Starting phenix.real_space_refine on Tue Aug 26 04:05:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua8_42054/08_2025/8ua8_42054_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua8_42054/08_2025/8ua8_42054.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ua8_42054/08_2025/8ua8_42054_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua8_42054/08_2025/8ua8_42054_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ua8_42054/08_2025/8ua8_42054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua8_42054/08_2025/8ua8_42054.map" } resolution = 3.7 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= 0.013 sd= 0.080 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 262 5.16 5 C 20931 2.51 5 N 5681 2.21 5 O 6337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s 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: 33212 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 28, 'TRANS': 409} Chain: "B" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3249 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 31, 'TRANS': 385} Chain: "C" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 392 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 5, 'TRANS': 45} Chain: "D" Number of atoms: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1163 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 28, 'TRANS': 409} Chain: "F" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3234 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 31, 'TRANS': 383} Chain: "G" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 46} Chain: "H" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1171 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 145} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 28, 'TRANS': 408} Chain: "J" Number of atoms: 3249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3249 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 31, 'TRANS': 385} Chain: "K" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 392 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 5, 'TRANS': 45} Chain: "L" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1165 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 145} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3318 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 28, 'TRANS': 408} Chain: "N" Number of atoms: 3218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3218 Classifications: {'peptide': 413} Link IDs: {'PTRANS': 31, 'TRANS': 381} Chain: "O" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 404 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 5, 'TRANS': 47} Chain: "P" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1171 Classifications: {'peptide': 153} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 145} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 275 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.27, per 1000 atoms: 0.22 Number of scatterers: 33212 At special positions: 0 Unit cell: (201.3, 161.7, 194.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 262 16.00 O 6337 8.00 N 5681 7.00 C 20931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=68, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.02 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.04 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.01 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.01 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 28 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " distance=2.02 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 220 " distance=2.04 Simple disulfide: pdb=" SG CYS C 9 " - pdb=" SG CYS C 18 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 27 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 58 " distance=2.04 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 78 " distance=2.06 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.02 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.02 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.01 Simple disulfide: pdb=" SG CYS F 19 " - pdb=" SG CYS F 125 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 28 " distance=2.03 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 105 " distance=2.02 Simple disulfide: pdb=" SG CYS F 153 " - pdb=" SG CYS F 265 " distance=2.04 Simple disulfide: pdb=" SG CYS F 201 " - pdb=" SG CYS F 225 " distance=2.03 Simple disulfide: pdb=" SG CYS F 203 " - pdb=" SG CYS F 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 9 " - pdb=" SG CYS G 18 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 27 " distance=2.03 Simple disulfide: pdb=" SG CYS G 26 " - pdb=" SG CYS G 58 " distance=2.03 Simple disulfide: pdb=" SG CYS I 49 " - pdb=" SG CYS I 114 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 94 " distance=2.04 Simple disulfide: pdb=" SG CYS I 63 " - pdb=" SG CYS I 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 68 " - pdb=" SG CYS I 78 " distance=2.04 Simple disulfide: pdb=" SG CYS I 259 " - pdb=" SG CYS I 271 " distance=2.05 Simple disulfide: pdb=" SG CYS I 301 " - pdb=" SG CYS I 376 " distance=2.02 Simple disulfide: pdb=" SG CYS I 306 " - pdb=" SG CYS I 380 " distance=2.02 Simple disulfide: pdb=" SG CYS I 328 " - pdb=" SG CYS I 370 " distance=2.01 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 125 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 28 " distance=2.03 Simple disulfide: pdb=" SG CYS J 91 " - pdb=" SG CYS J 105 " distance=2.02 Simple disulfide: pdb=" SG CYS J 153 " - pdb=" SG CYS J 265 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 225 " distance=2.03 Simple disulfide: pdb=" SG CYS J 203 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS K 9 " - pdb=" SG CYS K 18 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 27 " distance=1.99 Simple disulfide: pdb=" SG CYS K 26 " - pdb=" SG CYS K 58 " distance=2.03 Simple disulfide: pdb=" SG CYS M 49 " - pdb=" SG CYS M 114 " distance=2.03 Simple disulfide: pdb=" SG CYS M 63 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 259 " - pdb=" SG CYS M 271 " distance=2.03 Simple disulfide: pdb=" SG CYS M 301 " - pdb=" SG CYS M 376 " distance=2.02 Simple disulfide: pdb=" SG CYS M 306 " - pdb=" SG CYS M 380 " distance=2.02 Simple disulfide: pdb=" SG CYS M 328 " - pdb=" SG CYS M 370 " distance=2.01 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 125 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 28 " distance=2.03 Simple disulfide: pdb=" SG CYS N 91 " - pdb=" SG CYS N 105 " distance=2.00 Simple disulfide: pdb=" SG CYS N 153 " - pdb=" SG CYS N 265 " distance=2.04 Simple disulfide: pdb=" SG CYS N 201 " - pdb=" SG CYS N 225 " distance=2.02 Simple disulfide: pdb=" SG CYS N 203 " - pdb=" SG CYS N 220 " distance=2.04 Simple disulfide: pdb=" SG CYS O 9 " - pdb=" SG CYS O 18 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 27 " distance=2.05 Simple disulfide: pdb=" SG CYS O 26 " - pdb=" SG CYS O 58 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 84 " distance=2.03 Simple disulfide: pdb=" SG CYS R 79 " - pdb=" SG CYS R 97 " distance=2.03 Simple disulfide: pdb=" SG CYS R 91 " - pdb=" SG CYS R 108 " distance=2.03 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 Links applied BETA1-4 " NAG Q 1 " - " NAG Q 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " NAG-ASN " NAG G 101 " - " ASN G 13 " " NAG K 101 " - " ASN K 13 " " NAG Q 1 " - " ASN A 141 " " NAG S 1 " - " ASN B 200 " " NAG T 1 " - " ASN B 262 " " NAG U 1 " - " ASN E 141 " " NAG V 1 " - " ASN F 200 " " NAG W 1 " - " ASN F 262 " " NAG X 1 " - " ASN I 141 " " NAG Y 1 " - " ASN J 200 " " NAG Z 1 " - " ASN J 262 " " NAG a 1 " - " ASN M 141 " " NAG b 1 " - " ASN N 200 " " NAG c 1 " - " ASN N 262 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 1.2 microseconds 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 101 sheets defined 16.1% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 254 Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.989A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 404 through 438 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 349 through 362 removed outlier: 3.845A pdb=" N GLN B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 354 " --> pdb=" O TRP B 350 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 401 Proline residue: B 398 - end of helix Processing helix chain 'B' and resid 408 through 415 Processing helix chain 'C' and resid 26 through 31 removed outlier: 3.741A pdb=" N ASN C 30 " --> pdb=" O CYS C 26 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN C 31 " --> pdb=" O CYS C 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 26 through 31' Processing helix chain 'C' and resid 31 through 42 removed outlier: 3.973A pdb=" N THR C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN C 42 " --> pdb=" O MET C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.718A pdb=" N THR C 57 " --> pdb=" O GLN C 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 175 through 181 removed outlier: 3.759A pdb=" N ARG D 178 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER D 179 " --> pdb=" O HIS D 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 246 Processing helix chain 'E' and resid 250 through 254 Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.881A pdb=" N GLY E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 287 Processing helix chain 'E' and resid 289 through 293 Processing helix chain 'E' and resid 404 through 438 removed outlier: 3.649A pdb=" N ARG E 437 " --> pdb=" O CYS E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 11 removed outlier: 3.606A pdb=" N ALA F 11 " --> pdb=" O VAL F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 221 through 225 Processing helix chain 'F' and resid 349 through 362 removed outlier: 3.795A pdb=" N GLN F 353 " --> pdb=" O GLY F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 397 Processing helix chain 'F' and resid 398 through 400 No H-bonds generated for 'chain 'F' and resid 398 through 400' Processing helix chain 'F' and resid 408 through 415 Processing helix chain 'G' and resid 26 through 31 removed outlier: 3.522A pdb=" N ASN G 31 " --> pdb=" O CYS G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 42 removed outlier: 3.855A pdb=" N ASN G 42 " --> pdb=" O MET G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 56 removed outlier: 3.672A pdb=" N LEU G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 157 removed outlier: 3.821A pdb=" N ALA H 156 " --> pdb=" O ASN H 152 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS H 157 " --> pdb=" O ALA H 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 152 through 157' Processing helix chain 'H' and resid 174 through 179 removed outlier: 4.528A pdb=" N SER H 179 " --> pdb=" O HIS H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 246 Processing helix chain 'I' and resid 250 through 254 Processing helix chain 'I' and resid 255 through 259 removed outlier: 4.024A pdb=" N CYS I 259 " --> pdb=" O PRO I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 291 through 293 No H-bonds generated for 'chain 'I' and resid 291 through 293' Processing helix chain 'I' and resid 404 through 437 removed outlier: 3.526A pdb=" N TRP I 409 " --> pdb=" O THR I 405 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL I 410 " --> pdb=" O ALA I 406 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG I 437 " --> pdb=" O CYS I 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 12 Processing helix chain 'J' and resid 81 through 83 No H-bonds generated for 'chain 'J' and resid 81 through 83' Processing helix chain 'J' and resid 349 through 362 removed outlier: 3.813A pdb=" N GLN J 353 " --> pdb=" O GLY J 349 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 401 Proline residue: J 398 - end of helix Processing helix chain 'J' and resid 408 through 415 Processing helix chain 'K' and resid 26 through 31 removed outlier: 3.635A pdb=" N ASN K 30 " --> pdb=" O CYS K 26 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN K 31 " --> pdb=" O CYS K 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 26 through 31' Processing helix chain 'K' and resid 31 through 42 removed outlier: 3.599A pdb=" N THR K 35 " --> pdb=" O ASN K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 47 through 57 removed outlier: 4.484A pdb=" N THR K 57 " --> pdb=" O GLN K 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 118 No H-bonds generated for 'chain 'L' and resid 116 through 118' Processing helix chain 'L' and resid 152 through 157 removed outlier: 3.991A pdb=" N LYS L 157 " --> pdb=" O ALA L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 178 removed outlier: 3.783A pdb=" N ARG L 178 " --> pdb=" O VAL L 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 246 removed outlier: 3.533A pdb=" N TYR M 242 " --> pdb=" O SER M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 254 Processing helix chain 'M' and resid 255 through 259 removed outlier: 3.928A pdb=" N GLY M 258 " --> pdb=" O ALA M 255 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS M 259 " --> pdb=" O PRO M 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 255 through 259' Processing helix chain 'M' and resid 283 through 287 Processing helix chain 'M' and resid 404 through 437 removed outlier: 3.529A pdb=" N VAL M 410 " --> pdb=" O ALA M 406 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG M 437 " --> pdb=" O CYS M 433 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 83 No H-bonds generated for 'chain 'N' and resid 81 through 83' Processing helix chain 'N' and resid 349 through 362 removed outlier: 3.612A pdb=" N GLN N 353 " --> pdb=" O GLY N 349 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL N 355 " --> pdb=" O PRO N 351 " (cutoff:3.500A) Processing helix chain 'N' and resid 365 through 395 Processing helix chain 'N' and resid 397 through 402 removed outlier: 3.534A pdb=" N THR N 402 " --> pdb=" O PRO N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 408 through 415 Processing helix chain 'O' and resid 26 through 31 removed outlier: 3.746A pdb=" N ASN O 31 " --> pdb=" O CYS O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 31 through 42 removed outlier: 3.726A pdb=" N THR O 35 " --> pdb=" O ASN O 31 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 45 No H-bonds generated for 'chain 'O' and resid 43 through 45' Processing helix chain 'O' and resid 47 through 57 removed outlier: 3.657A pdb=" N THR O 57 " --> pdb=" O GLN O 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 178 removed outlier: 3.619A pdb=" N ARG P 178 " --> pdb=" O VAL P 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 90 removed outlier: 3.857A pdb=" N LYS R 90 " --> pdb=" O SER R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 108 Proline residue: R 105 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.230A pdb=" N MET A 31 " --> pdb=" O MET A 136 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N MET A 136 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 35 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain 'A' and resid 24 through 25 removed outlier: 4.795A pdb=" N THR A 288 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 48 removed outlier: 3.854A pdb=" N TYR A 46 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA7, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA8, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA9, first strand: chain 'A' and resid 220 through 221 removed outlier: 3.646A pdb=" N THR A 234 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 297 through 306 removed outlier: 5.728A pdb=" N ASP A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS A 321 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AB3, first strand: chain 'A' and resid 331 through 332 Processing sheet with id=AB4, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB5, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB6, first strand: chain 'B' and resid 36 through 38 removed outlier: 3.974A pdb=" N ALA B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N HIS B 99 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N ALA B 52 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N MET B 97 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N ILE B 54 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 11.081A pdb=" N GLY B 95 " --> pdb=" O ILE B 54 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 66 through 71 Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'B' and resid 149 through 156 Processing sheet with id=AC1, first strand: chain 'B' and resid 166 through 169 Processing sheet with id=AC2, first strand: chain 'B' and resid 181 through 184 Processing sheet with id=AC3, first strand: chain 'B' and resid 208 through 211 Processing sheet with id=AC4, first strand: chain 'B' and resid 274 through 277 Processing sheet with id=AC5, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AC6, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.630A pdb=" N GLY D 131 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N HIS D 125 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N VAL D 129 " --> pdb=" O HIS D 125 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR D 132 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 191 through 194 removed outlier: 8.311A pdb=" N ALA D 199 " --> pdb=" O PRO D 210 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE D 207 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL D 249 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL D 234 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TRP D 251 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA D 232 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 222 through 223 removed outlier: 7.495A pdb=" N ALA D 232 " --> pdb=" O TRP D 251 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TRP D 251 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL D 234 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL D 249 " --> pdb=" O VAL D 234 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 3 through 8 Processing sheet with id=AD1, first strand: chain 'E' and resid 15 through 19 removed outlier: 5.168A pdb=" N MET E 31 " --> pdb=" O MET E 136 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N MET E 136 " --> pdb=" O MET E 31 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL E 33 " --> pdb=" O ARG E 134 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG E 134 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU E 35 " --> pdb=" O LYS E 132 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 15 through 19 Processing sheet with id=AD3, first strand: chain 'E' and resid 46 through 48 removed outlier: 3.599A pdb=" N TYR E 46 " --> pdb=" O ALA E 121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AD5, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AD6, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AD7, first strand: chain 'E' and resid 220 through 221 removed outlier: 3.580A pdb=" N THR E 234 " --> pdb=" O LYS E 220 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 297 through 306 removed outlier: 5.041A pdb=" N ASP E 298 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS E 321 " --> pdb=" O ASP E 298 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL E 315 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 326 through 329 Processing sheet with id=AE1, first strand: chain 'E' and resid 331 through 332 Processing sheet with id=AE2, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AE3, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=AE4, first strand: chain 'F' and resid 34 through 38 removed outlier: 6.496A pdb=" N GLN F 49 " --> pdb=" O GLU F 35 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL F 37 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS F 47 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N HIS F 99 " --> pdb=" O PHE F 50 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N ALA F 52 " --> pdb=" O MET F 97 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N MET F 97 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ILE F 54 " --> pdb=" O GLY F 95 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N GLY F 95 " --> pdb=" O ILE F 54 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 66 through 71 Processing sheet with id=AE6, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AE7, first strand: chain 'F' and resid 149 through 156 Processing sheet with id=AE8, first strand: chain 'F' and resid 236 through 237 Processing sheet with id=AE9, first strand: chain 'F' and resid 181 through 184 Processing sheet with id=AF1, first strand: chain 'F' and resid 208 through 211 Processing sheet with id=AF2, first strand: chain 'F' and resid 274 through 277 removed outlier: 3.542A pdb=" N THR F 274 " --> pdb=" O HIS F 285 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 129 through 134 removed outlier: 6.096A pdb=" N VAL H 123 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR H 132 " --> pdb=" O PHE H 121 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE H 121 " --> pdb=" O TYR H 132 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 139 through 143 Processing sheet with id=AF5, first strand: chain 'H' and resid 256 through 259 removed outlier: 7.847A pdb=" N ARG H 243 " --> pdb=" O ASN H 239 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ASN H 239 " --> pdb=" O ARG H 243 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA H 245 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY H 237 " --> pdb=" O ALA H 245 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER H 247 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TRP H 251 " --> pdb=" O VAL H 231 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N VAL H 231 " --> pdb=" O TRP H 251 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA H 232 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ALA H 199 " --> pdb=" O PRO H 210 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE H 207 " --> pdb=" O LEU H 246 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 2 through 8 Processing sheet with id=AF7, first strand: chain 'I' and resid 15 through 19 removed outlier: 5.087A pdb=" N MET I 31 " --> pdb=" O MET I 136 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N MET I 136 " --> pdb=" O MET I 31 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N VAL I 33 " --> pdb=" O ARG I 134 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG I 134 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU I 35 " --> pdb=" O LYS I 132 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LEU I 129 " --> pdb=" O VAL I 148 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AF9, first strand: chain 'I' and resid 24 through 25 removed outlier: 4.660A pdb=" N THR I 288 " --> pdb=" O SER I 25 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 46 through 48 removed outlier: 3.822A pdb=" N TYR I 46 " --> pdb=" O ALA I 121 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AG3, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AG4, first strand: chain 'I' and resid 87 through 88 Processing sheet with id=AG5, first strand: chain 'I' and resid 203 through 204 Processing sheet with id=AG6, first strand: chain 'I' and resid 297 through 306 removed outlier: 7.158A pdb=" N LEU I 299 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N LYS I 321 " --> pdb=" O LEU I 299 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N CYS I 301 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR I 319 " --> pdb=" O CYS I 301 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL I 303 " --> pdb=" O THR I 317 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR I 317 " --> pdb=" O VAL I 303 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 343 through 346 Processing sheet with id=AG8, first strand: chain 'I' and resid 387 through 388 Processing sheet with id=AG9, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AH1, first strand: chain 'J' and resid 36 through 38 removed outlier: 4.049A pdb=" N ALA J 36 " --> pdb=" O GLN J 49 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N HIS J 99 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 9.385A pdb=" N ALA J 52 " --> pdb=" O MET J 97 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N MET J 97 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N ILE J 54 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 10.814A pdb=" N GLY J 95 " --> pdb=" O ILE J 54 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 66 through 71 Processing sheet with id=AH3, first strand: chain 'J' and resid 84 through 86 Processing sheet with id=AH4, first strand: chain 'J' and resid 149 through 156 Processing sheet with id=AH5, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AH6, first strand: chain 'J' and resid 181 through 184 Processing sheet with id=AH7, first strand: chain 'J' and resid 208 through 211 Processing sheet with id=AH8, first strand: chain 'J' and resid 274 through 278 removed outlier: 3.754A pdb=" N THR J 274 " --> pdb=" O HIS J 285 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU J 281 " --> pdb=" O GLY J 278 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 149 through 150 removed outlier: 3.860A pdb=" N GLY L 131 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N HIS L 125 " --> pdb=" O VAL L 129 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL L 129 " --> pdb=" O HIS L 125 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 256 through 259 removed outlier: 4.986A pdb=" N PHE L 207 " --> pdb=" O LEU L 246 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ALA L 199 " --> pdb=" O PRO L 210 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 256 through 259 removed outlier: 4.238A pdb=" N ARG L 243 " --> pdb=" O GLU L 240 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU L 240 " --> pdb=" O ARG L 243 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL L 249 " --> pdb=" O VAL L 234 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL L 234 " --> pdb=" O VAL L 249 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TRP L 251 " --> pdb=" O ALA L 232 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ALA L 232 " --> pdb=" O TRP L 251 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'M' and resid 2 through 8 Processing sheet with id=AI4, first strand: chain 'M' and resid 15 through 19 removed outlier: 5.110A pdb=" N MET M 31 " --> pdb=" O MET M 136 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET M 136 " --> pdb=" O MET M 31 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N VAL M 33 " --> pdb=" O ARG M 134 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG M 134 " --> pdb=" O VAL M 33 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU M 35 " --> pdb=" O LYS M 132 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 15 through 19 Processing sheet with id=AI6, first strand: chain 'M' and resid 46 through 48 removed outlier: 3.546A pdb=" N TYR M 46 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'M' and resid 51 through 54 Processing sheet with id=AI8, first strand: chain 'M' and resid 51 through 54 Processing sheet with id=AI9, first strand: chain 'M' and resid 203 through 204 Processing sheet with id=AJ1, first strand: chain 'M' and resid 220 through 221 removed outlier: 3.644A pdb=" N THR M 234 " --> pdb=" O LYS M 220 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'M' and resid 297 through 306 removed outlier: 5.644A pdb=" N ASP M 298 " --> pdb=" O LYS M 321 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS M 321 " --> pdb=" O ASP M 298 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL M 315 " --> pdb=" O ALA M 304 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'M' and resid 326 through 329 Processing sheet with id=AJ4, first strand: chain 'M' and resid 331 through 332 Processing sheet with id=AJ5, first strand: chain 'M' and resid 387 through 388 Processing sheet with id=AJ6, first strand: chain 'N' and resid 17 through 19 Processing sheet with id=AJ7, first strand: chain 'N' and resid 36 through 38 removed outlier: 4.141A pdb=" N ALA N 36 " --> pdb=" O GLN N 49 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N HIS N 99 " --> pdb=" O PHE N 50 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ALA N 52 " --> pdb=" O MET N 97 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N MET N 97 " --> pdb=" O ALA N 52 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N ILE N 54 " --> pdb=" O GLY N 95 " (cutoff:3.500A) removed outlier: 11.545A pdb=" N GLY N 95 " --> pdb=" O ILE N 54 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'N' and resid 66 through 71 Processing sheet with id=AJ9, first strand: chain 'N' and resid 84 through 86 Processing sheet with id=AK1, first strand: chain 'N' and resid 148 through 156 Processing sheet with id=AK2, first strand: chain 'N' and resid 236 through 237 Processing sheet with id=AK3, first strand: chain 'N' and resid 181 through 184 Processing sheet with id=AK4, first strand: chain 'N' and resid 207 through 211 removed outlier: 3.889A pdb=" N ASN N 207 " --> pdb=" O CYS N 201 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'N' and resid 274 through 277 Processing sheet with id=AK6, first strand: chain 'O' and resid 8 through 9 Processing sheet with id=AK7, first strand: chain 'P' and resid 139 through 140 removed outlier: 5.743A pdb=" N VAL P 129 " --> pdb=" O HIS P 125 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N HIS P 125 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY P 131 " --> pdb=" O VAL P 123 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'P' and resid 142 through 143 Processing sheet with id=AK9, first strand: chain 'P' and resid 191 through 195 removed outlier: 8.574A pdb=" N ALA P 199 " --> pdb=" O PRO P 210 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N PHE P 207 " --> pdb=" O LEU P 246 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL P 249 " --> pdb=" O VAL P 234 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL P 234 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TRP P 251 " --> pdb=" O ALA P 232 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ALA P 232 " --> pdb=" O TRP P 251 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'P' and resid 222 through 223 removed outlier: 7.500A pdb=" N ALA P 232 " --> pdb=" O TRP P 251 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TRP P 251 " --> pdb=" O ALA P 232 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL P 234 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VAL P 249 " --> pdb=" O VAL P 234 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'R' and resid 77 through 78 1259 hydrogen bonds defined for protein. 3159 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: 7.02 Time building geometry restraints manager: 2.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.29: 5406 1.29 - 1.65: 28321 1.65 - 2.00: 350 2.00 - 2.36: 0 2.36 - 2.72: 1 Bond restraints: 34078 Sorted by residual: bond pdb=" CB PRO A 237 " pdb=" CG PRO A 237 " ideal model delta sigma weight residual 1.492 2.723 -1.231 5.00e-02 4.00e+02 6.06e+02 bond pdb=" CG PRO A 237 " pdb=" CD PRO A 237 " ideal model delta sigma weight residual 1.503 0.927 0.576 3.40e-02 8.65e+02 2.87e+02 bond pdb=" C THR A 236 " pdb=" N PRO A 237 " ideal model delta sigma weight residual 1.331 1.432 -0.101 1.21e-02 6.83e+03 6.90e+01 bond pdb=" N PRO A 237 " pdb=" CD PRO A 237 " ideal model delta sigma weight residual 1.473 1.583 -0.110 1.40e-02 5.10e+03 6.14e+01 bond pdb=" CA PRO A 237 " pdb=" CB PRO A 237 " ideal model delta sigma weight residual 1.532 1.431 0.100 1.48e-02 4.57e+03 4.60e+01 ... (remaining 34073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 18.49: 46442 18.49 - 36.98: 2 36.98 - 55.48: 0 55.48 - 73.97: 0 73.97 - 92.46: 1 Bond angle restraints: 46445 Sorted by residual: angle pdb=" CB PRO A 237 " pdb=" CG PRO A 237 " pdb=" CD PRO A 237 " ideal model delta sigma weight residual 106.10 13.64 92.46 3.20e+00 9.77e-02 8.35e+02 angle pdb=" CA PRO A 237 " pdb=" CB PRO A 237 " pdb=" CG PRO A 237 " ideal model delta sigma weight residual 104.50 85.47 19.03 1.90e+00 2.77e-01 1.00e+02 angle pdb=" CA PRO H 143 " pdb=" N PRO H 143 " pdb=" CD PRO H 143 " ideal model delta sigma weight residual 112.00 99.39 12.61 1.40e+00 5.10e-01 8.11e+01 angle pdb=" N PRO A 237 " pdb=" CD PRO A 237 " pdb=" CG PRO A 237 " ideal model delta sigma weight residual 103.20 90.56 12.64 1.50e+00 4.44e-01 7.10e+01 angle pdb=" N PRO A 237 " pdb=" CA PRO A 237 " pdb=" CB PRO A 237 " ideal model delta sigma weight residual 103.45 93.51 9.94 1.21e+00 6.83e-01 6.74e+01 ... (remaining 46440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 18288 22.12 - 44.24: 2172 44.24 - 66.36: 312 66.36 - 88.48: 100 88.48 - 110.59: 27 Dihedral angle restraints: 20899 sinusoidal: 8541 harmonic: 12358 Sorted by residual: dihedral pdb=" CA VAL C 24 " pdb=" C VAL C 24 " pdb=" N PRO C 25 " pdb=" CA PRO C 25 " ideal model delta harmonic sigma weight residual -180.00 -94.30 -85.70 0 5.00e+00 4.00e-02 2.94e+02 dihedral pdb=" CA GLU F 247 " pdb=" C GLU F 247 " pdb=" N PRO F 248 " pdb=" CA PRO F 248 " ideal model delta harmonic sigma weight residual 180.00 -101.07 -78.93 0 5.00e+00 4.00e-02 2.49e+02 dihedral pdb=" CA VAL K 24 " pdb=" C VAL K 24 " pdb=" N PRO K 25 " pdb=" CA PRO K 25 " ideal model delta harmonic sigma weight residual -180.00 -113.78 -66.22 0 5.00e+00 4.00e-02 1.75e+02 ... (remaining 20896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4906 0.128 - 0.257: 333 0.257 - 0.385: 20 0.385 - 0.513: 4 0.513 - 0.642: 3 Chirality restraints: 5266 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.03e+03 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-02 2.50e+03 8.04e+02 chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-02 2.50e+03 7.86e+02 ... (remaining 5263 not shown) Planarity restraints: 5986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN M 100 " 0.030 2.00e-02 2.50e+03 6.06e-02 3.68e+01 pdb=" CG ASN M 100 " -0.105 2.00e-02 2.50e+03 pdb=" OD1 ASN M 100 " 0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN M 100 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 37 " 0.470 9.50e-02 1.11e+02 2.12e-01 3.53e+01 pdb=" NE ARG K 37 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG K 37 " -0.055 2.00e-02 2.50e+03 pdb=" NH1 ARG K 37 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG K 37 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE G 16 " -0.097 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO G 17 " 0.240 5.00e-02 4.00e+02 pdb=" CA PRO G 17 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO G 17 " -0.073 5.00e-02 4.00e+02 ... (remaining 5983 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 384 2.56 - 3.14: 28721 3.14 - 3.73: 49442 3.73 - 4.31: 66884 4.31 - 4.90: 113218 Nonbonded interactions: 258649 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" O VAL B 242 " model vdw 1.974 3.040 nonbonded pdb=" OG SER A 25 " pdb=" OG1 THR A 288 " model vdw 1.976 3.040 nonbonded pdb=" OG SER F 59 " pdb=" OD1 ASN F 61 " model vdw 1.977 3.040 nonbonded pdb=" OE1 GLU B 40 " pdb=" OH TYR B 156 " model vdw 2.002 3.040 nonbonded pdb=" O VAL N 79 " pdb=" OG SER N 82 " model vdw 2.027 3.040 ... (remaining 258644 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 437) selection = (chain 'E' and resid 1 through 437) selection = chain 'I' selection = chain 'M' } ncs_group { reference = (chain 'B' and resid 6 through 418) selection = (chain 'F' and resid 6 through 418) selection = (chain 'J' and resid 6 through 418) selection = chain 'N' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 8 through 58) selection = (chain 'K' and resid 8 through 58) selection = (chain 'O' and resid 8 through 58) } ncs_group { reference = (chain 'D' and (resid 116 through 177 or (resid 178 and (name N or name CA or na \ me C or name O or name CB )) or resid 179 through 267)) selection = (chain 'H' and (resid 116 through 177 or (resid 178 and (name N or name CA or na \ me C or name O or name CB )) or resid 179 through 267)) selection = (chain 'L' and resid 116 through 267) selection = (chain 'P' and (resid 116 through 177 or (resid 178 and (name N or name CA or na \ me C or name O or name CB )) or resid 179 through 267)) } ncs_group { reference = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'a' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.400 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.014 1.231 34178 Z= 0.575 Angle : 1.399 92.462 46677 Z= 0.719 Chirality : 0.071 0.642 5266 Planarity : 0.012 0.212 5972 Dihedral : 18.917 110.595 12775 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.40 % Allowed : 0.35 % Favored : 99.24 % Rotamer: Outliers : 1.19 % Allowed : 35.57 % Favored : 63.24 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.13 % 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: -1.98 (0.12), residues: 4233 helix: 0.25 (0.23), residues: 468 sheet: -1.07 (0.14), residues: 1275 loop : -1.80 (0.12), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.002 ARG K 37 TYR 0.053 0.004 TYR N 305 PHE 0.059 0.004 PHE E 312 TRP 0.026 0.003 TRP N 235 HIS 0.022 0.003 HIS N 170 Details of bonding type rmsd covalent geometry : bond 0.01415 (34078) covalent geometry : angle 1.36736 (46445) SS BOND : bond 0.01107 ( 68) SS BOND : angle 4.28807 ( 136) hydrogen bonds : bond 0.13641 ( 1205) hydrogen bonds : angle 7.60747 ( 3159) link_BETA1-4 : bond 0.00533 ( 18) link_BETA1-4 : angle 5.21390 ( 54) link_NAG-ASN : bond 0.00983 ( 14) link_NAG-ASN : angle 3.56435 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1547 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 1504 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8380 (ttp-110) cc_final: 0.8095 (ttp-110) REVERT: A 139 ASN cc_start: 0.8587 (p0) cc_final: 0.8297 (p0) REVERT: B 60 ASP cc_start: 0.8684 (m-30) cc_final: 0.7384 (m-30) REVERT: B 129 TYR cc_start: 0.8341 (t80) cc_final: 0.7865 (t80) REVERT: B 326 GLU cc_start: 0.7384 (tt0) cc_final: 0.7133 (tt0) REVERT: D 206 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6965 (mtt180) REVERT: E 73 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7415 (mtmt) REVERT: E 186 ASN cc_start: 0.8034 (m-40) cc_final: 0.7803 (m-40) REVERT: E 199 ARG cc_start: 0.7634 (mmt180) cc_final: 0.7395 (mmt180) REVERT: E 204 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8062 (mm-40) REVERT: E 228 MET cc_start: 0.7644 (tpt) cc_final: 0.7054 (tpt) REVERT: E 311 ASP cc_start: 0.8168 (t0) cc_final: 0.7936 (t0) REVERT: E 340 GLN cc_start: 0.8586 (tp40) cc_final: 0.8266 (tp40) REVERT: F 15 TYR cc_start: 0.8164 (p90) cc_final: 0.7928 (p90) REVERT: F 169 MET cc_start: 0.7997 (mmp) cc_final: 0.7548 (mmp) REVERT: F 215 MET cc_start: 0.7787 (pmm) cc_final: 0.7444 (pmm) REVERT: F 235 TRP cc_start: 0.8106 (OUTLIER) cc_final: 0.7898 (t60) REVERT: F 284 LEU cc_start: 0.8797 (mt) cc_final: 0.8511 (mt) REVERT: H 177 MET cc_start: 0.8921 (mtt) cc_final: 0.8563 (mtt) REVERT: H 258 ARG cc_start: 0.8672 (ttm170) cc_final: 0.8393 (ttm170) REVERT: I 48 THR cc_start: 0.7726 (m) cc_final: 0.7352 (p) REVERT: I 61 LYS cc_start: 0.8157 (ttmt) cc_final: 0.7874 (ttmt) REVERT: I 73 LYS cc_start: 0.7722 (mtpp) cc_final: 0.7456 (mtpp) REVERT: I 76 TYR cc_start: 0.7795 (t80) cc_final: 0.7509 (t80) REVERT: I 146 VAL cc_start: 0.8536 (t) cc_final: 0.8190 (m) REVERT: I 356 PHE cc_start: 0.8519 (p90) cc_final: 0.8316 (p90) REVERT: J 10 LYS cc_start: 0.8648 (tttm) cc_final: 0.8113 (tttm) REVERT: J 81 SER cc_start: 0.9239 (p) cc_final: 0.8981 (p) REVERT: J 153 CYS cc_start: 0.5424 (m) cc_final: 0.5136 (m) REVERT: L 162 LYS cc_start: 0.8717 (mtpp) cc_final: 0.8421 (mtpp) REVERT: L 215 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7647 (mmtt) REVERT: L 255 MET cc_start: 0.7233 (mmp) cc_final: 0.7033 (mmp) REVERT: M 43 ASN cc_start: 0.7811 (m-40) cc_final: 0.7310 (m-40) REVERT: M 102 GLN cc_start: 0.8128 (tp-100) cc_final: 0.7466 (tp40) REVERT: M 167 SER cc_start: 0.8548 (t) cc_final: 0.8331 (p) REVERT: M 174 ASP cc_start: 0.7539 (m-30) cc_final: 0.7100 (m-30) REVERT: M 186 ASN cc_start: 0.8644 (p0) cc_final: 0.8014 (p0) REVERT: M 321 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7818 (mtmm) REVERT: M 351 LYS cc_start: 0.8498 (mmmt) cc_final: 0.8010 (mmmt) REVERT: N 104 LYS cc_start: 0.8516 (mtmm) cc_final: 0.7902 (mtmm) REVERT: N 234 LYS cc_start: 0.8423 (mmmm) cc_final: 0.8215 (mmmm) REVERT: N 286 LEU cc_start: 0.8660 (mt) cc_final: 0.8229 (mt) REVERT: N 329 TRP cc_start: 0.8942 (t-100) cc_final: 0.8725 (t-100) REVERT: N 394 LYS cc_start: 0.8859 (mmtm) cc_final: 0.8298 (mmtm) REVERT: O 8 MET cc_start: 0.7511 (ttp) cc_final: 0.6882 (ttp) REVERT: P 142 LYS cc_start: 0.8781 (tmtt) cc_final: 0.8173 (tmtt) REVERT: P 166 TYR cc_start: 0.7705 (m-10) cc_final: 0.7453 (m-80) REVERT: P 197 HIS cc_start: 0.8164 (m90) cc_final: 0.7820 (m90) outliers start: 43 outliers final: 27 residues processed: 1518 average time/residue: 0.1923 time to fit residues: 467.2632 Evaluate side-chains 1511 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 1482 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 235 TRP Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 357 SER Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain H residue 250 THR Chi-restraints excluded: chain I residue 160 GLN Chi-restraints excluded: chain I residue 328 CYS Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 370 CYS Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 62 HIS Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 171 MET Chi-restraints excluded: chain J residue 265 CYS Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 51 SER Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 307 GLU Chi-restraints excluded: chain P residue 250 THR Chi-restraints excluded: chain P residue 251 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 281 ASN B 49 GLN B 134 GLN B 226 HIS ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN E 139 ASN E 187 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 ASN F 73 HIS F 128 GLN F 170 HIS F 226 HIS H 201 GLN J 134 GLN J 236 GLN ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 HIS ** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 142 GLN M 204 GLN M 340 GLN ** N 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 255 HIS N 353 GLN O 42 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.121878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101474 restraints weight = 57079.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.104916 restraints weight = 23744.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107126 restraints weight = 12692.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108286 restraints weight = 8140.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109296 restraints weight = 6214.459| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 34178 Z= 0.203 Angle : 0.821 13.371 46677 Z= 0.414 Chirality : 0.050 0.316 5266 Planarity : 0.007 0.124 5972 Dihedral : 10.095 76.158 5314 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.72 % Favored : 93.91 % Rotamer: Outliers : 6.10 % Allowed : 29.16 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.62 (0.12), residues: 4233 helix: 0.87 (0.23), residues: 483 sheet: -1.04 (0.13), residues: 1294 loop : -1.51 (0.12), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 37 TYR 0.025 0.002 TYR N 296 PHE 0.023 0.002 PHE N 100 TRP 0.015 0.001 TRP H 195 HIS 0.009 0.001 HIS B 29 Details of bonding type rmsd covalent geometry : bond 0.00446 (34078) covalent geometry : angle 0.80123 (46445) SS BOND : bond 0.00422 ( 68) SS BOND : angle 1.77659 ( 136) hydrogen bonds : bond 0.04310 ( 1205) hydrogen bonds : angle 6.18519 ( 3159) link_BETA1-4 : bond 0.00897 ( 18) link_BETA1-4 : angle 4.07575 ( 54) link_NAG-ASN : bond 0.00489 ( 14) link_NAG-ASN : angle 2.89088 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1695 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 1475 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TYR cc_start: 0.8300 (m-80) cc_final: 0.7948 (m-80) REVERT: A 78 CYS cc_start: 0.5008 (OUTLIER) cc_final: 0.4763 (p) REVERT: A 115 ARG cc_start: 0.8285 (ttp-110) cc_final: 0.7878 (ttp-110) REVERT: A 183 GLU cc_start: 0.7113 (pm20) cc_final: 0.6862 (pm20) REVERT: A 257 PHE cc_start: 0.8780 (m-10) cc_final: 0.8395 (m-10) REVERT: A 292 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: A 306 CYS cc_start: 0.6913 (t) cc_final: 0.5960 (t) REVERT: A 317 THR cc_start: 0.8713 (t) cc_final: 0.8337 (p) REVERT: A 381 GLU cc_start: 0.7314 (pm20) cc_final: 0.6972 (pm20) REVERT: A 390 TYR cc_start: 0.8730 (p90) cc_final: 0.8521 (p90) REVERT: B 40 GLU cc_start: 0.7543 (mp0) cc_final: 0.7190 (mp0) REVERT: B 49 GLN cc_start: 0.8319 (tt0) cc_final: 0.8051 (tt0) REVERT: B 60 ASP cc_start: 0.8742 (m-30) cc_final: 0.7426 (m-30) REVERT: B 96 THR cc_start: 0.8038 (p) cc_final: 0.7817 (p) REVERT: B 109 GLU cc_start: 0.7267 (mm-30) cc_final: 0.7033 (mm-30) REVERT: B 129 TYR cc_start: 0.8204 (t80) cc_final: 0.7742 (t80) REVERT: B 156 TYR cc_start: 0.8454 (m-80) cc_final: 0.7576 (m-10) REVERT: B 157 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7446 (mm-40) REVERT: B 169 MET cc_start: 0.7301 (mmm) cc_final: 0.6401 (mmm) REVERT: B 242 VAL cc_start: 0.8554 (m) cc_final: 0.8331 (p) REVERT: B 261 ASP cc_start: 0.7791 (p0) cc_final: 0.7218 (p0) REVERT: B 265 CYS cc_start: 0.5026 (OUTLIER) cc_final: 0.4815 (t) REVERT: B 326 GLU cc_start: 0.7360 (tt0) cc_final: 0.7007 (tt0) REVERT: B 327 TYR cc_start: 0.8590 (p90) cc_final: 0.8250 (p90) REVERT: B 357 TYR cc_start: 0.8489 (t80) cc_final: 0.8187 (t80) REVERT: D 206 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7117 (mtt180) REVERT: D 218 ASP cc_start: 0.8154 (p0) cc_final: 0.7846 (p0) REVERT: E 27 LEU cc_start: 0.7948 (tp) cc_final: 0.7732 (tt) REVERT: E 73 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7447 (mtmt) REVERT: E 100 ASN cc_start: 0.7334 (m-40) cc_final: 0.7100 (m-40) REVERT: E 186 ASN cc_start: 0.8122 (m-40) cc_final: 0.7734 (m-40) REVERT: E 196 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8101 (mm-40) REVERT: E 199 ARG cc_start: 0.7828 (mmt180) cc_final: 0.7383 (mmt180) REVERT: E 202 ASP cc_start: 0.7142 (m-30) cc_final: 0.6858 (m-30) REVERT: E 204 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7828 (mm-40) REVERT: E 228 MET cc_start: 0.7447 (tpt) cc_final: 0.6917 (tpt) REVERT: E 234 THR cc_start: 0.7497 (p) cc_final: 0.7185 (t) REVERT: E 312 PHE cc_start: 0.7730 (m-80) cc_final: 0.7457 (m-80) REVERT: E 324 LYS cc_start: 0.8634 (pttm) cc_final: 0.8354 (pttm) REVERT: E 336 VAL cc_start: 0.8650 (t) cc_final: 0.8333 (p) REVERT: E 340 GLN cc_start: 0.8679 (tp40) cc_final: 0.8279 (tp40) REVERT: E 407 LEU cc_start: 0.8536 (tp) cc_final: 0.8131 (tp) REVERT: F 7 ASN cc_start: 0.8175 (t0) cc_final: 0.7386 (t0) REVERT: F 10 LYS cc_start: 0.8570 (mttp) cc_final: 0.7748 (mtmp) REVERT: F 40 GLU cc_start: 0.7064 (mp0) cc_final: 0.6861 (mp0) REVERT: F 112 GLN cc_start: 0.8550 (tt0) cc_final: 0.8279 (tt0) REVERT: F 126 ARG cc_start: 0.8394 (mtm180) cc_final: 0.7889 (mtp85) REVERT: F 196 LYS cc_start: 0.8474 (ttpt) cc_final: 0.8239 (ttpt) REVERT: F 215 MET cc_start: 0.7953 (pmm) cc_final: 0.7578 (pmm) REVERT: F 234 LYS cc_start: 0.8439 (mmmt) cc_final: 0.7838 (mmmm) REVERT: F 235 TRP cc_start: 0.8120 (OUTLIER) cc_final: 0.7764 (t60) REVERT: F 362 TYR cc_start: 0.8578 (m-80) cc_final: 0.8340 (m-80) REVERT: H 177 MET cc_start: 0.8753 (mtt) cc_final: 0.8494 (mtt) REVERT: H 223 ILE cc_start: 0.8397 (mt) cc_final: 0.8168 (mt) REVERT: H 258 ARG cc_start: 0.8677 (ttm170) cc_final: 0.8388 (ttm170) REVERT: I 2 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7348 (mm-30) REVERT: I 61 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7910 (ttmt) REVERT: I 67 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7003 (tm-30) REVERT: I 73 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7509 (mtpp) REVERT: I 146 VAL cc_start: 0.8591 (t) cc_final: 0.8305 (m) REVERT: I 228 MET cc_start: 0.7923 (tmt) cc_final: 0.7534 (ppp) REVERT: I 237 PRO cc_start: 0.8776 (Cg_exo) cc_final: 0.8516 (Cg_endo) REVERT: I 371 SER cc_start: 0.8760 (t) cc_final: 0.8493 (p) REVERT: I 381 GLU cc_start: 0.7347 (pm20) cc_final: 0.7076 (pm20) REVERT: I 402 MET cc_start: 0.7271 (mmm) cc_final: 0.7070 (mmm) REVERT: J 10 LYS cc_start: 0.8835 (tttm) cc_final: 0.8154 (tttm) REVERT: J 97 MET cc_start: 0.7432 (tmm) cc_final: 0.6969 (tmm) REVERT: J 129 TYR cc_start: 0.7747 (t80) cc_final: 0.7140 (t80) REVERT: J 153 CYS cc_start: 0.5374 (m) cc_final: 0.4911 (m) REVERT: J 304 GLN cc_start: 0.8465 (tt0) cc_final: 0.8251 (tt0) REVERT: J 331 ASN cc_start: 0.8849 (m-40) cc_final: 0.8580 (m-40) REVERT: J 362 TYR cc_start: 0.8032 (m-80) cc_final: 0.7388 (m-80) REVERT: J 379 ILE cc_start: 0.8378 (mt) cc_final: 0.8141 (mt) REVERT: L 121 PHE cc_start: 0.8268 (m-10) cc_final: 0.7972 (m-10) REVERT: L 188 LYS cc_start: 0.9124 (ptpp) cc_final: 0.8595 (ptpp) REVERT: L 215 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7686 (mmtt) REVERT: M 5 THR cc_start: 0.8635 (OUTLIER) cc_final: 0.8373 (t) REVERT: M 15 TYR cc_start: 0.7667 (t80) cc_final: 0.7022 (t80) REVERT: M 16 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8450 (mmmt) REVERT: M 28 THR cc_start: 0.8251 (p) cc_final: 0.8038 (p) REVERT: M 35 GLU cc_start: 0.7953 (pm20) cc_final: 0.7734 (pm20) REVERT: M 50 GLU cc_start: 0.6854 (tp30) cc_final: 0.6581 (tp30) REVERT: M 100 ASN cc_start: 0.7164 (m110) cc_final: 0.6930 (m-40) REVERT: M 139 ASN cc_start: 0.8449 (p0) cc_final: 0.8159 (p0) REVERT: M 174 ASP cc_start: 0.7497 (m-30) cc_final: 0.7135 (m-30) REVERT: M 183 GLU cc_start: 0.7151 (pm20) cc_final: 0.6757 (pm20) REVERT: M 186 ASN cc_start: 0.8678 (p0) cc_final: 0.8101 (p0) REVERT: M 204 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7140 (mm-40) REVERT: M 216 ASN cc_start: 0.8231 (p0) cc_final: 0.7861 (p0) REVERT: M 321 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7774 (mtmm) REVERT: M 351 LYS cc_start: 0.8264 (mmmt) cc_final: 0.7829 (mmmt) REVERT: M 411 GLN cc_start: 0.7857 (tp40) cc_final: 0.7249 (tp40) REVERT: N 40 GLU cc_start: 0.7637 (mp0) cc_final: 0.7091 (mp0) REVERT: N 49 GLN cc_start: 0.8046 (tt0) cc_final: 0.7401 (tp-100) REVERT: N 104 LYS cc_start: 0.8510 (mtmm) cc_final: 0.7903 (mtmm) REVERT: N 212 ASN cc_start: 0.8542 (t0) cc_final: 0.8278 (t0) REVERT: N 215 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5908 (ppp) REVERT: N 223 GLU cc_start: 0.7684 (mp0) cc_final: 0.7462 (mp0) REVERT: N 234 LYS cc_start: 0.8440 (mmmm) cc_final: 0.8112 (mmmm) REVERT: N 264 THR cc_start: 0.8218 (p) cc_final: 0.8005 (p) REVERT: N 286 LEU cc_start: 0.8542 (mt) cc_final: 0.8040 (mt) REVERT: N 329 TRP cc_start: 0.8965 (t-100) cc_final: 0.8489 (t-100) REVERT: N 394 LYS cc_start: 0.8711 (mmtm) cc_final: 0.8230 (mmtm) REVERT: O 8 MET cc_start: 0.7401 (ttp) cc_final: 0.6764 (ttp) REVERT: P 142 LYS cc_start: 0.8992 (tmtt) cc_final: 0.8427 (tmtt) REVERT: P 195 TRP cc_start: 0.8130 (t60) cc_final: 0.7909 (t60) REVERT: P 197 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7657 (m90) REVERT: P 258 ARG cc_start: 0.8377 (ttm110) cc_final: 0.8072 (ttm110) outliers start: 220 outliers final: 132 residues processed: 1560 average time/residue: 0.1968 time to fit residues: 494.1768 Evaluate side-chains 1580 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1439 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 235 TRP Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 346 LYS Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain H residue 170 CYS Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 328 CYS Chi-restraints excluded: chain I residue 341 GLU Chi-restraints excluded: chain I residue 347 LYS Chi-restraints excluded: chain I residue 364 SER Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 287 HIS Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 352 HIS Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 170 CYS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 20 GLU Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 78 CYS Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 252 ASN Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 398 VAL Chi-restraints excluded: chain M residue 407 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 215 MET Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 158 LEU Chi-restraints excluded: chain P residue 182 SER Chi-restraints excluded: chain P residue 188 LYS Chi-restraints excluded: chain P residue 197 HIS Chi-restraints excluded: chain P residue 234 VAL Chi-restraints excluded: chain P residue 250 THR Chi-restraints excluded: chain P residue 251 TRP Chi-restraints excluded: chain R residue 85 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 315 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 265 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 195 optimal weight: 10.0000 chunk 327 optimal weight: 10.0000 chunk 410 optimal weight: 0.0870 chunk 337 optimal weight: 8.9990 chunk 316 optimal weight: 0.0870 chunk 244 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 overall best weight: 4.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN C 42 ASN E 187 GLN F 207 ASN ** F 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 HIS ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN M 187 GLN M 204 GLN ** M 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 340 GLN ** N 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 255 HIS ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097482 restraints weight = 57654.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.100935 restraints weight = 23988.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103077 restraints weight = 12778.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104467 restraints weight = 8243.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105121 restraints weight = 6142.659| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 34178 Z= 0.252 Angle : 0.786 10.771 46677 Z= 0.394 Chirality : 0.050 0.295 5266 Planarity : 0.006 0.114 5972 Dihedral : 8.418 63.041 5287 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.72 % Favored : 93.95 % Rotamer: Outliers : 7.66 % Allowed : 28.63 % Favored : 63.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.48 (0.13), residues: 4233 helix: 1.05 (0.23), residues: 488 sheet: -0.94 (0.13), residues: 1306 loop : -1.45 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 271 TYR 0.026 0.002 TYR N 296 PHE 0.019 0.002 PHE F 50 TRP 0.014 0.002 TRP F 409 HIS 0.008 0.001 HIS J 170 Details of bonding type rmsd covalent geometry : bond 0.00535 (34078) covalent geometry : angle 0.76697 (46445) SS BOND : bond 0.00482 ( 68) SS BOND : angle 1.72934 ( 136) hydrogen bonds : bond 0.04031 ( 1205) hydrogen bonds : angle 5.78860 ( 3159) link_BETA1-4 : bond 0.00974 ( 18) link_BETA1-4 : angle 4.00096 ( 54) link_NAG-ASN : bond 0.00351 ( 14) link_NAG-ASN : angle 2.34846 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1763 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 1487 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8638 (mtp180) cc_final: 0.8405 (mtp180) REVERT: A 31 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.8060 (mtm) REVERT: A 44 LEU cc_start: 0.8863 (tp) cc_final: 0.8544 (tt) REVERT: A 51 TYR cc_start: 0.8035 (p90) cc_final: 0.7394 (p90) REVERT: A 77 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7812 (mm-40) REVERT: A 230 HIS cc_start: 0.8153 (p-80) cc_final: 0.7316 (p-80) REVERT: A 287 PHE cc_start: 0.8688 (m-80) cc_final: 0.8421 (m-10) REVERT: A 292 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7573 (mp0) REVERT: A 306 CYS cc_start: 0.6849 (t) cc_final: 0.6587 (t) REVERT: A 317 THR cc_start: 0.8748 (t) cc_final: 0.8426 (p) REVERT: A 381 GLU cc_start: 0.7308 (pm20) cc_final: 0.6958 (pm20) REVERT: B 40 GLU cc_start: 0.7518 (mp0) cc_final: 0.7154 (mp0) REVERT: B 60 ASP cc_start: 0.8741 (m-30) cc_final: 0.7998 (m-30) REVERT: B 97 MET cc_start: 0.7649 (tmm) cc_final: 0.7031 (tmm) REVERT: B 109 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7080 (mm-30) REVERT: B 129 TYR cc_start: 0.8257 (t80) cc_final: 0.7848 (t80) REVERT: B 156 TYR cc_start: 0.8545 (m-80) cc_final: 0.8116 (m-80) REVERT: B 158 GLN cc_start: 0.8690 (mp10) cc_final: 0.8478 (mp10) REVERT: B 169 MET cc_start: 0.7362 (mmm) cc_final: 0.6555 (mmm) REVERT: B 253 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7677 (mtpp) REVERT: B 326 GLU cc_start: 0.7351 (tt0) cc_final: 0.7041 (tt0) REVERT: B 327 TYR cc_start: 0.8674 (p90) cc_final: 0.8441 (p90) REVERT: B 362 TYR cc_start: 0.8487 (m-80) cc_final: 0.8230 (m-80) REVERT: D 141 MET cc_start: 0.7436 (mtp) cc_final: 0.7029 (mtp) REVERT: D 206 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7127 (mtt180) REVERT: D 265 GLU cc_start: 0.7363 (pp20) cc_final: 0.7005 (pp20) REVERT: E 79 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7571 (mtpt) REVERT: E 100 ASN cc_start: 0.7516 (m-40) cc_final: 0.7193 (m-40) REVERT: E 186 ASN cc_start: 0.8085 (m-40) cc_final: 0.7687 (m-40) REVERT: E 199 ARG cc_start: 0.7779 (mmt180) cc_final: 0.7297 (mmt180) REVERT: E 202 ASP cc_start: 0.7061 (m-30) cc_final: 0.6816 (m-30) REVERT: E 216 ASN cc_start: 0.8144 (p0) cc_final: 0.7908 (p0) REVERT: E 228 MET cc_start: 0.7426 (tpt) cc_final: 0.7039 (tpt) REVERT: E 234 THR cc_start: 0.7437 (p) cc_final: 0.7145 (t) REVERT: E 246 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6771 (tm-30) REVERT: E 324 LYS cc_start: 0.8654 (pttm) cc_final: 0.8363 (pttm) REVERT: E 336 VAL cc_start: 0.8696 (t) cc_final: 0.8394 (p) REVERT: E 340 GLN cc_start: 0.8738 (tp40) cc_final: 0.8114 (tp40) REVERT: E 407 LEU cc_start: 0.8617 (tp) cc_final: 0.8176 (tp) REVERT: F 7 ASN cc_start: 0.8311 (t0) cc_final: 0.7451 (t0) REVERT: F 10 LYS cc_start: 0.8576 (mtmp) cc_final: 0.7705 (mtmp) REVERT: F 40 GLU cc_start: 0.7145 (mp0) cc_final: 0.6900 (mp0) REVERT: F 50 PHE cc_start: 0.8393 (p90) cc_final: 0.8106 (p90) REVERT: F 92 PHE cc_start: 0.8585 (t80) cc_final: 0.8024 (t80) REVERT: F 94 HIS cc_start: 0.7953 (m170) cc_final: 0.7412 (m170) REVERT: F 97 MET cc_start: 0.7950 (tpp) cc_final: 0.7393 (tpp) REVERT: F 112 GLN cc_start: 0.8602 (tt0) cc_final: 0.8378 (tt0) REVERT: F 196 LYS cc_start: 0.8511 (ttpt) cc_final: 0.8298 (ttpt) REVERT: F 215 MET cc_start: 0.8007 (pmm) cc_final: 0.7748 (pmm) REVERT: F 234 LYS cc_start: 0.8495 (mmmt) cc_final: 0.7739 (mmmm) REVERT: F 246 ASP cc_start: 0.7642 (t0) cc_final: 0.7391 (t0) REVERT: F 272 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7470 (mm-30) REVERT: F 274 THR cc_start: 0.8637 (m) cc_final: 0.8317 (t) REVERT: F 362 TYR cc_start: 0.8548 (m-80) cc_final: 0.8146 (m-80) REVERT: H 177 MET cc_start: 0.8709 (mtt) cc_final: 0.8504 (mtt) REVERT: H 258 ARG cc_start: 0.8762 (ttm170) cc_final: 0.8249 (ttm170) REVERT: I 2 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7341 (mm-30) REVERT: I 61 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7784 (ttmt) REVERT: I 139 ASN cc_start: 0.8474 (p0) cc_final: 0.8252 (p0) REVERT: I 146 VAL cc_start: 0.8600 (t) cc_final: 0.8281 (m) REVERT: I 220 LYS cc_start: 0.8295 (ttmt) cc_final: 0.8053 (ttmt) REVERT: I 237 PRO cc_start: 0.8809 (Cg_exo) cc_final: 0.8553 (Cg_endo) REVERT: I 371 SER cc_start: 0.8831 (t) cc_final: 0.8504 (p) REVERT: I 381 GLU cc_start: 0.7277 (pm20) cc_final: 0.6904 (pm20) REVERT: I 402 MET cc_start: 0.7334 (mmm) cc_final: 0.7066 (mmm) REVERT: J 10 LYS cc_start: 0.8851 (tttm) cc_final: 0.8439 (tttm) REVERT: J 97 MET cc_start: 0.7443 (tmm) cc_final: 0.7044 (tmm) REVERT: J 235 TRP cc_start: 0.7812 (OUTLIER) cc_final: 0.7350 (m-10) REVERT: J 304 GLN cc_start: 0.8444 (tt0) cc_final: 0.8230 (tt0) REVERT: J 331 ASN cc_start: 0.8936 (m110) cc_final: 0.8643 (m110) REVERT: L 188 LYS cc_start: 0.9144 (ptpp) cc_final: 0.8566 (ptpp) REVERT: L 215 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7700 (mmtt) REVERT: L 218 ASP cc_start: 0.8318 (p0) cc_final: 0.6988 (p0) REVERT: L 221 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.6466 (ptp-110) REVERT: L 258 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7884 (ttm110) REVERT: M 5 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8343 (t) REVERT: M 15 TYR cc_start: 0.7725 (t80) cc_final: 0.6976 (t80) REVERT: M 16 LYS cc_start: 0.8678 (mmmt) cc_final: 0.8388 (mmmt) REVERT: M 35 GLU cc_start: 0.7861 (pm20) cc_final: 0.7424 (pm20) REVERT: M 50 GLU cc_start: 0.6894 (tp30) cc_final: 0.6547 (tp30) REVERT: M 100 ASN cc_start: 0.7554 (m110) cc_final: 0.7180 (m-40) REVERT: M 174 ASP cc_start: 0.7549 (m-30) cc_final: 0.7173 (m-30) REVERT: M 183 GLU cc_start: 0.7285 (pm20) cc_final: 0.6726 (pm20) REVERT: M 186 ASN cc_start: 0.8696 (p0) cc_final: 0.8156 (p0) REVERT: M 204 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7512 (mm-40) REVERT: M 216 ASN cc_start: 0.8285 (p0) cc_final: 0.7929 (p0) REVERT: M 321 LYS cc_start: 0.8266 (mtmm) cc_final: 0.7817 (mtmm) REVERT: M 351 LYS cc_start: 0.8306 (mmmt) cc_final: 0.7861 (mmmt) REVERT: M 411 GLN cc_start: 0.7846 (tp40) cc_final: 0.7221 (tp40) REVERT: N 40 GLU cc_start: 0.7663 (mp0) cc_final: 0.7108 (mp0) REVERT: N 53 GLN cc_start: 0.8314 (mp10) cc_final: 0.7997 (mp10) REVERT: N 104 LYS cc_start: 0.8562 (mtmm) cc_final: 0.7973 (mtmm) REVERT: N 166 GLU cc_start: 0.7931 (pm20) cc_final: 0.7505 (pm20) REVERT: N 212 ASN cc_start: 0.8557 (t0) cc_final: 0.8275 (t0) REVERT: N 215 MET cc_start: 0.6247 (ppp) cc_final: 0.5899 (ppp) REVERT: N 234 LYS cc_start: 0.8450 (mmmm) cc_final: 0.8066 (mmmm) REVERT: N 250 ARG cc_start: 0.7047 (mmm-85) cc_final: 0.6392 (mmm-85) REVERT: N 286 LEU cc_start: 0.8511 (mt) cc_final: 0.7862 (mt) REVERT: N 329 TRP cc_start: 0.8968 (t-100) cc_final: 0.8406 (t-100) REVERT: N 356 GLN cc_start: 0.8348 (tt0) cc_final: 0.7663 (tm-30) REVERT: N 394 LYS cc_start: 0.8801 (mmtm) cc_final: 0.8268 (mmtm) REVERT: O 8 MET cc_start: 0.7458 (ttp) cc_final: 0.6825 (ttp) REVERT: P 142 LYS cc_start: 0.8990 (tmtt) cc_final: 0.8472 (tmtt) REVERT: P 195 TRP cc_start: 0.8159 (t60) cc_final: 0.7862 (t60) REVERT: P 197 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.7705 (m90) REVERT: P 258 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8189 (ttm110) outliers start: 276 outliers final: 189 residues processed: 1601 average time/residue: 0.1859 time to fit residues: 480.3953 Evaluate side-chains 1658 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 1460 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 235 TRP Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 31 MET Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain H residue 170 CYS Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 166 LEU Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 301 CYS Chi-restraints excluded: chain I residue 328 CYS Chi-restraints excluded: chain I residue 340 GLN Chi-restraints excluded: chain I residue 341 GLU Chi-restraints excluded: chain I residue 351 LYS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 370 CYS Chi-restraints excluded: chain I residue 426 LEU Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 433 CYS Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 62 HIS Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 235 TRP Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 287 HIS Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 380 SER Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 170 CYS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 258 ARG Chi-restraints excluded: chain L residue 259 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 78 CYS Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 275 ASN Chi-restraints excluded: chain M residue 301 CYS Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 358 THR Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 398 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 162 LYS Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 307 GLU Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 320 VAL Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 147 LYS Chi-restraints excluded: chain P residue 158 LEU Chi-restraints excluded: chain P residue 182 SER Chi-restraints excluded: chain P residue 188 LYS Chi-restraints excluded: chain P residue 197 HIS Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 234 VAL Chi-restraints excluded: chain P residue 250 THR Chi-restraints excluded: chain P residue 251 TRP Chi-restraints excluded: chain P residue 252 ASN Chi-restraints excluded: chain P residue 258 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 150 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 371 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 23 optimal weight: 0.0040 chunk 304 optimal weight: 8.9990 chunk 414 optimal weight: 5.9990 overall best weight: 2.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN B 112 GLN ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 204 GLN ** E 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 170 HIS F 207 ASN F 236 GLN H 252 ASN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 9 ASN M 142 GLN M 204 GLN M 340 GLN ** N 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 255 HIS ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.119725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.099327 restraints weight = 56649.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.102773 restraints weight = 23440.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.104976 restraints weight = 12516.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106181 restraints weight = 7998.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.107064 restraints weight = 6073.518| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 34178 Z= 0.191 Angle : 0.751 9.482 46677 Z= 0.374 Chirality : 0.049 0.284 5266 Planarity : 0.006 0.105 5972 Dihedral : 7.602 61.548 5281 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.84 % Favored : 93.88 % Rotamer: Outliers : 7.88 % Allowed : 29.99 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.42 (0.13), residues: 4233 helix: 1.15 (0.23), residues: 490 sheet: -0.94 (0.14), residues: 1286 loop : -1.39 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 271 TYR 0.028 0.002 TYR N 296 PHE 0.025 0.002 PHE F 237 TRP 0.013 0.001 TRP N 329 HIS 0.010 0.001 HIS H 125 Details of bonding type rmsd covalent geometry : bond 0.00418 (34078) covalent geometry : angle 0.73411 (46445) SS BOND : bond 0.00390 ( 68) SS BOND : angle 1.50867 ( 136) hydrogen bonds : bond 0.03659 ( 1205) hydrogen bonds : angle 5.58460 ( 3159) link_BETA1-4 : bond 0.00887 ( 18) link_BETA1-4 : angle 3.79144 ( 54) link_NAG-ASN : bond 0.00343 ( 14) link_NAG-ASN : angle 2.39295 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1769 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 284 poor density : 1485 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.8829 (tp) cc_final: 0.8513 (tt) REVERT: A 51 TYR cc_start: 0.7988 (p90) cc_final: 0.7281 (p90) REVERT: A 77 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7698 (mm-40) REVERT: A 105 GLU cc_start: 0.7378 (tm-30) cc_final: 0.6942 (tm-30) REVERT: A 115 ARG cc_start: 0.8327 (ttp-110) cc_final: 0.8053 (mtm110) REVERT: A 170 TRP cc_start: 0.9022 (t60) cc_final: 0.8575 (t60) REVERT: A 183 GLU cc_start: 0.7088 (pm20) cc_final: 0.6726 (pm20) REVERT: A 230 HIS cc_start: 0.8224 (p-80) cc_final: 0.7517 (p-80) REVERT: A 257 PHE cc_start: 0.8679 (m-10) cc_final: 0.8353 (m-10) REVERT: A 287 PHE cc_start: 0.8683 (m-80) cc_final: 0.8418 (m-10) REVERT: A 292 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7586 (mp0) REVERT: A 306 CYS cc_start: 0.6810 (t) cc_final: 0.6506 (t) REVERT: A 317 THR cc_start: 0.8764 (t) cc_final: 0.8443 (p) REVERT: A 381 GLU cc_start: 0.7298 (pm20) cc_final: 0.6900 (pm20) REVERT: A 412 LYS cc_start: 0.8226 (mtmt) cc_final: 0.8025 (mtmt) REVERT: B 9 TYR cc_start: 0.8138 (m-80) cc_final: 0.7719 (m-80) REVERT: B 40 GLU cc_start: 0.7526 (mp0) cc_final: 0.7304 (mp0) REVERT: B 97 MET cc_start: 0.7535 (tmm) cc_final: 0.6876 (tmm) REVERT: B 109 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7063 (mm-30) REVERT: B 126 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7712 (mtt-85) REVERT: B 129 TYR cc_start: 0.8216 (t80) cc_final: 0.7818 (t80) REVERT: B 158 GLN cc_start: 0.8658 (mp10) cc_final: 0.8417 (mp10) REVERT: B 169 MET cc_start: 0.7374 (mmm) cc_final: 0.6569 (mmm) REVERT: B 253 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7782 (mtpp) REVERT: B 326 GLU cc_start: 0.7313 (tt0) cc_final: 0.6978 (tt0) REVERT: B 362 TYR cc_start: 0.8464 (m-80) cc_final: 0.8109 (m-80) REVERT: D 116 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7196 (pt0) REVERT: D 141 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7026 (mtp) REVERT: D 265 GLU cc_start: 0.7445 (pp20) cc_final: 0.7044 (pp20) REVERT: E 79 LYS cc_start: 0.7982 (ttpt) cc_final: 0.7582 (mtpt) REVERT: E 87 PHE cc_start: 0.8609 (OUTLIER) cc_final: 0.8398 (m-80) REVERT: E 100 ASN cc_start: 0.7602 (m-40) cc_final: 0.7302 (m-40) REVERT: E 140 VAL cc_start: 0.8277 (t) cc_final: 0.7934 (p) REVERT: E 186 ASN cc_start: 0.8097 (m-40) cc_final: 0.7652 (m-40) REVERT: E 199 ARG cc_start: 0.7790 (mmt180) cc_final: 0.7332 (mmt180) REVERT: E 202 ASP cc_start: 0.7108 (m-30) cc_final: 0.6856 (m-30) REVERT: E 204 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7962 (mm-40) REVERT: E 216 ASN cc_start: 0.8210 (p0) cc_final: 0.7889 (p0) REVERT: E 228 MET cc_start: 0.7403 (tpt) cc_final: 0.7119 (tpt) REVERT: E 246 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6673 (tm-30) REVERT: E 324 LYS cc_start: 0.8621 (pttm) cc_final: 0.8306 (pttm) REVERT: E 336 VAL cc_start: 0.8711 (t) cc_final: 0.8418 (p) REVERT: E 340 GLN cc_start: 0.8719 (tp40) cc_final: 0.8259 (tp40) REVERT: E 407 LEU cc_start: 0.8637 (tp) cc_final: 0.8140 (tp) REVERT: F 7 ASN cc_start: 0.8291 (t0) cc_final: 0.7451 (t0) REVERT: F 10 LYS cc_start: 0.8616 (mtmp) cc_final: 0.7719 (mtmp) REVERT: F 38 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7633 (mtm-85) REVERT: F 40 GLU cc_start: 0.7146 (mp0) cc_final: 0.6909 (mp0) REVERT: F 50 PHE cc_start: 0.8346 (p90) cc_final: 0.7981 (p90) REVERT: F 64 TYR cc_start: 0.8151 (p90) cc_final: 0.7811 (p90) REVERT: F 92 PHE cc_start: 0.8561 (t80) cc_final: 0.7993 (t80) REVERT: F 94 HIS cc_start: 0.7910 (m170) cc_final: 0.7370 (m170) REVERT: F 97 MET cc_start: 0.7909 (tpp) cc_final: 0.7323 (tpp) REVERT: F 112 GLN cc_start: 0.8587 (tt0) cc_final: 0.8354 (tt0) REVERT: F 166 GLU cc_start: 0.7964 (pm20) cc_final: 0.7610 (pm20) REVERT: F 215 MET cc_start: 0.8027 (pmm) cc_final: 0.7507 (pmm) REVERT: F 234 LYS cc_start: 0.8544 (mmmt) cc_final: 0.7839 (mmmm) REVERT: F 254 VAL cc_start: 0.8385 (t) cc_final: 0.8045 (p) REVERT: F 272 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7430 (mm-30) REVERT: F 274 THR cc_start: 0.8636 (m) cc_final: 0.8295 (t) REVERT: F 362 TYR cc_start: 0.8506 (m-80) cc_final: 0.8136 (m-80) REVERT: F 407 VAL cc_start: 0.7093 (t) cc_final: 0.6858 (p) REVERT: H 258 ARG cc_start: 0.8747 (ttm170) cc_final: 0.8283 (ttm170) REVERT: I 2 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7328 (mm-30) REVERT: I 61 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7935 (ttmt) REVERT: I 73 LYS cc_start: 0.7712 (mtpp) cc_final: 0.7486 (ttmm) REVERT: I 76 TYR cc_start: 0.8254 (t80) cc_final: 0.8034 (t80) REVERT: I 139 ASN cc_start: 0.8485 (p0) cc_final: 0.8217 (p0) REVERT: I 146 VAL cc_start: 0.8585 (t) cc_final: 0.8280 (m) REVERT: I 220 LYS cc_start: 0.8272 (ttmt) cc_final: 0.8027 (ttmt) REVERT: I 236 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8538 (p) REVERT: I 237 PRO cc_start: 0.8798 (Cg_exo) cc_final: 0.8499 (Cg_endo) REVERT: I 323 ASP cc_start: 0.7981 (p0) cc_final: 0.7600 (p0) REVERT: I 356 PHE cc_start: 0.8532 (p90) cc_final: 0.8271 (p90) REVERT: I 371 SER cc_start: 0.8839 (t) cc_final: 0.8494 (p) REVERT: I 381 GLU cc_start: 0.7280 (pm20) cc_final: 0.6917 (pm20) REVERT: J 10 LYS cc_start: 0.8823 (tttm) cc_final: 0.8374 (tttm) REVERT: J 97 MET cc_start: 0.7342 (tmm) cc_final: 0.7112 (tmm) REVERT: J 129 TYR cc_start: 0.7772 (t80) cc_final: 0.7188 (t80) REVERT: J 235 TRP cc_start: 0.7828 (OUTLIER) cc_final: 0.7478 (m-10) REVERT: J 331 ASN cc_start: 0.8898 (m110) cc_final: 0.8568 (m110) REVERT: J 362 TYR cc_start: 0.8069 (m-80) cc_final: 0.7634 (m-80) REVERT: L 188 LYS cc_start: 0.9170 (ptpp) cc_final: 0.8583 (ptpp) REVERT: L 218 ASP cc_start: 0.8304 (p0) cc_final: 0.6991 (p0) REVERT: L 221 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6440 (ptp-110) REVERT: L 227 LYS cc_start: 0.8811 (tppt) cc_final: 0.8443 (tppt) REVERT: L 258 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7816 (ttm110) REVERT: M 5 THR cc_start: 0.8652 (OUTLIER) cc_final: 0.8315 (t) REVERT: M 15 TYR cc_start: 0.7717 (t80) cc_final: 0.6895 (t80) REVERT: M 16 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8280 (mmmt) REVERT: M 30 GLN cc_start: 0.8408 (pt0) cc_final: 0.7729 (pt0) REVERT: M 35 GLU cc_start: 0.7859 (pm20) cc_final: 0.7433 (pm20) REVERT: M 50 GLU cc_start: 0.6928 (tp30) cc_final: 0.6702 (tp30) REVERT: M 105 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: M 174 ASP cc_start: 0.7558 (m-30) cc_final: 0.7199 (m-30) REVERT: M 186 ASN cc_start: 0.8667 (p0) cc_final: 0.8105 (p0) REVERT: M 204 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7218 (mm-40) REVERT: M 216 ASN cc_start: 0.8165 (p0) cc_final: 0.7881 (p0) REVERT: M 246 GLU cc_start: 0.7658 (mm-30) cc_final: 0.6919 (tm-30) REVERT: M 292 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7530 (mm-30) REVERT: M 321 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7767 (mtmm) REVERT: M 351 LYS cc_start: 0.8246 (mmmt) cc_final: 0.7844 (mmmt) REVERT: M 411 GLN cc_start: 0.7807 (tp40) cc_final: 0.7187 (tp40) REVERT: N 40 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7099 (mp0) REVERT: N 49 GLN cc_start: 0.8151 (tt0) cc_final: 0.7465 (tp-100) REVERT: N 104 LYS cc_start: 0.8533 (mtmm) cc_final: 0.7971 (mtmm) REVERT: N 140 LYS cc_start: 0.8706 (mmtp) cc_final: 0.8413 (mttp) REVERT: N 166 GLU cc_start: 0.7918 (pm20) cc_final: 0.7576 (pm20) REVERT: N 215 MET cc_start: 0.6121 (ppp) cc_final: 0.5745 (ppp) REVERT: N 224 GLN cc_start: 0.8118 (tp40) cc_final: 0.7496 (tp40) REVERT: N 234 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8078 (mmmm) REVERT: N 250 ARG cc_start: 0.7034 (mmm-85) cc_final: 0.6690 (mmm-85) REVERT: N 272 GLU cc_start: 0.8045 (mp0) cc_final: 0.7550 (mp0) REVERT: N 318 ILE cc_start: 0.8796 (pp) cc_final: 0.8427 (pp) REVERT: N 329 TRP cc_start: 0.8962 (t-100) cc_final: 0.8751 (t-100) REVERT: N 356 GLN cc_start: 0.8349 (tt0) cc_final: 0.7653 (tm-30) REVERT: N 394 LYS cc_start: 0.8847 (mmtm) cc_final: 0.8322 (mmtm) REVERT: O 8 MET cc_start: 0.7438 (ttp) cc_final: 0.6825 (ttp) REVERT: P 142 LYS cc_start: 0.9034 (tmtt) cc_final: 0.8535 (tmtt) REVERT: P 166 TYR cc_start: 0.7835 (m-10) cc_final: 0.7427 (m-10) REVERT: P 195 TRP cc_start: 0.8137 (t60) cc_final: 0.7914 (t60) REVERT: P 197 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7731 (m90) REVERT: P 256 VAL cc_start: 0.8872 (t) cc_final: 0.8624 (t) REVERT: P 258 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8142 (ttm110) outliers start: 284 outliers final: 204 residues processed: 1608 average time/residue: 0.2027 time to fit residues: 524.8319 Evaluate side-chains 1684 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 1466 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 235 TRP Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 204 GLN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 170 HIS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain H residue 170 CYS Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 301 CYS Chi-restraints excluded: chain I residue 328 CYS Chi-restraints excluded: chain I residue 340 GLN Chi-restraints excluded: chain I residue 341 GLU Chi-restraints excluded: chain I residue 351 LYS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 387 ILE Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 62 HIS Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 112 GLN Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 235 TRP Chi-restraints excluded: chain J residue 239 SER Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 287 HIS Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 380 SER Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 170 CYS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 258 ARG Chi-restraints excluded: chain L residue 259 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 112 ASP Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 204 GLN Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 275 ASN Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 301 CYS Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 398 VAL Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 162 LYS Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 307 GLU Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 147 LYS Chi-restraints excluded: chain P residue 158 LEU Chi-restraints excluded: chain P residue 177 MET Chi-restraints excluded: chain P residue 182 SER Chi-restraints excluded: chain P residue 188 LYS Chi-restraints excluded: chain P residue 197 HIS Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 234 VAL Chi-restraints excluded: chain P residue 250 THR Chi-restraints excluded: chain P residue 251 TRP Chi-restraints excluded: chain P residue 258 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 30 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 409 optimal weight: 6.9990 chunk 277 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 416 optimal weight: 50.0000 chunk 129 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 363 optimal weight: 0.0670 overall best weight: 5.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 212 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 204 GLN F 170 HIS F 207 ASN F 236 GLN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 ASN I 77 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 ASN ** N 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 212 ASN N 255 HIS P 186 HIS ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.098217 restraints weight = 56919.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.101583 restraints weight = 23551.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.103794 restraints weight = 12740.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.105038 restraints weight = 8118.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.105928 restraints weight = 6131.387| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.113 34178 Z= 0.315 Angle : 0.793 10.308 46677 Z= 0.398 Chirality : 0.050 0.289 5266 Planarity : 0.006 0.113 5972 Dihedral : 7.335 63.659 5277 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.64 % Favored : 93.08 % Rotamer: Outliers : 8.49 % Allowed : 29.77 % Favored : 61.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.46 (0.13), residues: 4233 helix: 1.11 (0.23), residues: 491 sheet: -0.93 (0.13), residues: 1306 loop : -1.45 (0.13), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 271 TYR 0.031 0.002 TYR N 296 PHE 0.025 0.002 PHE F 294 TRP 0.015 0.002 TRP N 329 HIS 0.024 0.001 HIS F 170 Details of bonding type rmsd covalent geometry : bond 0.00660 (34078) covalent geometry : angle 0.77571 (46445) SS BOND : bond 0.00545 ( 68) SS BOND : angle 1.70535 ( 136) hydrogen bonds : bond 0.03964 ( 1205) hydrogen bonds : angle 5.58771 ( 3159) link_BETA1-4 : bond 0.00735 ( 18) link_BETA1-4 : angle 3.76182 ( 54) link_NAG-ASN : bond 0.00315 ( 14) link_NAG-ASN : angle 2.36249 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1805 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 306 poor density : 1499 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7912 (p90) cc_final: 0.7231 (p90) REVERT: A 105 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6915 (tm-30) REVERT: A 115 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.7897 (mtm110) REVERT: A 170 TRP cc_start: 0.9046 (t60) cc_final: 0.8633 (t60) REVERT: A 230 HIS cc_start: 0.8291 (p-80) cc_final: 0.7692 (p-80) REVERT: A 257 PHE cc_start: 0.8727 (m-10) cc_final: 0.8399 (m-10) REVERT: A 287 PHE cc_start: 0.8722 (m-80) cc_final: 0.8441 (m-10) REVERT: A 292 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: A 306 CYS cc_start: 0.6788 (t) cc_final: 0.6574 (t) REVERT: A 317 THR cc_start: 0.8785 (t) cc_final: 0.8478 (p) REVERT: A 366 VAL cc_start: 0.8850 (OUTLIER) cc_final: 0.8647 (m) REVERT: A 381 GLU cc_start: 0.7308 (pm20) cc_final: 0.6916 (pm20) REVERT: B 9 TYR cc_start: 0.8224 (m-80) cc_final: 0.7752 (m-80) REVERT: B 40 GLU cc_start: 0.7559 (mp0) cc_final: 0.7328 (mp0) REVERT: B 69 TYR cc_start: 0.7926 (p90) cc_final: 0.7692 (p90) REVERT: B 75 ILE cc_start: 0.8711 (mp) cc_final: 0.8337 (mt) REVERT: B 97 MET cc_start: 0.7529 (tmm) cc_final: 0.6915 (tmm) REVERT: B 109 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7100 (mm-30) REVERT: B 129 TYR cc_start: 0.8272 (t80) cc_final: 0.7878 (t80) REVERT: B 156 TYR cc_start: 0.8604 (m-10) cc_final: 0.8231 (m-10) REVERT: B 169 MET cc_start: 0.7407 (mmm) cc_final: 0.6631 (mmm) REVERT: B 253 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7829 (mtpp) REVERT: B 280 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.7201 (mpp80) REVERT: B 326 GLU cc_start: 0.7349 (tt0) cc_final: 0.7038 (tt0) REVERT: B 327 TYR cc_start: 0.8681 (p90) cc_final: 0.8456 (p90) REVERT: B 362 TYR cc_start: 0.8519 (m-80) cc_final: 0.8073 (m-80) REVERT: D 116 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7233 (pt0) REVERT: D 141 MET cc_start: 0.7373 (OUTLIER) cc_final: 0.7029 (mtp) REVERT: D 265 GLU cc_start: 0.7592 (pp20) cc_final: 0.7207 (pp20) REVERT: E 77 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: E 79 LYS cc_start: 0.8004 (ttpt) cc_final: 0.7604 (mtpt) REVERT: E 100 ASN cc_start: 0.7796 (m-40) cc_final: 0.7509 (m-40) REVERT: E 140 VAL cc_start: 0.8250 (t) cc_final: 0.7788 (p) REVERT: E 176 LYS cc_start: 0.8504 (mmtp) cc_final: 0.7870 (mmtp) REVERT: E 186 ASN cc_start: 0.8126 (m-40) cc_final: 0.7681 (m-40) REVERT: E 199 ARG cc_start: 0.7799 (mmt180) cc_final: 0.7269 (mmt180) REVERT: E 216 ASN cc_start: 0.8285 (p0) cc_final: 0.7967 (p0) REVERT: E 238 SER cc_start: 0.8167 (t) cc_final: 0.7840 (t) REVERT: E 246 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6758 (tm-30) REVERT: E 324 LYS cc_start: 0.8663 (pttm) cc_final: 0.8391 (pttm) REVERT: E 336 VAL cc_start: 0.8717 (t) cc_final: 0.8398 (p) REVERT: E 407 LEU cc_start: 0.8674 (tp) cc_final: 0.8213 (tp) REVERT: F 7 ASN cc_start: 0.8323 (t0) cc_final: 0.7563 (t0) REVERT: F 10 LYS cc_start: 0.8626 (mtmp) cc_final: 0.7996 (mtmp) REVERT: F 13 ARG cc_start: 0.8522 (ptm160) cc_final: 0.8182 (ptm-80) REVERT: F 38 ARG cc_start: 0.8036 (mtm-85) cc_final: 0.7745 (mtm-85) REVERT: F 40 GLU cc_start: 0.7195 (mp0) cc_final: 0.6938 (mp0) REVERT: F 50 PHE cc_start: 0.8330 (p90) cc_final: 0.8072 (p90) REVERT: F 62 HIS cc_start: 0.7970 (OUTLIER) cc_final: 0.7486 (t70) REVERT: F 64 TYR cc_start: 0.8160 (p90) cc_final: 0.7814 (p90) REVERT: F 92 PHE cc_start: 0.8582 (t80) cc_final: 0.8027 (t80) REVERT: F 94 HIS cc_start: 0.7976 (m170) cc_final: 0.7363 (m170) REVERT: F 97 MET cc_start: 0.7943 (tpp) cc_final: 0.7343 (tpp) REVERT: F 112 GLN cc_start: 0.8594 (tt0) cc_final: 0.8334 (tt0) REVERT: F 166 GLU cc_start: 0.7959 (pm20) cc_final: 0.7649 (pm20) REVERT: F 272 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7469 (mm-30) REVERT: F 274 THR cc_start: 0.8632 (m) cc_final: 0.8347 (t) REVERT: F 361 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8237 (tp) REVERT: F 362 TYR cc_start: 0.8555 (m-80) cc_final: 0.8200 (m-80) REVERT: F 399 TYR cc_start: 0.8307 (m-10) cc_final: 0.8049 (m-10) REVERT: H 258 ARG cc_start: 0.8775 (ttm170) cc_final: 0.8298 (ttm170) REVERT: I 2 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7307 (mm-30) REVERT: I 50 GLU cc_start: 0.6786 (tp30) cc_final: 0.6537 (tp30) REVERT: I 61 LYS cc_start: 0.8384 (ttmt) cc_final: 0.7925 (ttmt) REVERT: I 73 LYS cc_start: 0.7819 (mtpp) cc_final: 0.7567 (ttmm) REVERT: I 76 TYR cc_start: 0.8244 (t80) cc_final: 0.7974 (t80) REVERT: I 139 ASN cc_start: 0.8483 (p0) cc_final: 0.8189 (p0) REVERT: I 146 VAL cc_start: 0.8619 (t) cc_final: 0.8287 (m) REVERT: I 220 LYS cc_start: 0.8331 (ttmt) cc_final: 0.8099 (ttmt) REVERT: I 221 LEU cc_start: 0.8518 (pt) cc_final: 0.8301 (pp) REVERT: I 356 PHE cc_start: 0.8554 (p90) cc_final: 0.8267 (p90) REVERT: I 371 SER cc_start: 0.8893 (t) cc_final: 0.8563 (p) REVERT: I 381 GLU cc_start: 0.7266 (pm20) cc_final: 0.6881 (pm20) REVERT: J 10 LYS cc_start: 0.8855 (tttm) cc_final: 0.8437 (tttm) REVERT: J 97 MET cc_start: 0.7418 (tmm) cc_final: 0.7185 (tmm) REVERT: J 153 CYS cc_start: 0.5582 (m) cc_final: 0.5061 (m) REVERT: J 169 MET cc_start: 0.7333 (mmt) cc_final: 0.7053 (mmt) REVERT: J 235 TRP cc_start: 0.7840 (OUTLIER) cc_final: 0.7489 (m-10) REVERT: J 250 ARG cc_start: 0.7605 (mmm-85) cc_final: 0.7318 (mmm-85) REVERT: J 331 ASN cc_start: 0.8871 (m110) cc_final: 0.8600 (m110) REVERT: J 362 TYR cc_start: 0.8165 (m-80) cc_final: 0.7802 (m-80) REVERT: L 188 LYS cc_start: 0.9177 (ptpp) cc_final: 0.8591 (ptpp) REVERT: L 215 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7736 (mmtt) REVERT: L 218 ASP cc_start: 0.8283 (p0) cc_final: 0.8052 (p0) REVERT: L 227 LYS cc_start: 0.8893 (tppt) cc_final: 0.8423 (tppt) REVERT: L 258 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.7876 (ttm110) REVERT: M 5 THR cc_start: 0.8659 (OUTLIER) cc_final: 0.8151 (t) REVERT: M 15 TYR cc_start: 0.7837 (t80) cc_final: 0.7098 (t80) REVERT: M 35 GLU cc_start: 0.7814 (pm20) cc_final: 0.7430 (pm20) REVERT: M 94 CYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7081 (m) REVERT: M 100 ASN cc_start: 0.7609 (m110) cc_final: 0.6619 (m-40) REVERT: M 105 GLU cc_start: 0.7522 (tt0) cc_final: 0.7236 (tt0) REVERT: M 174 ASP cc_start: 0.7609 (m-30) cc_final: 0.7231 (m-30) REVERT: M 186 ASN cc_start: 0.8663 (p0) cc_final: 0.8163 (p0) REVERT: M 204 GLN cc_start: 0.8085 (mm-40) cc_final: 0.7358 (mm-40) REVERT: M 216 ASN cc_start: 0.8221 (p0) cc_final: 0.7890 (p0) REVERT: M 246 GLU cc_start: 0.7666 (mm-30) cc_final: 0.6974 (tm-30) REVERT: M 292 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7545 (mm-30) REVERT: M 305 THR cc_start: 0.8666 (t) cc_final: 0.8303 (p) REVERT: M 321 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7778 (mtmm) REVERT: M 351 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7915 (mmmt) REVERT: M 381 GLU cc_start: 0.7640 (pm20) cc_final: 0.7384 (pm20) REVERT: N 40 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7169 (mp0) REVERT: N 53 GLN cc_start: 0.8321 (mp10) cc_final: 0.8087 (mp10) REVERT: N 96 THR cc_start: 0.8177 (p) cc_final: 0.7900 (p) REVERT: N 104 LYS cc_start: 0.8545 (mtmm) cc_final: 0.7953 (mtmm) REVERT: N 140 LYS cc_start: 0.8753 (mmtp) cc_final: 0.8441 (mttp) REVERT: N 166 GLU cc_start: 0.7855 (pm20) cc_final: 0.7477 (pm20) REVERT: N 177 ASP cc_start: 0.7958 (p0) cc_final: 0.7515 (p0) REVERT: N 215 MET cc_start: 0.6076 (ppp) cc_final: 0.5642 (ppp) REVERT: N 224 GLN cc_start: 0.8143 (tp40) cc_final: 0.7608 (tp40) REVERT: N 234 LYS cc_start: 0.8473 (mmmm) cc_final: 0.8078 (mmmm) REVERT: N 238 ASN cc_start: 0.8521 (t0) cc_final: 0.8276 (t0) REVERT: N 244 ARG cc_start: 0.7853 (mmm-85) cc_final: 0.7642 (mmm-85) REVERT: N 272 GLU cc_start: 0.8060 (mp0) cc_final: 0.7553 (mp0) REVERT: N 282 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8454 (t) REVERT: N 318 ILE cc_start: 0.8820 (pp) cc_final: 0.8527 (pp) REVERT: N 356 GLN cc_start: 0.8371 (tt0) cc_final: 0.7693 (tm-30) REVERT: N 394 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8376 (mmtm) REVERT: O 8 MET cc_start: 0.7487 (ttp) cc_final: 0.6901 (ttp) REVERT: P 142 LYS cc_start: 0.9090 (tmtt) cc_final: 0.8577 (tmtt) REVERT: P 162 LYS cc_start: 0.7954 (mttp) cc_final: 0.7693 (mmtp) REVERT: P 197 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7708 (m90) REVERT: P 258 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7814 (ttm110) outliers start: 306 outliers final: 219 residues processed: 1628 average time/residue: 0.2008 time to fit residues: 524.2326 Evaluate side-chains 1712 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 1478 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 235 TRP Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 62 HIS Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 387 MET Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain H residue 170 CYS Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 219 LEU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 301 CYS Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 328 CYS Chi-restraints excluded: chain I residue 347 LYS Chi-restraints excluded: chain I residue 351 LYS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 370 CYS Chi-restraints excluded: chain I residue 387 ILE Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 433 CYS Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 62 HIS Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 235 TRP Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 287 HIS Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 380 SER Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain J residue 394 LYS Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 170 CYS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 258 ARG Chi-restraints excluded: chain L residue 259 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 252 ASN Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 301 CYS Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 348 THR Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 398 VAL Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 162 LYS Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 274 THR Chi-restraints excluded: chain N residue 282 VAL Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 307 GLU Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain N residue 388 LEU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 158 LEU Chi-restraints excluded: chain P residue 177 MET Chi-restraints excluded: chain P residue 182 SER Chi-restraints excluded: chain P residue 197 HIS Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 234 VAL Chi-restraints excluded: chain P residue 250 THR Chi-restraints excluded: chain P residue 251 TRP Chi-restraints excluded: chain P residue 252 ASN Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 258 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 223 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 329 optimal weight: 2.9990 chunk 412 optimal weight: 7.9990 chunk 296 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 201 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS B 112 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 204 GLN E 260 GLN E 340 GLN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 252 ASN I 77 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 255 HIS P 192 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.120849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.100526 restraints weight = 56388.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104044 restraints weight = 23267.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.106186 restraints weight = 12295.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.107588 restraints weight = 7902.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108250 restraints weight = 5865.379| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34178 Z= 0.163 Angle : 0.753 13.655 46677 Z= 0.374 Chirality : 0.048 0.279 5266 Planarity : 0.006 0.110 5972 Dihedral : 7.062 63.897 5274 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.84 % Favored : 93.95 % Rotamer: Outliers : 7.77 % Allowed : 31.41 % Favored : 60.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.37 (0.13), residues: 4233 helix: 1.21 (0.23), residues: 493 sheet: -0.88 (0.13), residues: 1298 loop : -1.38 (0.13), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 271 TYR 0.028 0.002 TYR E 214 PHE 0.027 0.002 PHE E 312 TRP 0.012 0.001 TRP E 170 HIS 0.009 0.001 HIS L 196 Details of bonding type rmsd covalent geometry : bond 0.00365 (34078) covalent geometry : angle 0.73605 (46445) SS BOND : bond 0.00511 ( 68) SS BOND : angle 1.72318 ( 136) hydrogen bonds : bond 0.03503 ( 1205) hydrogen bonds : angle 5.45412 ( 3159) link_BETA1-4 : bond 0.00829 ( 18) link_BETA1-4 : angle 3.51241 ( 54) link_NAG-ASN : bond 0.00337 ( 14) link_NAG-ASN : angle 2.33206 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1747 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 280 poor density : 1467 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7875 (p90) cc_final: 0.7234 (p90) REVERT: A 115 ARG cc_start: 0.8264 (ttp-110) cc_final: 0.7828 (mtm110) REVERT: A 170 TRP cc_start: 0.9001 (t60) cc_final: 0.8688 (t60) REVERT: A 183 GLU cc_start: 0.7074 (pm20) cc_final: 0.6746 (pm20) REVERT: A 230 HIS cc_start: 0.8289 (p-80) cc_final: 0.7770 (p-80) REVERT: A 257 PHE cc_start: 0.8642 (m-10) cc_final: 0.8316 (m-10) REVERT: A 262 LYS cc_start: 0.8280 (mmtm) cc_final: 0.7978 (mmtm) REVERT: A 287 PHE cc_start: 0.8682 (m-80) cc_final: 0.8424 (m-10) REVERT: A 292 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: A 306 CYS cc_start: 0.6764 (t) cc_final: 0.6536 (t) REVERT: A 317 THR cc_start: 0.8779 (t) cc_final: 0.8481 (p) REVERT: A 354 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8148 (mt) REVERT: A 366 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8600 (m) REVERT: A 381 GLU cc_start: 0.7279 (pm20) cc_final: 0.6890 (pm20) REVERT: B 9 TYR cc_start: 0.8123 (m-80) cc_final: 0.7653 (m-80) REVERT: B 40 GLU cc_start: 0.7518 (mp0) cc_final: 0.7104 (mp0) REVERT: B 69 TYR cc_start: 0.7856 (p90) cc_final: 0.7634 (p90) REVERT: B 97 MET cc_start: 0.7437 (tmm) cc_final: 0.6879 (tmm) REVERT: B 109 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7044 (mm-30) REVERT: B 129 TYR cc_start: 0.8211 (t80) cc_final: 0.7790 (t80) REVERT: B 156 TYR cc_start: 0.8576 (m-10) cc_final: 0.8175 (m-10) REVERT: B 169 MET cc_start: 0.7385 (mmm) cc_final: 0.6578 (mmm) REVERT: B 196 LYS cc_start: 0.8513 (ttmp) cc_final: 0.7902 (tptt) REVERT: B 254 VAL cc_start: 0.8125 (OUTLIER) cc_final: 0.7531 (m) REVERT: B 280 ARG cc_start: 0.8859 (OUTLIER) cc_final: 0.7124 (mpp80) REVERT: B 326 GLU cc_start: 0.7294 (tt0) cc_final: 0.6960 (tt0) REVERT: B 357 TYR cc_start: 0.8542 (t80) cc_final: 0.8170 (t80) REVERT: B 362 TYR cc_start: 0.8433 (m-80) cc_final: 0.7972 (m-80) REVERT: D 116 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7177 (pt0) REVERT: D 206 ARG cc_start: 0.7510 (mtt180) cc_final: 0.7080 (mtt180) REVERT: D 265 GLU cc_start: 0.7592 (pp20) cc_final: 0.7202 (pp20) REVERT: E 79 LYS cc_start: 0.7957 (ttpt) cc_final: 0.7545 (mtpt) REVERT: E 100 ASN cc_start: 0.7706 (m-40) cc_final: 0.7457 (m-40) REVERT: E 140 VAL cc_start: 0.8196 (t) cc_final: 0.7840 (p) REVERT: E 176 LYS cc_start: 0.8514 (mmtp) cc_final: 0.7845 (mmtp) REVERT: E 186 ASN cc_start: 0.8081 (m-40) cc_final: 0.7591 (m-40) REVERT: E 199 ARG cc_start: 0.7764 (mmt180) cc_final: 0.7427 (mmt180) REVERT: E 216 ASN cc_start: 0.8112 (p0) cc_final: 0.7817 (p0) REVERT: E 246 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6704 (tm-30) REVERT: E 324 LYS cc_start: 0.8594 (pttm) cc_final: 0.8292 (pttm) REVERT: E 336 VAL cc_start: 0.8720 (t) cc_final: 0.8411 (p) REVERT: E 407 LEU cc_start: 0.8640 (tp) cc_final: 0.8090 (tp) REVERT: F 7 ASN cc_start: 0.8298 (t0) cc_final: 0.7573 (t0) REVERT: F 10 LYS cc_start: 0.8705 (mtmp) cc_final: 0.7788 (mtmp) REVERT: F 35 GLU cc_start: 0.7064 (tt0) cc_final: 0.6833 (tt0) REVERT: F 38 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7663 (mtm-85) REVERT: F 40 GLU cc_start: 0.7154 (mp0) cc_final: 0.6877 (mp0) REVERT: F 64 TYR cc_start: 0.8127 (p90) cc_final: 0.7765 (p90) REVERT: F 97 MET cc_start: 0.7892 (tpp) cc_final: 0.7262 (tpp) REVERT: F 112 GLN cc_start: 0.8546 (tt0) cc_final: 0.8267 (tt0) REVERT: F 166 GLU cc_start: 0.7928 (pm20) cc_final: 0.7623 (pm20) REVERT: F 195 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7614 (tptp) REVERT: F 234 LYS cc_start: 0.8551 (mmmt) cc_final: 0.7814 (mmmm) REVERT: F 272 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7430 (mm-30) REVERT: F 274 THR cc_start: 0.8612 (m) cc_final: 0.8271 (t) REVERT: F 326 GLU cc_start: 0.7538 (tt0) cc_final: 0.7286 (tt0) REVERT: F 346 LYS cc_start: 0.8363 (mptt) cc_final: 0.7920 (mptt) REVERT: H 170 CYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7466 (p) REVERT: H 258 ARG cc_start: 0.8756 (ttm170) cc_final: 0.8294 (ttm170) REVERT: I 2 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7292 (mm-30) REVERT: I 61 LYS cc_start: 0.8276 (ttmt) cc_final: 0.7896 (ttmt) REVERT: I 73 LYS cc_start: 0.7769 (mtpp) cc_final: 0.7523 (ttmm) REVERT: I 146 VAL cc_start: 0.8586 (t) cc_final: 0.8285 (m) REVERT: I 220 LYS cc_start: 0.8302 (ttmt) cc_final: 0.8049 (ttmt) REVERT: I 221 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8273 (pp) REVERT: I 234 THR cc_start: 0.8216 (t) cc_final: 0.7713 (t) REVERT: I 236 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8525 (p) REVERT: I 356 PHE cc_start: 0.8553 (p90) cc_final: 0.8292 (p90) REVERT: I 371 SER cc_start: 0.8808 (t) cc_final: 0.8561 (p) REVERT: I 381 GLU cc_start: 0.7263 (pm20) cc_final: 0.6862 (pm20) REVERT: J 10 LYS cc_start: 0.8820 (tttm) cc_final: 0.8386 (tttm) REVERT: J 61 ASN cc_start: 0.7907 (t0) cc_final: 0.7559 (t0) REVERT: J 129 TYR cc_start: 0.7759 (t80) cc_final: 0.7167 (t80) REVERT: J 169 MET cc_start: 0.7324 (mmt) cc_final: 0.7066 (mmt) REVERT: J 235 TRP cc_start: 0.7794 (OUTLIER) cc_final: 0.7464 (m-10) REVERT: J 320 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8488 (t) REVERT: J 331 ASN cc_start: 0.8839 (m110) cc_final: 0.8489 (m110) REVERT: J 362 TYR cc_start: 0.8091 (m-80) cc_final: 0.7777 (m-80) REVERT: L 161 LYS cc_start: 0.8515 (tttm) cc_final: 0.8268 (pttm) REVERT: L 188 LYS cc_start: 0.9178 (ptpp) cc_final: 0.8580 (ptpp) REVERT: L 218 ASP cc_start: 0.8276 (p0) cc_final: 0.7821 (p0) REVERT: L 227 LYS cc_start: 0.8846 (tppt) cc_final: 0.8343 (tppt) REVERT: L 258 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7885 (ttm110) REVERT: M 15 TYR cc_start: 0.7783 (t80) cc_final: 0.7281 (t80) REVERT: M 35 GLU cc_start: 0.7821 (pm20) cc_final: 0.7422 (pm20) REVERT: M 59 TYR cc_start: 0.8622 (t80) cc_final: 0.8359 (t80) REVERT: M 94 CYS cc_start: 0.7423 (OUTLIER) cc_final: 0.7064 (m) REVERT: M 100 ASN cc_start: 0.7512 (m110) cc_final: 0.6581 (m-40) REVERT: M 105 GLU cc_start: 0.7531 (tt0) cc_final: 0.7254 (tt0) REVERT: M 174 ASP cc_start: 0.7615 (m-30) cc_final: 0.7265 (m-30) REVERT: M 183 GLU cc_start: 0.7346 (pm20) cc_final: 0.6930 (pm20) REVERT: M 186 ASN cc_start: 0.8627 (p0) cc_final: 0.8085 (p0) REVERT: M 216 ASN cc_start: 0.8107 (p0) cc_final: 0.7851 (p0) REVERT: M 246 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6918 (tm-30) REVERT: M 292 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7524 (mm-30) REVERT: M 305 THR cc_start: 0.8586 (t) cc_final: 0.8252 (p) REVERT: M 321 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7723 (mtmm) REVERT: M 351 LYS cc_start: 0.8252 (mmmt) cc_final: 0.7832 (mmmt) REVERT: M 381 GLU cc_start: 0.7621 (pm20) cc_final: 0.7350 (pm20) REVERT: M 411 GLN cc_start: 0.7811 (tp40) cc_final: 0.7199 (tp40) REVERT: N 40 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7178 (mp0) REVERT: N 49 GLN cc_start: 0.8195 (tt0) cc_final: 0.7485 (tp-100) REVERT: N 104 LYS cc_start: 0.8538 (mtmm) cc_final: 0.7958 (mtmm) REVERT: N 140 LYS cc_start: 0.8719 (mmtp) cc_final: 0.8399 (mttp) REVERT: N 157 GLN cc_start: 0.7836 (tt0) cc_final: 0.7614 (tt0) REVERT: N 166 GLU cc_start: 0.7811 (pm20) cc_final: 0.7460 (pm20) REVERT: N 177 ASP cc_start: 0.7871 (p0) cc_final: 0.7321 (p0) REVERT: N 215 MET cc_start: 0.6047 (ppp) cc_final: 0.5655 (ppp) REVERT: N 223 GLU cc_start: 0.7728 (mp0) cc_final: 0.7489 (mp0) REVERT: N 234 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8120 (mmmm) REVERT: N 250 ARG cc_start: 0.7080 (mmm-85) cc_final: 0.6375 (mmm-85) REVERT: N 272 GLU cc_start: 0.8060 (mp0) cc_final: 0.7565 (mp0) REVERT: N 356 GLN cc_start: 0.8349 (tt0) cc_final: 0.7659 (tm-30) REVERT: N 394 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8289 (mmtm) REVERT: O 8 MET cc_start: 0.7489 (ttp) cc_final: 0.6887 (ttp) REVERT: P 142 LYS cc_start: 0.9074 (tmtt) cc_final: 0.8559 (tmtt) REVERT: P 166 TYR cc_start: 0.7825 (m-10) cc_final: 0.7347 (m-10) REVERT: P 197 HIS cc_start: 0.7973 (OUTLIER) cc_final: 0.7676 (m90) REVERT: P 215 LYS cc_start: 0.8500 (pmtt) cc_final: 0.8197 (pmtt) REVERT: P 255 MET cc_start: 0.5993 (tpp) cc_final: 0.5751 (tpp) REVERT: P 258 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7715 (ttm110) outliers start: 280 outliers final: 217 residues processed: 1582 average time/residue: 0.1920 time to fit residues: 487.5810 Evaluate side-chains 1687 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 1453 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 139 GLU Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 235 TRP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 MET Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain H residue 170 CYS Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 219 LEU Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 328 CYS Chi-restraints excluded: chain I residue 341 GLU Chi-restraints excluded: chain I residue 347 LYS Chi-restraints excluded: chain I residue 351 LYS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 387 ILE Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 62 HIS Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 235 TRP Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 287 HIS Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 320 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 352 HIS Chi-restraints excluded: chain J residue 375 LEU Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain J residue 393 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 170 CYS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 258 ARG Chi-restraints excluded: chain L residue 259 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 266 VAL Chi-restraints excluded: chain M residue 301 CYS Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 348 THR Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 398 VAL Chi-restraints excluded: chain M residue 436 LEU Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 162 LYS Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 307 GLU Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 158 LEU Chi-restraints excluded: chain P residue 177 MET Chi-restraints excluded: chain P residue 182 SER Chi-restraints excluded: chain P residue 197 HIS Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 234 VAL Chi-restraints excluded: chain P residue 250 THR Chi-restraints excluded: chain P residue 251 TRP Chi-restraints excluded: chain P residue 258 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 59 optimal weight: 3.9990 chunk 293 optimal weight: 30.0000 chunk 320 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 401 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 327 optimal weight: 7.9990 chunk 410 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 204 GLN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 255 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.099591 restraints weight = 56485.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.103053 restraints weight = 23317.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.105265 restraints weight = 12416.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.106487 restraints weight = 7912.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107422 restraints weight = 5981.753| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 34178 Z= 0.246 Angle : 0.776 13.224 46677 Z= 0.387 Chirality : 0.049 0.276 5266 Planarity : 0.006 0.107 5972 Dihedral : 7.017 65.079 5274 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.57 % Favored : 93.17 % Rotamer: Outliers : 7.91 % Allowed : 31.85 % Favored : 60.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.40 (0.13), residues: 4233 helix: 1.21 (0.23), residues: 494 sheet: -0.84 (0.13), residues: 1304 loop : -1.45 (0.13), residues: 2435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 271 TYR 0.028 0.002 TYR N 296 PHE 0.023 0.002 PHE F 294 TRP 0.030 0.002 TRP I 170 HIS 0.013 0.001 HIS F 287 Details of bonding type rmsd covalent geometry : bond 0.00525 (34078) covalent geometry : angle 0.75987 (46445) SS BOND : bond 0.00453 ( 68) SS BOND : angle 1.75385 ( 136) hydrogen bonds : bond 0.03706 ( 1205) hydrogen bonds : angle 5.45827 ( 3159) link_BETA1-4 : bond 0.00732 ( 18) link_BETA1-4 : angle 3.45825 ( 54) link_NAG-ASN : bond 0.00266 ( 14) link_NAG-ASN : angle 2.37406 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1764 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 285 poor density : 1479 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7813 (p90) cc_final: 0.7132 (p90) REVERT: A 115 ARG cc_start: 0.8293 (ttp-110) cc_final: 0.7973 (mtm110) REVERT: A 155 THR cc_start: 0.8609 (m) cc_final: 0.8378 (t) REVERT: A 170 TRP cc_start: 0.9023 (t60) cc_final: 0.8692 (t60) REVERT: A 174 ASP cc_start: 0.7655 (m-30) cc_final: 0.7131 (m-30) REVERT: A 230 HIS cc_start: 0.8330 (p-80) cc_final: 0.7849 (p-80) REVERT: A 257 PHE cc_start: 0.8671 (m-10) cc_final: 0.8376 (m-10) REVERT: A 262 LYS cc_start: 0.8322 (mmtm) cc_final: 0.7999 (mmtm) REVERT: A 287 PHE cc_start: 0.8704 (m-80) cc_final: 0.8405 (m-10) REVERT: A 292 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: A 306 CYS cc_start: 0.6722 (t) cc_final: 0.6514 (t) REVERT: A 317 THR cc_start: 0.8783 (t) cc_final: 0.8498 (p) REVERT: A 366 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8633 (m) REVERT: A 381 GLU cc_start: 0.7269 (pm20) cc_final: 0.6888 (pm20) REVERT: A 401 ASP cc_start: 0.7484 (t0) cc_final: 0.7243 (t0) REVERT: B 9 TYR cc_start: 0.8165 (m-80) cc_final: 0.7817 (m-80) REVERT: B 40 GLU cc_start: 0.7544 (mp0) cc_final: 0.7126 (mp0) REVERT: B 96 THR cc_start: 0.8257 (m) cc_final: 0.7675 (p) REVERT: B 97 MET cc_start: 0.7467 (tmm) cc_final: 0.7162 (tmm) REVERT: B 109 GLU cc_start: 0.7328 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 129 TYR cc_start: 0.8230 (t80) cc_final: 0.7840 (t80) REVERT: B 156 TYR cc_start: 0.8628 (m-10) cc_final: 0.8238 (m-10) REVERT: B 169 MET cc_start: 0.7415 (mmm) cc_final: 0.6548 (mmm) REVERT: B 254 VAL cc_start: 0.8203 (OUTLIER) cc_final: 0.7635 (m) REVERT: B 280 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.7207 (mpp80) REVERT: B 326 GLU cc_start: 0.7378 (tt0) cc_final: 0.7092 (tt0) REVERT: B 357 TYR cc_start: 0.8567 (t80) cc_final: 0.8181 (t80) REVERT: B 362 TYR cc_start: 0.8485 (m-80) cc_final: 0.7972 (m-80) REVERT: D 116 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7112 (pt0) REVERT: D 141 MET cc_start: 0.7402 (mtp) cc_final: 0.7060 (mtp) REVERT: D 206 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7057 (mtt180) REVERT: D 215 LYS cc_start: 0.8539 (mttt) cc_final: 0.7989 (mttt) REVERT: D 265 GLU cc_start: 0.7648 (pp20) cc_final: 0.7259 (pp20) REVERT: E 79 LYS cc_start: 0.7957 (ttpt) cc_final: 0.7554 (mtpt) REVERT: E 100 ASN cc_start: 0.7794 (m-40) cc_final: 0.7512 (m-40) REVERT: E 140 VAL cc_start: 0.8200 (t) cc_final: 0.7840 (p) REVERT: E 176 LYS cc_start: 0.8524 (mmtp) cc_final: 0.7791 (mmtp) REVERT: E 186 ASN cc_start: 0.8092 (m-40) cc_final: 0.7691 (m-40) REVERT: E 199 ARG cc_start: 0.7777 (mmt180) cc_final: 0.7394 (mmt180) REVERT: E 216 ASN cc_start: 0.8252 (p0) cc_final: 0.7935 (p0) REVERT: E 228 MET cc_start: 0.7206 (tpt) cc_final: 0.6830 (tpt) REVERT: E 246 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6798 (tm-30) REVERT: E 324 LYS cc_start: 0.8631 (pttm) cc_final: 0.8337 (pttm) REVERT: E 336 VAL cc_start: 0.8706 (t) cc_final: 0.8407 (p) REVERT: E 340 GLN cc_start: 0.8843 (tp40) cc_final: 0.8546 (tp40) REVERT: E 407 LEU cc_start: 0.8679 (tp) cc_final: 0.8176 (tp) REVERT: F 10 LYS cc_start: 0.8702 (mtmp) cc_final: 0.8371 (mtmp) REVERT: F 13 ARG cc_start: 0.8496 (ptm160) cc_final: 0.8154 (ptm-80) REVERT: F 35 GLU cc_start: 0.7066 (tt0) cc_final: 0.6657 (tt0) REVERT: F 38 ARG cc_start: 0.8012 (mtm-85) cc_final: 0.7758 (mtm-85) REVERT: F 40 GLU cc_start: 0.7140 (mp0) cc_final: 0.6884 (mp0) REVERT: F 64 TYR cc_start: 0.8091 (p90) cc_final: 0.7785 (p90) REVERT: F 97 MET cc_start: 0.7894 (tpp) cc_final: 0.7249 (tpp) REVERT: F 111 LEU cc_start: 0.8375 (tp) cc_final: 0.8171 (tt) REVERT: F 112 GLN cc_start: 0.8576 (tt0) cc_final: 0.8329 (tt0) REVERT: F 166 GLU cc_start: 0.7921 (pm20) cc_final: 0.7627 (pm20) REVERT: F 195 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7671 (tptp) REVERT: F 272 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7457 (mm-30) REVERT: F 274 THR cc_start: 0.8622 (m) cc_final: 0.8298 (t) REVERT: F 326 GLU cc_start: 0.7546 (tt0) cc_final: 0.7283 (tt0) REVERT: F 346 LYS cc_start: 0.8382 (mptt) cc_final: 0.7901 (mptt) REVERT: F 399 TYR cc_start: 0.8271 (m-10) cc_final: 0.8037 (m-10) REVERT: H 170 CYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7416 (p) REVERT: H 258 ARG cc_start: 0.8775 (ttm170) cc_final: 0.8304 (ttm170) REVERT: I 2 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7294 (mm-30) REVERT: I 50 GLU cc_start: 0.6776 (tp30) cc_final: 0.6551 (tp30) REVERT: I 61 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7915 (ttmt) REVERT: I 73 LYS cc_start: 0.7809 (mtpp) cc_final: 0.7561 (ttmm) REVERT: I 102 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: I 146 VAL cc_start: 0.8599 (t) cc_final: 0.8273 (m) REVERT: I 221 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8290 (pp) REVERT: I 356 PHE cc_start: 0.8537 (p90) cc_final: 0.8261 (p90) REVERT: I 371 SER cc_start: 0.8849 (t) cc_final: 0.8584 (p) REVERT: I 381 GLU cc_start: 0.7290 (pm20) cc_final: 0.6877 (pm20) REVERT: J 10 LYS cc_start: 0.8841 (tttm) cc_final: 0.8387 (tttm) REVERT: J 61 ASN cc_start: 0.7932 (t0) cc_final: 0.7578 (t0) REVERT: J 68 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7806 (ttp80) REVERT: J 129 TYR cc_start: 0.7795 (t80) cc_final: 0.7224 (t80) REVERT: J 169 MET cc_start: 0.7338 (mmt) cc_final: 0.7057 (mmt) REVERT: J 235 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.7455 (m-10) REVERT: J 320 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8433 (t) REVERT: J 331 ASN cc_start: 0.8839 (m110) cc_final: 0.8512 (m110) REVERT: J 362 TYR cc_start: 0.8153 (m-80) cc_final: 0.7871 (m-80) REVERT: L 188 LYS cc_start: 0.9180 (ptpp) cc_final: 0.8612 (ptpp) REVERT: L 215 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7728 (mmtt) REVERT: L 218 ASP cc_start: 0.8222 (p0) cc_final: 0.7763 (p0) REVERT: L 227 LYS cc_start: 0.8868 (tppt) cc_final: 0.8349 (tppt) REVERT: L 258 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7853 (ttm110) REVERT: M 5 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8256 (t) REVERT: M 15 TYR cc_start: 0.7896 (t80) cc_final: 0.6979 (t80) REVERT: M 16 LYS cc_start: 0.8650 (mmtt) cc_final: 0.8354 (mmtt) REVERT: M 35 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7404 (pm20) REVERT: M 59 TYR cc_start: 0.8683 (t80) cc_final: 0.8400 (t80) REVERT: M 94 CYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7180 (m) REVERT: M 100 ASN cc_start: 0.7615 (m110) cc_final: 0.6688 (m-40) REVERT: M 174 ASP cc_start: 0.7639 (m-30) cc_final: 0.7247 (m-30) REVERT: M 183 GLU cc_start: 0.7376 (pm20) cc_final: 0.6849 (pm20) REVERT: M 186 ASN cc_start: 0.8630 (p0) cc_final: 0.8136 (p0) REVERT: M 216 ASN cc_start: 0.8170 (p0) cc_final: 0.7893 (p0) REVERT: M 246 GLU cc_start: 0.7693 (mm-30) cc_final: 0.6998 (tm-30) REVERT: M 292 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7528 (mm-30) REVERT: M 305 THR cc_start: 0.8677 (t) cc_final: 0.8350 (p) REVERT: M 321 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7733 (mtmm) REVERT: M 351 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7875 (mmmt) REVERT: M 364 SER cc_start: 0.8474 (p) cc_final: 0.8262 (p) REVERT: M 381 GLU cc_start: 0.7649 (pm20) cc_final: 0.7361 (pm20) REVERT: M 411 GLN cc_start: 0.7825 (tp40) cc_final: 0.7185 (tp40) REVERT: N 40 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7202 (mp0) REVERT: N 96 THR cc_start: 0.8203 (p) cc_final: 0.7893 (p) REVERT: N 104 LYS cc_start: 0.8551 (mtmm) cc_final: 0.7987 (mtmm) REVERT: N 140 LYS cc_start: 0.8754 (mmtp) cc_final: 0.8421 (mttp) REVERT: N 166 GLU cc_start: 0.7721 (pm20) cc_final: 0.7389 (pm20) REVERT: N 177 ASP cc_start: 0.7810 (p0) cc_final: 0.7387 (p0) REVERT: N 215 MET cc_start: 0.6075 (ppp) cc_final: 0.5665 (ppp) REVERT: N 234 LYS cc_start: 0.8481 (mmmm) cc_final: 0.8097 (mmmm) REVERT: N 238 ASN cc_start: 0.8526 (t0) cc_final: 0.8277 (t0) REVERT: N 250 ARG cc_start: 0.7135 (mmm-85) cc_final: 0.6454 (mmm-85) REVERT: N 272 GLU cc_start: 0.8064 (mp0) cc_final: 0.7546 (mp0) REVERT: N 356 GLN cc_start: 0.8360 (tt0) cc_final: 0.7689 (tm-30) REVERT: N 394 LYS cc_start: 0.8877 (mmtm) cc_final: 0.8286 (mmtm) REVERT: O 8 MET cc_start: 0.7475 (ttp) cc_final: 0.6902 (ttp) REVERT: P 142 LYS cc_start: 0.9066 (tmtt) cc_final: 0.8553 (tmtt) REVERT: P 166 TYR cc_start: 0.7862 (m-10) cc_final: 0.7409 (m-80) REVERT: P 196 HIS cc_start: 0.8984 (t-90) cc_final: 0.8696 (t70) REVERT: P 197 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7614 (m90) REVERT: P 215 LYS cc_start: 0.8564 (pmtt) cc_final: 0.8297 (pmtt) REVERT: P 255 MET cc_start: 0.6093 (tpp) cc_final: 0.5865 (tpp) REVERT: P 258 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7773 (ttm110) outliers start: 285 outliers final: 217 residues processed: 1602 average time/residue: 0.2228 time to fit residues: 574.1624 Evaluate side-chains 1697 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 235 poor density : 1462 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 235 TRP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 MET Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain H residue 170 CYS Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 244 THR Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 87 PHE Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 301 CYS Chi-restraints excluded: chain I residue 305 THR Chi-restraints excluded: chain I residue 328 CYS Chi-restraints excluded: chain I residue 351 LYS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 387 ILE Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain J residue 27 SER Chi-restraints excluded: chain J residue 62 HIS Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 235 TRP Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 287 HIS Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 320 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 380 SER Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain J residue 393 SER Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 170 CYS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 258 ARG Chi-restraints excluded: chain L residue 259 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 301 CYS Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 348 THR Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 398 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 162 LYS Chi-restraints excluded: chain N residue 198 LYS Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 307 GLU Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 333 ASP Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain N residue 388 LEU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 177 MET Chi-restraints excluded: chain P residue 182 SER Chi-restraints excluded: chain P residue 197 HIS Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 234 VAL Chi-restraints excluded: chain P residue 250 THR Chi-restraints excluded: chain P residue 251 TRP Chi-restraints excluded: chain P residue 252 ASN Chi-restraints excluded: chain P residue 258 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 101 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 230 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN E 204 GLN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN ** M 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 212 ASN N 255 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.119710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099317 restraints weight = 56578.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.102791 restraints weight = 23361.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.104992 restraints weight = 12444.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.106375 restraints weight = 7948.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107099 restraints weight = 5908.133| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 34178 Z= 0.255 Angle : 0.790 14.619 46677 Z= 0.393 Chirality : 0.050 0.283 5266 Planarity : 0.006 0.117 5972 Dihedral : 6.927 65.332 5274 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.54 % Favored : 93.17 % Rotamer: Outliers : 7.46 % Allowed : 32.85 % Favored : 59.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.40 (0.13), residues: 4233 helix: 1.21 (0.23), residues: 494 sheet: -0.79 (0.14), residues: 1270 loop : -1.48 (0.12), residues: 2469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 271 TYR 0.037 0.002 TYR N 296 PHE 0.022 0.002 PHE F 294 TRP 0.030 0.002 TRP I 170 HIS 0.012 0.001 HIS F 287 Details of bonding type rmsd covalent geometry : bond 0.00542 (34078) covalent geometry : angle 0.77272 (46445) SS BOND : bond 0.00513 ( 68) SS BOND : angle 1.82926 ( 136) hydrogen bonds : bond 0.03728 ( 1205) hydrogen bonds : angle 5.44568 ( 3159) link_BETA1-4 : bond 0.00718 ( 18) link_BETA1-4 : angle 3.34599 ( 54) link_NAG-ASN : bond 0.00516 ( 14) link_NAG-ASN : angle 2.79004 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1756 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 1487 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7711 (p90) cc_final: 0.7141 (p90) REVERT: A 139 ASN cc_start: 0.8509 (p0) cc_final: 0.8204 (p0) REVERT: A 155 THR cc_start: 0.8601 (m) cc_final: 0.8386 (t) REVERT: A 170 TRP cc_start: 0.9039 (t60) cc_final: 0.8758 (t60) REVERT: A 183 GLU cc_start: 0.6983 (pm20) cc_final: 0.6504 (pm20) REVERT: A 186 ASN cc_start: 0.8419 (p0) cc_final: 0.8007 (p0) REVERT: A 230 HIS cc_start: 0.8411 (p-80) cc_final: 0.8034 (p-80) REVERT: A 244 LEU cc_start: 0.8648 (mt) cc_final: 0.8267 (mp) REVERT: A 246 GLU cc_start: 0.7464 (tt0) cc_final: 0.7141 (tt0) REVERT: A 247 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8207 (mtmm) REVERT: A 257 PHE cc_start: 0.8766 (m-10) cc_final: 0.8471 (m-10) REVERT: A 287 PHE cc_start: 0.8697 (m-80) cc_final: 0.8463 (m-10) REVERT: A 292 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7623 (mp0) REVERT: A 317 THR cc_start: 0.8774 (t) cc_final: 0.8507 (p) REVERT: A 366 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8629 (m) REVERT: A 381 GLU cc_start: 0.7248 (pm20) cc_final: 0.6904 (pm20) REVERT: A 401 ASP cc_start: 0.7483 (t0) cc_final: 0.7244 (t0) REVERT: B 9 TYR cc_start: 0.8195 (m-80) cc_final: 0.7835 (m-80) REVERT: B 40 GLU cc_start: 0.7547 (mp0) cc_final: 0.7178 (mp0) REVERT: B 85 VAL cc_start: 0.8884 (m) cc_final: 0.8549 (p) REVERT: B 96 THR cc_start: 0.8256 (m) cc_final: 0.7733 (p) REVERT: B 97 MET cc_start: 0.7419 (tmm) cc_final: 0.7173 (tmm) REVERT: B 109 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7083 (mm-30) REVERT: B 254 VAL cc_start: 0.8215 (OUTLIER) cc_final: 0.7651 (m) REVERT: B 280 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7207 (mpp80) REVERT: B 362 TYR cc_start: 0.8477 (m-80) cc_final: 0.7957 (m-80) REVERT: D 116 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: D 141 MET cc_start: 0.7435 (mtp) cc_final: 0.7036 (mtp) REVERT: D 265 GLU cc_start: 0.7644 (pp20) cc_final: 0.7269 (pp20) REVERT: E 77 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7006 (mp10) REVERT: E 79 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7559 (mtpt) REVERT: E 100 ASN cc_start: 0.7828 (m-40) cc_final: 0.7545 (m-40) REVERT: E 140 VAL cc_start: 0.8194 (t) cc_final: 0.7813 (p) REVERT: E 176 LYS cc_start: 0.8478 (mmtp) cc_final: 0.7758 (mmtp) REVERT: E 186 ASN cc_start: 0.8094 (m-40) cc_final: 0.7679 (m-40) REVERT: E 216 ASN cc_start: 0.8256 (p0) cc_final: 0.7958 (p0) REVERT: E 228 MET cc_start: 0.7172 (tpt) cc_final: 0.6964 (tpt) REVERT: E 246 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6829 (tm-30) REVERT: E 262 LYS cc_start: 0.8446 (mmtm) cc_final: 0.8228 (mttm) REVERT: E 324 LYS cc_start: 0.8639 (pttm) cc_final: 0.8370 (pttm) REVERT: E 336 VAL cc_start: 0.8715 (t) cc_final: 0.8396 (p) REVERT: E 340 GLN cc_start: 0.8838 (tp40) cc_final: 0.8490 (tp40) REVERT: E 407 LEU cc_start: 0.8679 (tp) cc_final: 0.8220 (tp) REVERT: F 10 LYS cc_start: 0.8716 (mtmp) cc_final: 0.8393 (mtmp) REVERT: F 13 ARG cc_start: 0.8487 (ptm160) cc_final: 0.8152 (ptm-80) REVERT: F 38 ARG cc_start: 0.8009 (mtm-85) cc_final: 0.7753 (mtm-85) REVERT: F 40 GLU cc_start: 0.7143 (mp0) cc_final: 0.6893 (mp0) REVERT: F 64 TYR cc_start: 0.8073 (p90) cc_final: 0.7781 (p90) REVERT: F 92 PHE cc_start: 0.8584 (t80) cc_final: 0.8085 (t80) REVERT: F 97 MET cc_start: 0.7845 (tpp) cc_final: 0.7201 (tpp) REVERT: F 111 LEU cc_start: 0.8378 (tp) cc_final: 0.8171 (tt) REVERT: F 112 GLN cc_start: 0.8558 (tt0) cc_final: 0.8315 (tt0) REVERT: F 166 GLU cc_start: 0.7923 (pm20) cc_final: 0.7633 (pm20) REVERT: F 195 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7654 (tptp) REVERT: F 272 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7454 (mm-30) REVERT: F 274 THR cc_start: 0.8641 (m) cc_final: 0.8321 (t) REVERT: F 326 GLU cc_start: 0.7549 (tt0) cc_final: 0.7269 (tt0) REVERT: F 346 LYS cc_start: 0.8384 (mptt) cc_final: 0.7919 (mptt) REVERT: F 387 MET cc_start: 0.7521 (mmt) cc_final: 0.7308 (mmp) REVERT: F 399 TYR cc_start: 0.8269 (m-10) cc_final: 0.8048 (m-10) REVERT: H 258 ARG cc_start: 0.8780 (ttm170) cc_final: 0.8327 (ttm170) REVERT: I 2 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7288 (mm-30) REVERT: I 50 GLU cc_start: 0.6797 (tp30) cc_final: 0.6589 (tp30) REVERT: I 61 LYS cc_start: 0.8332 (ttmt) cc_final: 0.7915 (ttmt) REVERT: I 73 LYS cc_start: 0.7790 (mtpp) cc_final: 0.7567 (ttmm) REVERT: I 102 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: I 139 ASN cc_start: 0.8412 (p0) cc_final: 0.8159 (p0) REVERT: I 146 VAL cc_start: 0.8600 (t) cc_final: 0.8281 (m) REVERT: I 221 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8303 (pp) REVERT: I 234 THR cc_start: 0.8273 (t) cc_final: 0.7770 (t) REVERT: I 356 PHE cc_start: 0.8513 (p90) cc_final: 0.8253 (p90) REVERT: I 371 SER cc_start: 0.8819 (t) cc_final: 0.8550 (p) REVERT: I 381 GLU cc_start: 0.7230 (pm20) cc_final: 0.6808 (pm20) REVERT: J 10 LYS cc_start: 0.8862 (tttm) cc_final: 0.8422 (tttm) REVERT: J 43 ASP cc_start: 0.8070 (t0) cc_final: 0.7670 (t0) REVERT: J 61 ASN cc_start: 0.7964 (t0) cc_final: 0.7634 (t0) REVERT: J 68 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7780 (ttp80) REVERT: J 111 LEU cc_start: 0.8326 (tp) cc_final: 0.8104 (tt) REVERT: J 169 MET cc_start: 0.7325 (mmt) cc_final: 0.7027 (mmt) REVERT: J 235 TRP cc_start: 0.7772 (OUTLIER) cc_final: 0.7487 (m-10) REVERT: J 331 ASN cc_start: 0.8849 (m110) cc_final: 0.8612 (m110) REVERT: J 362 TYR cc_start: 0.8160 (m-80) cc_final: 0.7816 (m-80) REVERT: L 161 LYS cc_start: 0.8609 (tttm) cc_final: 0.8275 (pttm) REVERT: L 188 LYS cc_start: 0.9185 (ptpp) cc_final: 0.8613 (ptpp) REVERT: L 215 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7711 (mmtt) REVERT: L 218 ASP cc_start: 0.8225 (p0) cc_final: 0.7778 (p0) REVERT: L 227 LYS cc_start: 0.8850 (tppt) cc_final: 0.8312 (tppt) REVERT: L 258 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7827 (ttm110) REVERT: M 15 TYR cc_start: 0.7889 (t80) cc_final: 0.7336 (t80) REVERT: M 16 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8436 (mmtt) REVERT: M 35 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: M 59 TYR cc_start: 0.8703 (t80) cc_final: 0.8459 (t80) REVERT: M 94 CYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7166 (m) REVERT: M 100 ASN cc_start: 0.7654 (m110) cc_final: 0.6665 (m-40) REVERT: M 174 ASP cc_start: 0.7642 (m-30) cc_final: 0.7284 (m-30) REVERT: M 181 LYS cc_start: 0.8437 (mtmm) cc_final: 0.8022 (mtmm) REVERT: M 183 GLU cc_start: 0.7413 (pm20) cc_final: 0.6839 (pm20) REVERT: M 186 ASN cc_start: 0.8623 (p0) cc_final: 0.8165 (p0) REVERT: M 188 ASP cc_start: 0.7662 (m-30) cc_final: 0.7439 (m-30) REVERT: M 204 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7233 (mm-40) REVERT: M 216 ASN cc_start: 0.8198 (p0) cc_final: 0.7891 (p0) REVERT: M 246 GLU cc_start: 0.7686 (mm-30) cc_final: 0.6984 (tm-30) REVERT: M 292 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7545 (mm-30) REVERT: M 305 THR cc_start: 0.8719 (t) cc_final: 0.8365 (p) REVERT: M 321 LYS cc_start: 0.8223 (mtmm) cc_final: 0.7730 (mtmm) REVERT: M 351 LYS cc_start: 0.8316 (mmmt) cc_final: 0.7892 (mmmt) REVERT: M 364 SER cc_start: 0.8502 (p) cc_final: 0.8263 (p) REVERT: M 381 GLU cc_start: 0.7641 (pm20) cc_final: 0.7344 (pm20) REVERT: M 411 GLN cc_start: 0.7835 (tp40) cc_final: 0.7216 (tp40) REVERT: N 40 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7159 (mp0) REVERT: N 96 THR cc_start: 0.8245 (p) cc_final: 0.7962 (p) REVERT: N 104 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8021 (mtmm) REVERT: N 140 LYS cc_start: 0.8768 (mmtp) cc_final: 0.8429 (mttp) REVERT: N 166 GLU cc_start: 0.7663 (pm20) cc_final: 0.7329 (pm20) REVERT: N 177 ASP cc_start: 0.7823 (p0) cc_final: 0.7296 (p0) REVERT: N 215 MET cc_start: 0.6040 (ppp) cc_final: 0.5659 (ppp) REVERT: N 223 GLU cc_start: 0.7813 (mp0) cc_final: 0.7463 (mp0) REVERT: N 234 LYS cc_start: 0.8494 (mmmm) cc_final: 0.8123 (mmmm) REVERT: N 238 ASN cc_start: 0.8525 (t0) cc_final: 0.8262 (t0) REVERT: N 250 ARG cc_start: 0.7108 (mmm-85) cc_final: 0.6464 (mmm-85) REVERT: N 272 GLU cc_start: 0.8071 (mp0) cc_final: 0.7592 (mp0) REVERT: N 356 GLN cc_start: 0.8366 (tt0) cc_final: 0.7700 (tm-30) REVERT: N 394 LYS cc_start: 0.8869 (mmtm) cc_final: 0.8269 (mmtm) REVERT: O 8 MET cc_start: 0.7491 (ttp) cc_final: 0.6940 (ttp) REVERT: P 142 LYS cc_start: 0.9066 (tmtt) cc_final: 0.8535 (tmtt) REVERT: P 166 TYR cc_start: 0.7867 (m-10) cc_final: 0.7322 (m-10) REVERT: P 196 HIS cc_start: 0.8997 (t-90) cc_final: 0.8708 (t70) REVERT: P 197 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7665 (m90) REVERT: P 215 LYS cc_start: 0.8595 (pmtt) cc_final: 0.8278 (pmtt) REVERT: P 255 MET cc_start: 0.6143 (tpp) cc_final: 0.5880 (tpp) REVERT: P 258 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7789 (ttm110) outliers start: 269 outliers final: 225 residues processed: 1598 average time/residue: 0.2249 time to fit residues: 575.8076 Evaluate side-chains 1726 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 1483 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 380 CYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 235 TRP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 203 ILE Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 263 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 MET Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 151 ASP Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 301 CYS Chi-restraints excluded: chain I residue 328 CYS Chi-restraints excluded: chain I residue 351 LYS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 370 CYS Chi-restraints excluded: chain I residue 387 ILE Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain J residue 28 CYS Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 62 HIS Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 235 TRP Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 287 HIS Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 380 SER Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain J residue 393 SER Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 170 CYS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 258 ARG Chi-restraints excluded: chain L residue 259 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 301 CYS Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 348 THR Chi-restraints excluded: chain M residue 353 THR Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 398 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 162 LYS Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 307 GLU Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain N residue 388 LEU Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 177 MET Chi-restraints excluded: chain P residue 182 SER Chi-restraints excluded: chain P residue 197 HIS Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 234 VAL Chi-restraints excluded: chain P residue 250 THR Chi-restraints excluded: chain P residue 251 TRP Chi-restraints excluded: chain P residue 258 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 143 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 262 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 327 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 255 optimal weight: 8.9990 chunk 165 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 187 GLN E 204 GLN I 3 HIS I 77 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 ASN ** N 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 212 ASN N 255 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.096984 restraints weight = 56500.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100453 restraints weight = 23401.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102574 restraints weight = 12445.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.103922 restraints weight = 7996.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104554 restraints weight = 5955.439| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 34178 Z= 0.359 Angle : 0.850 14.723 46677 Z= 0.428 Chirality : 0.052 0.314 5266 Planarity : 0.006 0.116 5972 Dihedral : 7.077 65.985 5273 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.47 % Favored : 92.27 % Rotamer: Outliers : 7.46 % Allowed : 33.05 % Favored : 59.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.57 (0.13), residues: 4233 helix: 0.97 (0.23), residues: 506 sheet: -0.90 (0.14), residues: 1294 loop : -1.59 (0.12), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 271 TYR 0.032 0.002 TYR N 296 PHE 0.032 0.002 PHE F 294 TRP 0.028 0.002 TRP I 170 HIS 0.012 0.001 HIS F 287 Details of bonding type rmsd covalent geometry : bond 0.00747 (34078) covalent geometry : angle 0.83301 (46445) SS BOND : bond 0.00583 ( 68) SS BOND : angle 2.10770 ( 136) hydrogen bonds : bond 0.04108 ( 1205) hydrogen bonds : angle 5.60605 ( 3159) link_BETA1-4 : bond 0.00687 ( 18) link_BETA1-4 : angle 3.40565 ( 54) link_NAG-ASN : bond 0.00499 ( 14) link_NAG-ASN : angle 2.65980 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1789 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 1520 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7702 (p90) cc_final: 0.7054 (p90) REVERT: A 105 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7019 (tm-30) REVERT: A 155 THR cc_start: 0.8604 (m) cc_final: 0.8288 (p) REVERT: A 170 TRP cc_start: 0.9062 (t60) cc_final: 0.8751 (t60) REVERT: A 183 GLU cc_start: 0.6992 (pm20) cc_final: 0.6504 (pm20) REVERT: A 186 ASN cc_start: 0.8484 (p0) cc_final: 0.7918 (p0) REVERT: A 230 HIS cc_start: 0.8427 (p-80) cc_final: 0.8121 (p-80) REVERT: A 241 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.8025 (mmtp) REVERT: A 244 LEU cc_start: 0.8637 (mt) cc_final: 0.8354 (mp) REVERT: A 257 PHE cc_start: 0.8873 (m-10) cc_final: 0.8580 (m-10) REVERT: A 262 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8167 (mmtm) REVERT: A 287 PHE cc_start: 0.8744 (m-80) cc_final: 0.8452 (m-10) REVERT: A 292 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: A 317 THR cc_start: 0.8791 (t) cc_final: 0.8501 (p) REVERT: A 366 VAL cc_start: 0.8860 (OUTLIER) cc_final: 0.8651 (m) REVERT: A 381 GLU cc_start: 0.7418 (pm20) cc_final: 0.7075 (pm20) REVERT: B 9 TYR cc_start: 0.8264 (m-80) cc_final: 0.7925 (m-80) REVERT: B 40 GLU cc_start: 0.7577 (mp0) cc_final: 0.7206 (mp0) REVERT: B 43 ASP cc_start: 0.8168 (t0) cc_final: 0.7868 (t0) REVERT: B 85 VAL cc_start: 0.8884 (m) cc_final: 0.8532 (p) REVERT: B 96 THR cc_start: 0.8360 (m) cc_final: 0.8086 (p) REVERT: B 97 MET cc_start: 0.7483 (tmm) cc_final: 0.7201 (tmm) REVERT: B 109 GLU cc_start: 0.7370 (mm-30) cc_final: 0.7131 (mm-30) REVERT: B 120 ASN cc_start: 0.8493 (t0) cc_final: 0.8138 (t0) REVERT: B 129 TYR cc_start: 0.8280 (t80) cc_final: 0.7899 (t80) REVERT: B 150 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 169 MET cc_start: 0.7522 (mmm) cc_final: 0.7131 (mmm) REVERT: B 254 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7735 (m) REVERT: B 280 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7253 (mpp80) REVERT: B 359 TYR cc_start: 0.8283 (t80) cc_final: 0.8072 (t80) REVERT: B 362 TYR cc_start: 0.8484 (m-80) cc_final: 0.7839 (m-80) REVERT: D 116 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7214 (pt0) REVERT: D 141 MET cc_start: 0.7477 (mtp) cc_final: 0.7103 (mtp) REVERT: D 227 LYS cc_start: 0.8700 (tppt) cc_final: 0.8255 (mppt) REVERT: D 265 GLU cc_start: 0.7685 (pp20) cc_final: 0.7326 (pp20) REVERT: E 77 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7020 (mp10) REVERT: E 100 ASN cc_start: 0.7923 (m-40) cc_final: 0.7609 (m-40) REVERT: E 140 VAL cc_start: 0.8201 (t) cc_final: 0.7792 (p) REVERT: E 176 LYS cc_start: 0.8505 (mmtp) cc_final: 0.7778 (mmtp) REVERT: E 186 ASN cc_start: 0.8121 (m-40) cc_final: 0.7701 (m-40) REVERT: E 204 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7766 (mm-40) REVERT: E 216 ASN cc_start: 0.8326 (p0) cc_final: 0.8018 (p0) REVERT: E 246 GLU cc_start: 0.7352 (tm-30) cc_final: 0.6870 (tm-30) REVERT: E 324 LYS cc_start: 0.8671 (pttm) cc_final: 0.8389 (pttm) REVERT: E 336 VAL cc_start: 0.8715 (t) cc_final: 0.8399 (p) REVERT: E 340 GLN cc_start: 0.8769 (tp40) cc_final: 0.8477 (tp40) REVERT: E 364 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7965 (p) REVERT: E 407 LEU cc_start: 0.8669 (tp) cc_final: 0.8175 (tp) REVERT: F 10 LYS cc_start: 0.8738 (mtmp) cc_final: 0.8421 (mtmp) REVERT: F 13 ARG cc_start: 0.8487 (ptm160) cc_final: 0.8161 (ptm-80) REVERT: F 38 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7784 (mtm-85) REVERT: F 40 GLU cc_start: 0.7198 (mp0) cc_final: 0.6957 (mp0) REVERT: F 64 TYR cc_start: 0.8079 (p90) cc_final: 0.7826 (p90) REVERT: F 92 PHE cc_start: 0.8571 (t80) cc_final: 0.8031 (t80) REVERT: F 97 MET cc_start: 0.7887 (tpp) cc_final: 0.7292 (tpp) REVERT: F 111 LEU cc_start: 0.8426 (tp) cc_final: 0.8162 (tt) REVERT: F 112 GLN cc_start: 0.8584 (tt0) cc_final: 0.8323 (tt0) REVERT: F 166 GLU cc_start: 0.7939 (pm20) cc_final: 0.7659 (pm20) REVERT: F 177 ASP cc_start: 0.7743 (p0) cc_final: 0.7494 (p0) REVERT: F 195 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7749 (tptp) REVERT: F 272 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7531 (mm-30) REVERT: F 274 THR cc_start: 0.8643 (m) cc_final: 0.8371 (t) REVERT: F 326 GLU cc_start: 0.7526 (tt0) cc_final: 0.7266 (tt0) REVERT: F 387 MET cc_start: 0.7557 (mmt) cc_final: 0.7346 (mmp) REVERT: F 399 TYR cc_start: 0.8308 (m-10) cc_final: 0.8093 (m-10) REVERT: H 258 ARG cc_start: 0.8783 (ttm170) cc_final: 0.8338 (ttm170) REVERT: I 2 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7282 (mm-30) REVERT: I 50 GLU cc_start: 0.6840 (tp30) cc_final: 0.6634 (tp30) REVERT: I 61 LYS cc_start: 0.8375 (ttmt) cc_final: 0.7941 (ttmt) REVERT: I 67 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7299 (tm-30) REVERT: I 77 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8271 (mm110) REVERT: I 102 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7910 (tt0) REVERT: I 105 GLU cc_start: 0.7465 (tt0) cc_final: 0.7249 (tt0) REVERT: I 146 VAL cc_start: 0.8628 (t) cc_final: 0.8283 (m) REVERT: I 221 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8329 (pp) REVERT: I 230 HIS cc_start: 0.8538 (p-80) cc_final: 0.7968 (p90) REVERT: I 234 THR cc_start: 0.8324 (t) cc_final: 0.7933 (t) REVERT: I 356 PHE cc_start: 0.8520 (p90) cc_final: 0.8277 (p90) REVERT: I 371 SER cc_start: 0.8859 (t) cc_final: 0.8576 (p) REVERT: I 381 GLU cc_start: 0.7250 (pm20) cc_final: 0.6835 (pm20) REVERT: I 390 TYR cc_start: 0.8670 (p90) cc_final: 0.8463 (p90) REVERT: J 10 LYS cc_start: 0.8910 (tttm) cc_final: 0.8218 (tttm) REVERT: J 43 ASP cc_start: 0.8061 (t0) cc_final: 0.7696 (t0) REVERT: J 61 ASN cc_start: 0.8006 (t0) cc_final: 0.7685 (t0) REVERT: J 68 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7815 (ttp80) REVERT: J 166 GLU cc_start: 0.7739 (pm20) cc_final: 0.7431 (pm20) REVERT: J 169 MET cc_start: 0.7322 (mmt) cc_final: 0.7000 (mmt) REVERT: J 235 TRP cc_start: 0.7771 (OUTLIER) cc_final: 0.7480 (m-10) REVERT: J 331 ASN cc_start: 0.8862 (m110) cc_final: 0.8620 (m110) REVERT: J 362 TYR cc_start: 0.8242 (m-80) cc_final: 0.7932 (m-80) REVERT: L 162 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8345 (mtpp) REVERT: L 188 LYS cc_start: 0.9181 (ptpp) cc_final: 0.8662 (ptpp) REVERT: L 215 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7762 (mmtt) REVERT: L 218 ASP cc_start: 0.8245 (p0) cc_final: 0.7810 (p0) REVERT: L 227 LYS cc_start: 0.8881 (tppt) cc_final: 0.8344 (tppt) REVERT: L 248 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8754 (t) REVERT: L 258 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7834 (ttm110) REVERT: M 15 TYR cc_start: 0.7970 (t80) cc_final: 0.7549 (t80) REVERT: M 35 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7398 (pm20) REVERT: M 50 GLU cc_start: 0.6946 (tp30) cc_final: 0.6733 (tp30) REVERT: M 59 TYR cc_start: 0.8749 (t80) cc_final: 0.8504 (t80) REVERT: M 76 TYR cc_start: 0.7945 (t80) cc_final: 0.7694 (t80) REVERT: M 94 CYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7139 (m) REVERT: M 100 ASN cc_start: 0.7640 (m110) cc_final: 0.6641 (m-40) REVERT: M 174 ASP cc_start: 0.7651 (m-30) cc_final: 0.7309 (m-30) REVERT: M 183 GLU cc_start: 0.7413 (pm20) cc_final: 0.6769 (pm20) REVERT: M 186 ASN cc_start: 0.8636 (p0) cc_final: 0.8169 (p0) REVERT: M 188 ASP cc_start: 0.7682 (m-30) cc_final: 0.7467 (m-30) REVERT: M 204 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7311 (mm-40) REVERT: M 216 ASN cc_start: 0.8245 (p0) cc_final: 0.7869 (p0) REVERT: M 246 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6975 (tm-30) REVERT: M 292 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7579 (mm-30) REVERT: M 305 THR cc_start: 0.8787 (t) cc_final: 0.8452 (p) REVERT: M 321 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7697 (mtmm) REVERT: M 351 LYS cc_start: 0.8395 (mmmt) cc_final: 0.7958 (mmmt) REVERT: M 381 GLU cc_start: 0.7634 (pm20) cc_final: 0.7340 (pm20) REVERT: N 40 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7182 (mp0) REVERT: N 65 THR cc_start: 0.8462 (p) cc_final: 0.8237 (t) REVERT: N 96 THR cc_start: 0.8297 (p) cc_final: 0.7988 (p) REVERT: N 140 LYS cc_start: 0.8783 (mttp) cc_final: 0.8424 (mttp) REVERT: N 166 GLU cc_start: 0.7648 (pm20) cc_final: 0.7304 (pm20) REVERT: N 177 ASP cc_start: 0.7811 (p0) cc_final: 0.7283 (p0) REVERT: N 215 MET cc_start: 0.6136 (ppp) cc_final: 0.5708 (ppp) REVERT: N 223 GLU cc_start: 0.7872 (mp0) cc_final: 0.7482 (mp0) REVERT: N 234 LYS cc_start: 0.8509 (mmmm) cc_final: 0.8135 (mmmm) REVERT: N 238 ASN cc_start: 0.8493 (t0) cc_final: 0.8231 (t0) REVERT: N 241 PHE cc_start: 0.8763 (m-80) cc_final: 0.8531 (m-80) REVERT: N 272 GLU cc_start: 0.8070 (mp0) cc_final: 0.7608 (mp0) REVERT: N 318 ILE cc_start: 0.8776 (pp) cc_final: 0.8553 (pp) REVERT: N 356 GLN cc_start: 0.8388 (tt0) cc_final: 0.7735 (tm-30) REVERT: N 394 LYS cc_start: 0.8909 (mmtm) cc_final: 0.8294 (mmtm) REVERT: P 142 LYS cc_start: 0.9062 (tmtt) cc_final: 0.8544 (tmtt) REVERT: P 154 ASP cc_start: 0.8139 (p0) cc_final: 0.7883 (p0) REVERT: P 196 HIS cc_start: 0.9022 (t-90) cc_final: 0.8741 (t70) REVERT: P 197 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7669 (m90) REVERT: P 227 LYS cc_start: 0.8174 (tppt) cc_final: 0.7419 (tppt) REVERT: P 255 MET cc_start: 0.6283 (tpp) cc_final: 0.5854 (mpp) REVERT: P 258 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.7678 (ttm110) outliers start: 269 outliers final: 224 residues processed: 1630 average time/residue: 0.2247 time to fit residues: 585.6455 Evaluate side-chains 1748 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 244 poor density : 1504 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain A residue 433 CYS Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 81 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 235 TRP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 47 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 77 GLN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain F residue 215 MET Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 409 TRP Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain H residue 125 HIS Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 87 PHE Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 219 LEU Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 291 VAL Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 301 CYS Chi-restraints excluded: chain I residue 328 CYS Chi-restraints excluded: chain I residue 351 LYS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 370 CYS Chi-restraints excluded: chain I residue 387 ILE Chi-restraints excluded: chain I residue 388 VAL Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain I residue 433 CYS Chi-restraints excluded: chain J residue 62 HIS Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 235 TRP Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 287 HIS Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 380 SER Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain J residue 388 LEU Chi-restraints excluded: chain J residue 393 SER Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 170 CYS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 258 ARG Chi-restraints excluded: chain L residue 259 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 7 MET Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 252 ASN Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 301 CYS Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 353 THR Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 398 VAL Chi-restraints excluded: chain N residue 58 LYS Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 88 SER Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 162 LYS Chi-restraints excluded: chain N residue 198 LYS Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 251 LYS Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 307 GLU Chi-restraints excluded: chain N residue 308 GLU Chi-restraints excluded: chain N residue 311 THR Chi-restraints excluded: chain N residue 333 ASP Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 177 MET Chi-restraints excluded: chain P residue 182 SER Chi-restraints excluded: chain P residue 197 HIS Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 234 VAL Chi-restraints excluded: chain P residue 250 THR Chi-restraints excluded: chain P residue 251 TRP Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain P residue 258 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 287 optimal weight: 0.9990 chunk 368 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 chunk 356 optimal weight: 5.9990 chunk 337 optimal weight: 0.0370 chunk 317 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 141 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN E 43 ASN E 187 GLN F 158 GLN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 197 HIS ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 212 ASN N 255 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.100890 restraints weight = 56799.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.104420 restraints weight = 23316.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.106636 restraints weight = 12354.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108048 restraints weight = 7887.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.108769 restraints weight = 5827.217| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34178 Z= 0.153 Angle : 0.795 12.141 46677 Z= 0.396 Chirality : 0.049 0.309 5266 Planarity : 0.006 0.116 5972 Dihedral : 6.839 65.153 5273 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.74 % Favored : 94.00 % Rotamer: Outliers : 5.99 % Allowed : 35.04 % Favored : 58.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.41 (0.13), residues: 4233 helix: 1.25 (0.23), residues: 494 sheet: -0.87 (0.14), residues: 1274 loop : -1.45 (0.12), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 229 TYR 0.030 0.002 TYR P 202 PHE 0.046 0.002 PHE F 237 TRP 0.030 0.001 TRP I 170 HIS 0.010 0.001 HIS F 287 Details of bonding type rmsd covalent geometry : bond 0.00349 (34078) covalent geometry : angle 0.77819 (46445) SS BOND : bond 0.00428 ( 68) SS BOND : angle 2.02374 ( 136) hydrogen bonds : bond 0.03455 ( 1205) hydrogen bonds : angle 5.46315 ( 3159) link_BETA1-4 : bond 0.00813 ( 18) link_BETA1-4 : angle 3.17805 ( 54) link_NAG-ASN : bond 0.00511 ( 14) link_NAG-ASN : angle 2.64488 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8466 Ramachandran restraints generated. 4233 Oldfield, 0 Emsley, 4233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1723 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1507 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 TYR cc_start: 0.7783 (p90) cc_final: 0.7288 (p90) REVERT: A 105 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6923 (tm-30) REVERT: A 115 ARG cc_start: 0.8302 (ttp-110) cc_final: 0.7825 (mtm110) REVERT: A 139 ASN cc_start: 0.8510 (p0) cc_final: 0.8220 (p0) REVERT: A 155 THR cc_start: 0.8588 (m) cc_final: 0.8367 (t) REVERT: A 170 TRP cc_start: 0.8995 (t60) cc_final: 0.8598 (t60) REVERT: A 176 LYS cc_start: 0.8447 (mtmm) cc_final: 0.7743 (mttm) REVERT: A 183 GLU cc_start: 0.6904 (pm20) cc_final: 0.6440 (pm20) REVERT: A 186 ASN cc_start: 0.8300 (p0) cc_final: 0.7807 (p0) REVERT: A 228 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6853 (ppp) REVERT: A 230 HIS cc_start: 0.8429 (p-80) cc_final: 0.7847 (p-80) REVERT: A 241 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7857 (mmmm) REVERT: A 245 LYS cc_start: 0.8377 (mttp) cc_final: 0.8037 (mttt) REVERT: A 246 GLU cc_start: 0.7369 (tt0) cc_final: 0.6931 (tt0) REVERT: A 257 PHE cc_start: 0.8845 (m-10) cc_final: 0.8542 (m-10) REVERT: A 262 LYS cc_start: 0.8276 (mmtm) cc_final: 0.8054 (mmtm) REVERT: A 287 PHE cc_start: 0.8680 (m-80) cc_final: 0.8449 (m-10) REVERT: A 292 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7647 (mp0) REVERT: A 317 THR cc_start: 0.8726 (t) cc_final: 0.8465 (p) REVERT: A 366 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8589 (m) REVERT: A 381 GLU cc_start: 0.7429 (pm20) cc_final: 0.7036 (pm20) REVERT: B 9 TYR cc_start: 0.8118 (m-80) cc_final: 0.7737 (m-80) REVERT: B 40 GLU cc_start: 0.7512 (mp0) cc_final: 0.7058 (mp0) REVERT: B 43 ASP cc_start: 0.8140 (t0) cc_final: 0.7854 (t0) REVERT: B 85 VAL cc_start: 0.8834 (m) cc_final: 0.8538 (p) REVERT: B 96 THR cc_start: 0.8211 (m) cc_final: 0.7614 (p) REVERT: B 97 MET cc_start: 0.7347 (tmm) cc_final: 0.7085 (tmm) REVERT: B 109 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 129 TYR cc_start: 0.8172 (t80) cc_final: 0.7793 (t80) REVERT: B 156 TYR cc_start: 0.8582 (m-10) cc_final: 0.8104 (m-10) REVERT: B 157 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7447 (mm-40) REVERT: B 254 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7628 (m) REVERT: B 280 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7114 (mpp80) REVERT: B 320 VAL cc_start: 0.8712 (t) cc_final: 0.8371 (m) REVERT: B 362 TYR cc_start: 0.8378 (m-80) cc_final: 0.7864 (m-80) REVERT: D 141 MET cc_start: 0.7378 (mtp) cc_final: 0.6987 (mtp) REVERT: D 227 LYS cc_start: 0.8627 (tppt) cc_final: 0.8163 (mppt) REVERT: D 248 VAL cc_start: 0.8984 (OUTLIER) cc_final: 0.8739 (t) REVERT: D 265 GLU cc_start: 0.7672 (pp20) cc_final: 0.7303 (pp20) REVERT: E 100 ASN cc_start: 0.7861 (m-40) cc_final: 0.7611 (m-40) REVERT: E 114 CYS cc_start: 0.6670 (t) cc_final: 0.6311 (t) REVERT: E 116 HIS cc_start: 0.8639 (m-70) cc_final: 0.8302 (m-70) REVERT: E 132 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8451 (mtpp) REVERT: E 140 VAL cc_start: 0.8148 (t) cc_final: 0.7775 (p) REVERT: E 176 LYS cc_start: 0.8458 (mmtp) cc_final: 0.7942 (mmtp) REVERT: E 186 ASN cc_start: 0.8054 (m-40) cc_final: 0.7621 (m-40) REVERT: E 216 ASN cc_start: 0.8036 (p0) cc_final: 0.7810 (p0) REVERT: E 246 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6697 (tm-30) REVERT: E 324 LYS cc_start: 0.8577 (pttm) cc_final: 0.8268 (pttm) REVERT: E 336 VAL cc_start: 0.8674 (t) cc_final: 0.8325 (p) REVERT: E 340 GLN cc_start: 0.8778 (tp40) cc_final: 0.8458 (tp40) REVERT: E 364 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7964 (p) REVERT: E 394 HIS cc_start: 0.8616 (p90) cc_final: 0.8099 (p90) REVERT: E 407 LEU cc_start: 0.8622 (tp) cc_final: 0.8186 (tp) REVERT: F 10 LYS cc_start: 0.8723 (mtmp) cc_final: 0.8401 (mtmp) REVERT: F 13 ARG cc_start: 0.8483 (ptm160) cc_final: 0.8144 (ptm-80) REVERT: F 38 ARG cc_start: 0.7956 (mtm-85) cc_final: 0.7722 (mtm-85) REVERT: F 40 GLU cc_start: 0.7067 (mp0) cc_final: 0.6839 (mp0) REVERT: F 50 PHE cc_start: 0.8187 (p90) cc_final: 0.7867 (p90) REVERT: F 64 TYR cc_start: 0.8016 (p90) cc_final: 0.7744 (p90) REVERT: F 92 PHE cc_start: 0.8515 (t80) cc_final: 0.8029 (t80) REVERT: F 97 MET cc_start: 0.7769 (tpp) cc_final: 0.7198 (tpp) REVERT: F 111 LEU cc_start: 0.8358 (tp) cc_final: 0.8127 (tt) REVERT: F 112 GLN cc_start: 0.8514 (tt0) cc_final: 0.8226 (tt0) REVERT: F 129 TYR cc_start: 0.7707 (t80) cc_final: 0.7492 (t80) REVERT: F 166 GLU cc_start: 0.7956 (pm20) cc_final: 0.7654 (pm20) REVERT: F 177 ASP cc_start: 0.7688 (p0) cc_final: 0.7371 (p0) REVERT: F 195 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7654 (tptp) REVERT: F 272 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7453 (mm-30) REVERT: F 274 THR cc_start: 0.8591 (m) cc_final: 0.8281 (t) REVERT: F 326 GLU cc_start: 0.7512 (tt0) cc_final: 0.7211 (tt0) REVERT: F 387 MET cc_start: 0.7535 (mmt) cc_final: 0.7295 (mmp) REVERT: H 258 ARG cc_start: 0.8763 (ttm170) cc_final: 0.8367 (ttm170) REVERT: I 2 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7276 (mm-30) REVERT: I 61 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7885 (ttmt) REVERT: I 102 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: I 146 VAL cc_start: 0.8598 (t) cc_final: 0.8308 (m) REVERT: I 221 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8303 (pp) REVERT: I 230 HIS cc_start: 0.8473 (p-80) cc_final: 0.7629 (p-80) REVERT: I 234 THR cc_start: 0.8144 (t) cc_final: 0.7614 (t) REVERT: I 270 ASN cc_start: 0.8666 (m110) cc_final: 0.8448 (m110) REVERT: I 278 VAL cc_start: 0.8704 (OUTLIER) cc_final: 0.8503 (p) REVERT: I 292 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.6836 (tm-30) REVERT: I 356 PHE cc_start: 0.8516 (p90) cc_final: 0.8264 (p90) REVERT: I 371 SER cc_start: 0.8773 (t) cc_final: 0.8555 (p) REVERT: I 381 GLU cc_start: 0.7252 (pm20) cc_final: 0.6851 (pm20) REVERT: J 10 LYS cc_start: 0.8913 (tttm) cc_final: 0.8519 (tttm) REVERT: J 43 ASP cc_start: 0.8099 (t0) cc_final: 0.7727 (t0) REVERT: J 61 ASN cc_start: 0.7965 (t0) cc_final: 0.7645 (t0) REVERT: J 129 TYR cc_start: 0.7733 (t80) cc_final: 0.7161 (t80) REVERT: J 157 GLN cc_start: 0.7341 (mm110) cc_final: 0.6781 (mm110) REVERT: J 166 GLU cc_start: 0.7695 (pm20) cc_final: 0.7467 (pm20) REVERT: J 169 MET cc_start: 0.7305 (mmt) cc_final: 0.7042 (mmt) REVERT: J 235 TRP cc_start: 0.7745 (OUTLIER) cc_final: 0.7450 (m-10) REVERT: J 251 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7666 (mtpp) REVERT: J 331 ASN cc_start: 0.8798 (m110) cc_final: 0.8448 (m110) REVERT: J 362 TYR cc_start: 0.8077 (m-80) cc_final: 0.7740 (m-80) REVERT: L 162 LYS cc_start: 0.8544 (mtpp) cc_final: 0.8307 (mtpp) REVERT: L 188 LYS cc_start: 0.9223 (ptpp) cc_final: 0.8604 (ptpp) REVERT: L 215 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7698 (mmtt) REVERT: L 218 ASP cc_start: 0.8214 (p0) cc_final: 0.7705 (p0) REVERT: L 227 LYS cc_start: 0.8809 (tppt) cc_final: 0.8232 (tppt) REVERT: L 258 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7779 (ttm110) REVERT: M 15 TYR cc_start: 0.7910 (t80) cc_final: 0.7376 (t80) REVERT: M 16 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8316 (mmtt) REVERT: M 35 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: M 59 TYR cc_start: 0.8717 (t80) cc_final: 0.8442 (t80) REVERT: M 94 CYS cc_start: 0.7544 (OUTLIER) cc_final: 0.7030 (m) REVERT: M 100 ASN cc_start: 0.7567 (m110) cc_final: 0.6652 (m-40) REVERT: M 174 ASP cc_start: 0.7671 (m-30) cc_final: 0.7311 (m-30) REVERT: M 181 LYS cc_start: 0.8338 (mtmm) cc_final: 0.7958 (mtmm) REVERT: M 183 GLU cc_start: 0.7414 (pm20) cc_final: 0.6846 (pm20) REVERT: M 186 ASN cc_start: 0.8561 (p0) cc_final: 0.8107 (p0) REVERT: M 216 ASN cc_start: 0.8077 (p0) cc_final: 0.7849 (p0) REVERT: M 244 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8553 (mp) REVERT: M 246 GLU cc_start: 0.7677 (mm-30) cc_final: 0.6960 (tm-30) REVERT: M 292 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7531 (mm-30) REVERT: M 305 THR cc_start: 0.8671 (t) cc_final: 0.8305 (p) REVERT: M 321 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7710 (mtmm) REVERT: M 351 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7884 (mmmt) REVERT: M 364 SER cc_start: 0.8515 (p) cc_final: 0.8256 (p) REVERT: M 381 GLU cc_start: 0.7622 (pm20) cc_final: 0.7328 (pm20) REVERT: M 411 GLN cc_start: 0.7815 (tp40) cc_final: 0.7186 (tp40) REVERT: N 40 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7060 (mp0) REVERT: N 96 THR cc_start: 0.8154 (p) cc_final: 0.7837 (p) REVERT: N 104 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8204 (mtmm) REVERT: N 140 LYS cc_start: 0.8739 (mttp) cc_final: 0.8393 (mttp) REVERT: N 166 GLU cc_start: 0.7599 (pm20) cc_final: 0.7266 (pm20) REVERT: N 177 ASP cc_start: 0.7758 (p0) cc_final: 0.7043 (p0) REVERT: N 215 MET cc_start: 0.6009 (ppp) cc_final: 0.5589 (ppp) REVERT: N 223 GLU cc_start: 0.7832 (mp0) cc_final: 0.7463 (mp0) REVERT: N 234 LYS cc_start: 0.8483 (mmmm) cc_final: 0.8074 (mmmm) REVERT: N 241 PHE cc_start: 0.8719 (m-80) cc_final: 0.8493 (m-80) REVERT: N 272 GLU cc_start: 0.8017 (mp0) cc_final: 0.7530 (mp0) REVERT: N 356 GLN cc_start: 0.8343 (tt0) cc_final: 0.7658 (tm-30) REVERT: N 394 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8252 (mmtm) REVERT: P 142 LYS cc_start: 0.9031 (tmtt) cc_final: 0.8507 (tmtt) REVERT: P 161 LYS cc_start: 0.8172 (tttt) cc_final: 0.7700 (tttt) REVERT: P 196 HIS cc_start: 0.8960 (t-90) cc_final: 0.8654 (t70) REVERT: P 197 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7654 (m90) REVERT: P 255 MET cc_start: 0.6076 (tpp) cc_final: 0.5680 (mpp) REVERT: P 258 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7723 (ttm110) outliers start: 216 outliers final: 173 residues processed: 1595 average time/residue: 0.2268 time to fit residues: 579.8309 Evaluate side-chains 1686 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 1489 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 160 GLN Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 241 LYS Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 77 ASN Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 235 TRP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 161 LYS Chi-restraints excluded: chain D residue 170 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 251 TRP Chi-restraints excluded: chain E residue 7 MET Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 398 VAL Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 67 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 101 ILE Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 162 LYS Chi-restraints excluded: chain F residue 195 LYS Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 215 MET Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 235 TRP Chi-restraints excluded: chain F residue 284 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 354 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 415 CYS Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 234 VAL Chi-restraints excluded: chain H residue 255 MET Chi-restraints excluded: chain H residue 257 THR Chi-restraints excluded: chain I residue 20 GLU Chi-restraints excluded: chain I residue 35 GLU Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 102 GLN Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 171 THR Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 221 LEU Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 236 THR Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 290 ILE Chi-restraints excluded: chain I residue 292 GLU Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 301 CYS Chi-restraints excluded: chain I residue 328 CYS Chi-restraints excluded: chain I residue 366 VAL Chi-restraints excluded: chain I residue 387 ILE Chi-restraints excluded: chain I residue 427 VAL Chi-restraints excluded: chain J residue 32 VAL Chi-restraints excluded: chain J residue 62 HIS Chi-restraints excluded: chain J residue 63 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 179 THR Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 214 ASP Chi-restraints excluded: chain J residue 228 SER Chi-restraints excluded: chain J residue 235 TRP Chi-restraints excluded: chain J residue 272 GLU Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 287 HIS Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 352 HIS Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain L residue 120 ILE Chi-restraints excluded: chain L residue 135 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 145 HIS Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain L residue 249 VAL Chi-restraints excluded: chain L residue 250 THR Chi-restraints excluded: chain L residue 258 ARG Chi-restraints excluded: chain L residue 259 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 7 MET Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 45 GLU Chi-restraints excluded: chain M residue 57 SER Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 263 THR Chi-restraints excluded: chain M residue 295 THR Chi-restraints excluded: chain M residue 301 CYS Chi-restraints excluded: chain M residue 330 VAL Chi-restraints excluded: chain M residue 348 THR Chi-restraints excluded: chain M residue 351 LYS Chi-restraints excluded: chain M residue 353 THR Chi-restraints excluded: chain M residue 369 LEU Chi-restraints excluded: chain M residue 385 ASP Chi-restraints excluded: chain M residue 398 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 104 LYS Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 212 ASN Chi-restraints excluded: chain N residue 235 TRP Chi-restraints excluded: chain N residue 251 LYS Chi-restraints excluded: chain N residue 301 GLU Chi-restraints excluded: chain N residue 307 GLU Chi-restraints excluded: chain N residue 373 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 52 LEU Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 128 LYS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 140 VAL Chi-restraints excluded: chain P residue 145 HIS Chi-restraints excluded: chain P residue 146 VAL Chi-restraints excluded: chain P residue 177 MET Chi-restraints excluded: chain P residue 197 HIS Chi-restraints excluded: chain P residue 206 ARG Chi-restraints excluded: chain P residue 234 VAL Chi-restraints excluded: chain P residue 250 THR Chi-restraints excluded: chain P residue 251 TRP Chi-restraints excluded: chain P residue 258 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 340 optimal weight: 8.9990 chunk 363 optimal weight: 10.0000 chunk 162 optimal weight: 4.9990 chunk 233 optimal weight: 0.5980 chunk 240 optimal weight: 0.9990 chunk 384 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 154 optimal weight: 0.0020 chunk 175 optimal weight: 10.0000 chunk 376 optimal weight: 6.9990 chunk 356 optimal weight: 10.0000 overall best weight: 2.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN F 61 ASN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 77 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN ** M 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 212 ASN N 255 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.120428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.100148 restraints weight = 56556.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.103614 restraints weight = 23303.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.105826 restraints weight = 12399.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107128 restraints weight = 7928.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.108000 restraints weight = 5941.868| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34178 Z= 0.194 Angle : 0.794 11.722 46677 Z= 0.396 Chirality : 0.049 0.301 5266 Planarity : 0.006 0.116 5972 Dihedral : 6.756 65.502 5273 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.24 % Favored : 93.55 % Rotamer: Outliers : 5.66 % Allowed : 35.57 % Favored : 58.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % 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: -1.38 (0.13), residues: 4233 helix: 1.28 (0.23), residues: 494 sheet: -0.87 (0.14), residues: 1292 loop : -1.42 (0.13), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 271 TYR 0.036 0.002 TYR A 81 PHE 0.040 0.002 PHE F 237 TRP 0.027 0.001 TRP I 170 HIS 0.010 0.001 HIS F 287 Details of bonding type rmsd covalent geometry : bond 0.00430 (34078) covalent geometry : angle 0.77730 (46445) SS BOND : bond 0.00453 ( 68) SS BOND : angle 2.06983 ( 136) hydrogen bonds : bond 0.03555 ( 1205) hydrogen bonds : angle 5.39778 ( 3159) link_BETA1-4 : bond 0.00728 ( 18) link_BETA1-4 : angle 3.10774 ( 54) link_NAG-ASN : bond 0.00410 ( 14) link_NAG-ASN : angle 2.64110 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9356.35 seconds wall clock time: 161 minutes 19.54 seconds (9679.54 seconds total)