Starting phenix.real_space_refine on Fri May 30 07:13:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ua8_42054/05_2025/8ua8_42054_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ua8_42054/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ua8_42054/05_2025/8ua8_42054.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ua8_42054/05_2025/8ua8_42054.map" model { file = "/net/cci-nas-00/data/ceres_data/8ua8_42054/05_2025/8ua8_42054_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ua8_42054/05_2025/8ua8_42054_neut.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.013 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 19.83, per 1000 atoms: 0.60 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: 10.14 Conformation dependent library (CDL) restraints added in 4.8 seconds 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: 5.27 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: 16.75 Time building geometry restraints manager: 10.94 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: 3.260 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: 0.030 Extract box with map and model: 1.480 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 82.300 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.240 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:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.460 ------------------------------------------------------------------------------- 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 : 8.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (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 TRP 0.026 0.003 TRP N 235 HIS 0.022 0.003 HIS N 170 PHE 0.059 0.004 PHE E 312 TYR 0.053 0.004 TYR N 305 ARG 0.050 0.002 ARG K 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00983 ( 14) link_NAG-ASN : angle 3.56435 ( 42) link_BETA1-4 : bond 0.00533 ( 18) link_BETA1-4 : angle 5.21390 ( 54) hydrogen bonds : bond 0.13641 ( 1205) hydrogen bonds : angle 7.60747 ( 3159) SS BOND : bond 0.01107 ( 68) SS BOND : angle 4.28807 ( 136) covalent geometry : bond 0.01415 (34078) covalent geometry : angle 1.36736 (46445) *********************** 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 : 3.833 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: 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: 0.7438 (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: 0.7549 (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: 0.7446 (mtpp) REVERT: I 76 TYR cc_start: 0.7795 (t80) cc_final: 0.7559 (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: 0.8315 (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: 0.7821 (m90) outliers start: 43 outliers final: 27 residues processed: 1518 average time/residue: 0.4633 time to fit residues: 1121.1790 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 : 3.750 ------------------------------------------------------------------------------- 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 353 optimal weight: 5.9990 chunk 317 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 214 optimal weight: 30.0000 chunk 169 optimal weight: 6.9990 chunk 328 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 chunk 244 optimal weight: 0.9990 chunk 380 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 I 235 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 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 255 HIS N 353 GLN O 42 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.101990 restraints weight = 56705.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.105470 restraints weight = 23637.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.107678 restraints weight = 12566.484| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34178 Z= 0.186 Angle : 0.816 13.532 46677 Z= 0.411 Chirality : 0.050 0.320 5266 Planarity : 0.007 0.123 5972 Dihedral : 10.111 76.466 5314 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.67 % Favored : 93.95 % Rotamer: Outliers : 5.99 % Allowed : 29.22 % Favored : 64.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.12), residues: 4233 helix: 0.87 (0.23), residues: 483 sheet: -1.05 (0.13), residues: 1322 loop : -1.51 (0.12), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 195 HIS 0.009 0.001 HIS B 29 PHE 0.023 0.002 PHE N 100 TYR 0.025 0.002 TYR N 296 ARG 0.010 0.001 ARG K 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 14) link_NAG-ASN : angle 2.88619 ( 42) link_BETA1-4 : bond 0.01145 ( 18) link_BETA1-4 : angle 4.02162 ( 54) hydrogen bonds : bond 0.04200 ( 1205) hydrogen bonds : angle 6.18517 ( 3159) SS BOND : bond 0.00378 ( 68) SS BOND : angle 1.72659 ( 136) covalent geometry : bond 0.00410 (34078) covalent geometry : angle 0.79607 (46445) *********************** 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 1679 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1463 time to evaluate : 3.613 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: 0.8293 (m-80) cc_final: 0.7946 (m-80) REVERT: A 78 CYS cc_start: 0.5057 (OUTLIER) cc_final: 0.4816 (p) REVERT: A 115 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.7892 (ttp-110) REVERT: A 183 GLU cc_start: 0.7117 (pm20) cc_final: 0.6875 (pm20) REVERT: A 257 PHE cc_start: 0.8771 (m-10) cc_final: 0.8378 (m-10) REVERT: A 292 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: A 306 CYS cc_start: 0.6924 (t) cc_final: 0.5963 (t) REVERT: A 317 THR cc_start: 0.8709 (t) cc_final: 0.8326 (p) REVERT: A 381 GLU cc_start: 0.7339 (pm20) cc_final: 0.6991 (pm20) REVERT: A 390 TYR cc_start: 0.8734 (p90) cc_final: 0.8481 (p90) REVERT: B 40 GLU cc_start: 0.7563 (mp0) cc_final: 0.7363 (mp0) REVERT: B 49 GLN cc_start: 0.8323 (tt0) cc_final: 0.8036 (tt0) REVERT: B 60 ASP cc_start: 0.8715 (m-30) cc_final: 0.7436 (m-30) REVERT: B 96 THR cc_start: 0.8009 (p) cc_final: 0.7803 (p) REVERT: B 97 MET cc_start: 0.7605 (tmm) cc_final: 0.6934 (tmm) REVERT: B 109 GLU cc_start: 0.7246 (mm-30) cc_final: 0.7039 (mm-30) REVERT: B 129 TYR cc_start: 0.8192 (t80) cc_final: 0.7740 (t80) REVERT: B 156 TYR cc_start: 0.8429 (m-80) cc_final: 0.7614 (m-10) REVERT: B 157 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7574 (mm-40) REVERT: B 169 MET cc_start: 0.7303 (mmm) cc_final: 0.6408 (mmm) REVERT: B 237 PHE cc_start: 0.8576 (t80) cc_final: 0.8355 (t80) REVERT: B 242 VAL cc_start: 0.8562 (m) cc_final: 0.8334 (p) REVERT: B 253 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7653 (mtpp) REVERT: B 261 ASP cc_start: 0.7809 (p0) cc_final: 0.7239 (p0) REVERT: B 326 GLU cc_start: 0.7345 (tt0) cc_final: 0.6982 (tt0) REVERT: B 327 TYR cc_start: 0.8598 (p90) cc_final: 0.8327 (p90) REVERT: B 357 TYR cc_start: 0.8472 (t80) cc_final: 0.8182 (t80) REVERT: D 206 ARG cc_start: 0.7460 (mtt180) cc_final: 0.7118 (mtt180) REVERT: D 218 ASP cc_start: 0.8183 (p0) cc_final: 0.7862 (p0) REVERT: E 27 LEU cc_start: 0.7943 (tp) cc_final: 0.7722 (tt) REVERT: E 73 LYS cc_start: 0.7822 (mtmm) cc_final: 0.7476 (mtmt) REVERT: E 100 ASN cc_start: 0.7379 (m-40) cc_final: 0.7130 (m-40) REVERT: E 186 ASN cc_start: 0.8115 (m-40) cc_final: 0.7731 (m-40) REVERT: E 196 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8051 (mm-40) REVERT: E 199 ARG cc_start: 0.7830 (mmt180) cc_final: 0.7545 (mmt180) REVERT: E 204 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.7825 (mm-40) REVERT: E 228 MET cc_start: 0.7454 (tpt) cc_final: 0.6912 (tpt) REVERT: E 234 THR cc_start: 0.7533 (p) cc_final: 0.7230 (t) REVERT: E 312 PHE cc_start: 0.7729 (m-80) cc_final: 0.7458 (m-80) REVERT: E 324 LYS cc_start: 0.8632 (pttm) cc_final: 0.8346 (pttm) REVERT: E 336 VAL cc_start: 0.8655 (t) cc_final: 0.8334 (p) REVERT: E 340 GLN cc_start: 0.8678 (tp40) cc_final: 0.8277 (tp40) REVERT: E 407 LEU cc_start: 0.8514 (tp) cc_final: 0.8100 (tp) REVERT: F 7 ASN cc_start: 0.8201 (t0) cc_final: 0.7796 (t0) REVERT: F 40 GLU cc_start: 0.7081 (mp0) cc_final: 0.6867 (mp0) REVERT: F 112 GLN cc_start: 0.8551 (tt0) cc_final: 0.8342 (tt0) REVERT: F 196 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8214 (ttpt) REVERT: F 215 MET cc_start: 0.7924 (pmm) cc_final: 0.7545 (pmm) REVERT: F 234 LYS cc_start: 0.8408 (mmmt) cc_final: 0.7831 (mmmm) REVERT: F 235 TRP cc_start: 0.8103 (OUTLIER) cc_final: 0.7773 (t60) REVERT: F 274 THR cc_start: 0.8678 (m) cc_final: 0.8182 (p) REVERT: F 362 TYR cc_start: 0.8563 (m-80) cc_final: 0.8318 (m-80) REVERT: H 177 MET cc_start: 0.8750 (mtt) cc_final: 0.8504 (mtt) REVERT: H 223 ILE cc_start: 0.8358 (mt) cc_final: 0.8131 (mt) REVERT: H 258 ARG cc_start: 0.8672 (ttm170) cc_final: 0.8443 (ttm170) REVERT: I 2 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7359 (mm-30) REVERT: I 73 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7533 (mtpp) REVERT: I 146 VAL cc_start: 0.8594 (t) cc_final: 0.8310 (m) REVERT: I 228 MET cc_start: 0.7945 (tmt) cc_final: 0.7647 (ppp) REVERT: I 237 PRO cc_start: 0.8775 (Cg_exo) cc_final: 0.8516 (Cg_endo) REVERT: I 371 SER cc_start: 0.8744 (t) cc_final: 0.8482 (p) REVERT: I 381 GLU cc_start: 0.7367 (pm20) cc_final: 0.7092 (pm20) REVERT: I 402 MET cc_start: 0.7303 (mmm) cc_final: 0.7091 (mmm) REVERT: J 10 LYS cc_start: 0.8843 (tttm) cc_final: 0.8363 (tttm) REVERT: J 97 MET cc_start: 0.7436 (tmm) cc_final: 0.6972 (tmm) REVERT: J 129 TYR cc_start: 0.7774 (t80) cc_final: 0.7170 (t80) REVERT: J 153 CYS cc_start: 0.5415 (m) cc_final: 0.4939 (m) REVERT: J 304 GLN cc_start: 0.8463 (tt0) cc_final: 0.8255 (tt0) REVERT: J 331 ASN cc_start: 0.8838 (m-40) cc_final: 0.8602 (m-40) REVERT: J 362 TYR cc_start: 0.8006 (m-80) cc_final: 0.7368 (m-80) REVERT: J 379 ILE cc_start: 0.8343 (mt) cc_final: 0.8107 (mt) REVERT: L 121 PHE cc_start: 0.8274 (m-10) cc_final: 0.7975 (m-10) REVERT: L 188 LYS cc_start: 0.9125 (ptpp) cc_final: 0.8600 (ptpp) REVERT: M 5 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8375 (t) REVERT: M 15 TYR cc_start: 0.7647 (t80) cc_final: 0.7000 (t80) REVERT: M 16 LYS cc_start: 0.8693 (mmmt) cc_final: 0.8484 (mmmt) REVERT: M 28 THR cc_start: 0.8268 (p) cc_final: 0.8044 (p) REVERT: M 35 GLU cc_start: 0.7973 (pm20) cc_final: 0.7747 (pm20) REVERT: M 139 ASN cc_start: 0.8428 (p0) cc_final: 0.8123 (p0) REVERT: M 174 ASP cc_start: 0.7509 (m-30) cc_final: 0.7154 (m-30) REVERT: M 183 GLU cc_start: 0.7173 (pm20) cc_final: 0.6800 (pm20) REVERT: M 186 ASN cc_start: 0.8675 (p0) cc_final: 0.8097 (p0) REVERT: M 204 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7167 (mm-40) REVERT: M 216 ASN cc_start: 0.8240 (p0) cc_final: 0.7879 (p0) REVERT: M 321 LYS cc_start: 0.8226 (mtmm) cc_final: 0.7765 (mtmm) REVERT: M 351 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7818 (mmmt) REVERT: M 411 GLN cc_start: 0.7862 (tp40) cc_final: 0.7269 (tp40) REVERT: N 40 GLU cc_start: 0.7670 (mp0) cc_final: 0.7129 (mp0) REVERT: N 49 GLN cc_start: 0.8016 (tt0) cc_final: 0.7394 (tp-100) REVERT: N 104 LYS cc_start: 0.8499 (mtmm) cc_final: 0.7909 (mtmm) REVERT: N 212 ASN cc_start: 0.8556 (t0) cc_final: 0.8299 (t0) REVERT: N 215 MET cc_start: 0.6232 (OUTLIER) cc_final: 0.5879 (ppp) REVERT: N 223 GLU cc_start: 0.7688 (mp0) cc_final: 0.7459 (mp0) REVERT: N 234 LYS cc_start: 0.8431 (mmmm) cc_final: 0.8077 (mmmm) REVERT: N 264 THR cc_start: 0.8181 (p) cc_final: 0.7972 (p) REVERT: N 286 LEU cc_start: 0.8549 (mt) cc_final: 0.8072 (mt) REVERT: N 329 TRP cc_start: 0.8965 (t-100) cc_final: 0.8508 (t-100) REVERT: N 394 LYS cc_start: 0.8705 (mmtm) cc_final: 0.8220 (mmtm) REVERT: O 8 MET cc_start: 0.7486 (ttp) cc_final: 0.6818 (ttp) REVERT: P 142 LYS cc_start: 0.8981 (tmtt) cc_final: 0.8422 (tmtt) REVERT: P 195 TRP cc_start: 0.8103 (t60) cc_final: 0.7903 (t60) REVERT: P 197 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7645 (m90) REVERT: P 258 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8062 (ttm110) outliers start: 216 outliers final: 128 residues processed: 1551 average time/residue: 0.4458 time to fit residues: 1101.8930 Evaluate side-chains 1559 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 1423 time to evaluate : 3.676 ------------------------------------------------------------------------------- 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 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 162 LYS Chi-restraints excluded: chain B residue 235 TRP Chi-restraints excluded: chain B residue 264 THR 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 G residue 15 THR 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 130 LYS Chi-restraints excluded: chain I residue 136 MET 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 235 GLN 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 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 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 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 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 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 37 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 236 optimal weight: 0.5980 chunk 235 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 413 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 319 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 overall best weight: 3.5188 ------------------------------------------------------------------------------- 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** I 235 GLN ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 GLN ** M 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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 = 0.3451 r_free = 0.3451 target = 0.120125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.099685 restraints weight = 56957.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.103134 restraints weight = 23570.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.105338 restraints weight = 12572.703| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 34178 Z= 0.227 Angle : 0.777 9.736 46677 Z= 0.388 Chirality : 0.050 0.297 5266 Planarity : 0.006 0.115 5972 Dihedral : 8.398 63.024 5284 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.55 % Favored : 94.12 % Rotamer: Outliers : 7.27 % Allowed : 28.91 % Favored : 63.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.13), residues: 4233 helix: 1.09 (0.23), residues: 487 sheet: -0.92 (0.13), residues: 1304 loop : -1.45 (0.13), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 409 HIS 0.007 0.001 HIS J 170 PHE 0.018 0.002 PHE I 420 TYR 0.027 0.002 TYR N 296 ARG 0.009 0.001 ARG N 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 14) link_NAG-ASN : angle 2.39407 ( 42) link_BETA1-4 : bond 0.00839 ( 18) link_BETA1-4 : angle 3.94985 ( 54) hydrogen bonds : bond 0.03941 ( 1205) hydrogen bonds : angle 5.77789 ( 3159) SS BOND : bond 0.00535 ( 68) SS BOND : angle 1.66092 ( 136) covalent geometry : bond 0.00488 (34078) covalent geometry : angle 0.75883 (46445) *********************** 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 1729 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 1467 time to evaluate : 3.608 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: A 24 TYR cc_start: 0.8295 (m-80) cc_final: 0.7954 (m-80) REVERT: A 51 TYR cc_start: 0.8091 (p90) cc_final: 0.7462 (p90) REVERT: A 174 ASP cc_start: 0.7637 (m-30) cc_final: 0.7273 (m-30) REVERT: A 183 GLU cc_start: 0.7144 (pm20) cc_final: 0.6926 (pm20) REVERT: A 230 HIS cc_start: 0.8145 (p-80) cc_final: 0.7305 (p-80) REVERT: A 246 GLU cc_start: 0.7477 (tp30) cc_final: 0.7246 (tt0) REVERT: A 257 PHE cc_start: 0.8715 (m-10) cc_final: 0.8362 (m-10) REVERT: A 287 PHE cc_start: 0.8668 (m-80) cc_final: 0.8424 (m-10) REVERT: A 292 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: A 317 THR cc_start: 0.8748 (t) cc_final: 0.8429 (p) REVERT: B 40 GLU cc_start: 0.7517 (mp0) cc_final: 0.7310 (mp0) REVERT: B 49 GLN cc_start: 0.8331 (tt0) cc_final: 0.8086 (tt0) REVERT: B 60 ASP cc_start: 0.8746 (m-30) cc_final: 0.8011 (m-30) REVERT: B 97 MET cc_start: 0.7612 (tmm) cc_final: 0.7069 (tmm) REVERT: B 109 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7078 (mm-30) REVERT: B 129 TYR cc_start: 0.8244 (t80) cc_final: 0.7866 (t80) REVERT: B 153 CYS cc_start: 0.5126 (m) cc_final: 0.4830 (m) REVERT: B 157 GLN cc_start: 0.7870 (mm-40) cc_final: 0.7553 (mm-40) REVERT: B 169 MET cc_start: 0.7370 (mmm) cc_final: 0.6573 (mmm) REVERT: B 253 LYS cc_start: 0.7987 (mtpp) cc_final: 0.7737 (mtpp) REVERT: B 261 ASP cc_start: 0.7864 (p0) cc_final: 0.7359 (p0) REVERT: B 326 GLU cc_start: 0.7323 (tt0) cc_final: 0.7020 (tt0) REVERT: B 327 TYR cc_start: 0.8689 (p90) cc_final: 0.8457 (p90) REVERT: B 362 TYR cc_start: 0.8491 (m-80) cc_final: 0.8229 (m-80) REVERT: D 141 MET cc_start: 0.7386 (mtp) cc_final: 0.6990 (mtp) REVERT: D 206 ARG cc_start: 0.7447 (mtt180) cc_final: 0.7107 (mtt180) REVERT: D 265 GLU cc_start: 0.7332 (pp20) cc_final: 0.6962 (pp20) REVERT: E 79 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7549 (mtpt) REVERT: E 100 ASN cc_start: 0.7432 (m-40) cc_final: 0.7114 (m-40) REVERT: E 109 ASP cc_start: 0.7910 (p0) cc_final: 0.7601 (p0) REVERT: E 186 ASN cc_start: 0.8112 (m-40) cc_final: 0.7666 (m-40) REVERT: E 199 ARG cc_start: 0.7811 (mmt180) cc_final: 0.7348 (mmt180) REVERT: E 202 ASP cc_start: 0.7099 (m-30) cc_final: 0.6840 (m-30) REVERT: E 216 ASN cc_start: 0.8145 (p0) cc_final: 0.7866 (p0) REVERT: E 228 MET cc_start: 0.7446 (tpt) cc_final: 0.7001 (tpt) REVERT: E 234 THR cc_start: 0.7459 (p) cc_final: 0.7139 (t) REVERT: E 246 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6748 (tm-30) REVERT: E 324 LYS cc_start: 0.8638 (pttm) cc_final: 0.8337 (pttm) REVERT: E 336 VAL cc_start: 0.8688 (t) cc_final: 0.8373 (p) REVERT: E 340 GLN cc_start: 0.8747 (tp40) cc_final: 0.8152 (tp40) REVERT: E 407 LEU cc_start: 0.8625 (tp) cc_final: 0.8149 (tp) REVERT: F 7 ASN cc_start: 0.8285 (t0) cc_final: 0.7437 (t0) REVERT: F 10 LYS cc_start: 0.8578 (mtmp) cc_final: 0.7718 (mtmp) REVERT: F 40 GLU cc_start: 0.7123 (mp0) cc_final: 0.6874 (mp0) REVERT: F 50 PHE cc_start: 0.8402 (p90) cc_final: 0.8113 (p90) REVERT: F 92 PHE cc_start: 0.8576 (t80) cc_final: 0.8031 (t80) REVERT: F 94 HIS cc_start: 0.7922 (m170) cc_final: 0.7401 (m170) REVERT: F 97 MET cc_start: 0.7937 (tpp) cc_final: 0.7390 (tpp) REVERT: F 112 GLN cc_start: 0.8643 (tt0) cc_final: 0.8441 (tt0) REVERT: F 196 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8302 (ttpt) REVERT: F 215 MET cc_start: 0.8011 (pmm) cc_final: 0.7470 (pmm) REVERT: F 234 LYS cc_start: 0.8479 (mmmt) cc_final: 0.7765 (mmmm) REVERT: F 246 ASP cc_start: 0.7659 (t0) cc_final: 0.7418 (t0) REVERT: F 272 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7488 (mm-30) REVERT: F 274 THR cc_start: 0.8632 (m) cc_final: 0.8112 (p) REVERT: F 362 TYR cc_start: 0.8572 (m-80) cc_final: 0.8232 (m-80) REVERT: H 177 MET cc_start: 0.8688 (mtt) cc_final: 0.8488 (mtt) REVERT: H 258 ARG cc_start: 0.8754 (ttm170) cc_final: 0.8241 (ttm170) REVERT: I 2 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7347 (mm-30) REVERT: I 77 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8047 (mm-40) REVERT: I 139 ASN cc_start: 0.8458 (p0) cc_final: 0.8245 (p0) REVERT: I 146 VAL cc_start: 0.8585 (t) cc_final: 0.8285 (m) REVERT: I 235 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7591 (tt0) REVERT: I 237 PRO cc_start: 0.8785 (Cg_exo) cc_final: 0.8556 (Cg_endo) REVERT: I 371 SER cc_start: 0.8792 (t) cc_final: 0.8485 (p) REVERT: I 381 GLU cc_start: 0.7318 (pm20) cc_final: 0.6947 (pm20) REVERT: I 402 MET cc_start: 0.7342 (mmm) cc_final: 0.7079 (mmm) REVERT: J 10 LYS cc_start: 0.8813 (tttm) cc_final: 0.8369 (tttm) REVERT: J 97 MET cc_start: 0.7385 (tmm) cc_final: 0.7013 (tmm) REVERT: J 129 TYR cc_start: 0.7799 (t80) cc_final: 0.7209 (t80) REVERT: J 235 TRP cc_start: 0.7825 (OUTLIER) cc_final: 0.7394 (m-10) REVERT: J 304 GLN cc_start: 0.8455 (tt0) cc_final: 0.8241 (tt0) REVERT: J 331 ASN cc_start: 0.8928 (m110) cc_final: 0.8596 (m110) REVERT: L 188 LYS cc_start: 0.9151 (ptpp) cc_final: 0.8564 (ptpp) REVERT: L 215 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7691 (mmtt) REVERT: L 218 ASP cc_start: 0.8338 (p0) cc_final: 0.6911 (p0) REVERT: L 221 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6356 (ptp-110) REVERT: L 258 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7792 (ttm110) REVERT: M 5 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8340 (t) REVERT: M 15 TYR cc_start: 0.7713 (t80) cc_final: 0.6957 (t80) REVERT: M 16 LYS cc_start: 0.8671 (mmmt) cc_final: 0.8385 (mmmt) REVERT: M 35 GLU cc_start: 0.7916 (pm20) cc_final: 0.7490 (pm20) REVERT: M 50 GLU cc_start: 0.6925 (tp30) cc_final: 0.6578 (tp30) REVERT: M 100 ASN cc_start: 0.7715 (m110) cc_final: 0.7513 (m-40) REVERT: M 174 ASP cc_start: 0.7519 (m-30) cc_final: 0.7150 (m-30) REVERT: M 183 GLU cc_start: 0.7273 (pm20) cc_final: 0.6683 (pm20) REVERT: M 186 ASN cc_start: 0.8692 (p0) cc_final: 0.8118 (p0) REVERT: M 204 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7465 (mm-40) REVERT: M 216 ASN cc_start: 0.8292 (p0) cc_final: 0.7956 (p0) REVERT: M 321 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7812 (mtmm) REVERT: M 351 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7859 (mmmt) REVERT: M 411 GLN cc_start: 0.7826 (tp40) cc_final: 0.7207 (tp40) REVERT: N 40 GLU cc_start: 0.7680 (mp0) cc_final: 0.7147 (mp0) REVERT: N 49 GLN cc_start: 0.8168 (tt0) cc_final: 0.7469 (tp-100) REVERT: N 104 LYS cc_start: 0.8542 (mtmm) cc_final: 0.7979 (mtmm) REVERT: N 166 GLU cc_start: 0.7955 (pm20) cc_final: 0.7526 (pm20) REVERT: N 212 ASN cc_start: 0.8559 (t0) cc_final: 0.8277 (t0) REVERT: N 215 MET cc_start: 0.6256 (ppp) cc_final: 0.5921 (ppp) REVERT: N 234 LYS cc_start: 0.8451 (mmmm) cc_final: 0.8080 (mmmm) REVERT: N 250 ARG cc_start: 0.7049 (mmm-85) cc_final: 0.6643 (mmm-85) REVERT: N 286 LEU cc_start: 0.8542 (mt) cc_final: 0.7925 (mt) REVERT: N 329 TRP cc_start: 0.8966 (t-100) cc_final: 0.8434 (t-100) REVERT: N 356 GLN cc_start: 0.8343 (tt0) cc_final: 0.7659 (tm-30) REVERT: N 394 LYS cc_start: 0.8804 (mmtm) cc_final: 0.8257 (mmtm) REVERT: O 8 MET cc_start: 0.7495 (ttp) cc_final: 0.6850 (ttp) REVERT: P 142 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8491 (tmtt) REVERT: P 166 TYR cc_start: 0.7796 (m-10) cc_final: 0.7535 (m-80) REVERT: P 195 TRP cc_start: 0.8116 (t60) cc_final: 0.7864 (t60) REVERT: P 197 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7687 (m90) REVERT: P 255 MET cc_start: 0.5693 (mpp) cc_final: 0.5445 (mpp) REVERT: P 258 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8163 (ttm110) outliers start: 262 outliers final: 186 residues processed: 1575 average time/residue: 0.4400 time to fit residues: 1106.0796 Evaluate side-chains 1638 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 1443 time to evaluate : 3.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 113 VAL Chi-restraints excluded: chain A residue 120 SER 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 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 142 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 LYS 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 343 THR 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 219 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 231 VAL 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 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 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 286 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 354 ILE 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 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 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 136 MET Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 235 GLN 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 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 388 VAL 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 65 THR Chi-restraints excluded: chain J residue 88 SER 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 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 381 ILE Chi-restraints excluded: chain J residue 394 LYS 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 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 62 CYS 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 419 random chunks: chunk 164 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 292 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 233 optimal weight: 0.0770 chunk 269 optimal weight: 50.0000 chunk 362 optimal weight: 6.9990 chunk 319 optimal weight: 0.9980 overall best weight: 3.0144 ------------------------------------------------------------------------------- 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 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 F 170 HIS F 207 ASN F 236 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 9 ASN ** 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 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 = 0.3449 r_free = 0.3449 target = 0.120147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.099680 restraints weight = 57287.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103178 restraints weight = 23738.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105372 restraints weight = 12592.399| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34178 Z= 0.200 Angle : 0.748 9.607 46677 Z= 0.372 Chirality : 0.049 0.285 5266 Planarity : 0.006 0.106 5972 Dihedral : 7.540 61.177 5277 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.93 % Favored : 93.79 % Rotamer: Outliers : 7.99 % Allowed : 29.77 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.13), residues: 4233 helix: 1.15 (0.23), residues: 490 sheet: -0.91 (0.13), residues: 1304 loop : -1.40 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 329 HIS 0.008 0.001 HIS J 170 PHE 0.031 0.002 PHE F 237 TYR 0.027 0.002 TYR N 296 ARG 0.010 0.001 ARG N 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00368 ( 14) link_NAG-ASN : angle 2.34253 ( 42) link_BETA1-4 : bond 0.00882 ( 18) link_BETA1-4 : angle 3.82052 ( 54) hydrogen bonds : bond 0.03686 ( 1205) hydrogen bonds : angle 5.57564 ( 3159) SS BOND : bond 0.00377 ( 68) SS BOND : angle 1.51057 ( 136) covalent geometry : bond 0.00436 (34078) covalent geometry : angle 0.73092 (46445) *********************** 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 1760 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 288 poor density : 1472 time to evaluate : 3.537 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 24 TYR cc_start: 0.8285 (m-80) cc_final: 0.7963 (m-80) REVERT: A 31 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8042 (mtm) REVERT: A 44 LEU cc_start: 0.8825 (tp) cc_final: 0.8519 (tt) REVERT: A 51 TYR cc_start: 0.8001 (p90) cc_final: 0.7292 (p90) REVERT: A 77 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7737 (mm-40) REVERT: A 105 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6931 (tm-30) REVERT: A 230 HIS cc_start: 0.8201 (p-80) cc_final: 0.7519 (p-80) REVERT: A 246 GLU cc_start: 0.7506 (tp30) cc_final: 0.7209 (tt0) REVERT: A 247 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8302 (mtmm) REVERT: A 257 PHE cc_start: 0.8682 (m-10) cc_final: 0.8328 (m-10) REVERT: A 287 PHE cc_start: 0.8665 (m-80) cc_final: 0.8383 (m-10) REVERT: A 292 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: A 317 THR cc_start: 0.8769 (t) cc_final: 0.8429 (p) REVERT: A 354 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8195 (mt) REVERT: A 432 THR cc_start: 0.8369 (m) cc_final: 0.8162 (t) REVERT: B 40 GLU cc_start: 0.7544 (mp0) cc_final: 0.7299 (mp0) REVERT: B 49 GLN cc_start: 0.8359 (tt0) cc_final: 0.8086 (tt0) REVERT: B 60 ASP cc_start: 0.8705 (m-30) cc_final: 0.7540 (m-30) REVERT: B 75 ILE cc_start: 0.8697 (mp) cc_final: 0.8213 (mt) REVERT: B 97 MET cc_start: 0.7595 (tmm) cc_final: 0.7107 (tmm) REVERT: B 109 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7053 (mm-30) REVERT: B 126 ARG cc_start: 0.7960 (mtt-85) cc_final: 0.7750 (mtt-85) REVERT: B 129 TYR cc_start: 0.8222 (t80) cc_final: 0.7802 (t80) REVERT: B 153 CYS cc_start: 0.5109 (m) cc_final: 0.4791 (m) REVERT: B 156 TYR cc_start: 0.8519 (m-10) cc_final: 0.8261 (m-10) REVERT: B 169 MET cc_start: 0.7333 (mmm) cc_final: 0.6508 (mmm) REVERT: B 253 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7788 (mtpp) REVERT: B 326 GLU cc_start: 0.7329 (tt0) cc_final: 0.7003 (tt0) REVERT: B 362 TYR cc_start: 0.8471 (m-80) cc_final: 0.8106 (m-80) REVERT: D 116 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7187 (pt0) REVERT: D 141 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7064 (mtp) REVERT: D 218 ASP cc_start: 0.8194 (p0) cc_final: 0.7943 (p0) REVERT: D 265 GLU cc_start: 0.7422 (pp20) cc_final: 0.7021 (pp20) REVERT: E 38 LEU cc_start: 0.8551 (tp) cc_final: 0.8266 (tt) REVERT: E 79 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7568 (mtpt) REVERT: E 87 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: E 100 ASN cc_start: 0.7591 (m-40) cc_final: 0.7291 (m-40) REVERT: E 140 VAL cc_start: 0.8247 (t) cc_final: 0.7897 (p) REVERT: E 186 ASN cc_start: 0.8123 (m-40) cc_final: 0.7665 (m-40) REVERT: E 199 ARG cc_start: 0.7805 (mmt180) cc_final: 0.7316 (mmt180) REVERT: E 202 ASP cc_start: 0.7130 (m-30) cc_final: 0.6866 (m-30) REVERT: E 216 ASN cc_start: 0.8185 (p0) cc_final: 0.7914 (p0) REVERT: E 228 MET cc_start: 0.7445 (tpt) cc_final: 0.7142 (tpt) REVERT: E 246 GLU cc_start: 0.7045 (tm-30) cc_final: 0.6677 (tm-30) REVERT: E 324 LYS cc_start: 0.8608 (pttm) cc_final: 0.8300 (pttm) REVERT: E 336 VAL cc_start: 0.8735 (t) cc_final: 0.8443 (p) REVERT: E 340 GLN cc_start: 0.8736 (tp40) cc_final: 0.8256 (tp40) REVERT: E 407 LEU cc_start: 0.8621 (tp) cc_final: 0.8102 (tp) REVERT: F 7 ASN cc_start: 0.8345 (t0) cc_final: 0.7446 (t0) REVERT: F 10 LYS cc_start: 0.8600 (mtmp) cc_final: 0.7698 (mtmp) REVERT: F 38 ARG cc_start: 0.7981 (mtm-85) cc_final: 0.7630 (mtm-85) REVERT: F 40 GLU cc_start: 0.7174 (mp0) cc_final: 0.6925 (mp0) REVERT: F 50 PHE cc_start: 0.8302 (p90) cc_final: 0.7902 (p90) REVERT: F 64 TYR cc_start: 0.8190 (p90) cc_final: 0.7837 (p90) REVERT: F 92 PHE cc_start: 0.8559 (t80) cc_final: 0.8032 (t80) REVERT: F 94 HIS cc_start: 0.7901 (m170) cc_final: 0.7399 (m170) REVERT: F 97 MET cc_start: 0.7914 (tpp) cc_final: 0.7339 (tpp) REVERT: F 112 GLN cc_start: 0.8602 (tt0) cc_final: 0.8350 (tt0) REVERT: F 196 LYS cc_start: 0.8458 (ttpt) cc_final: 0.8237 (ttpt) REVERT: F 215 MET cc_start: 0.8001 (pmm) cc_final: 0.7457 (pmm) REVERT: F 234 LYS cc_start: 0.8513 (mmmt) cc_final: 0.7789 (mmmm) REVERT: F 269 MET cc_start: 0.8253 (mtp) cc_final: 0.8053 (mtp) REVERT: F 272 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7439 (mm-30) REVERT: F 274 THR cc_start: 0.8650 (m) cc_final: 0.8297 (t) REVERT: F 362 TYR cc_start: 0.8497 (m-80) cc_final: 0.8116 (m-80) REVERT: F 407 VAL cc_start: 0.7131 (t) cc_final: 0.6900 (p) REVERT: H 258 ARG cc_start: 0.8753 (ttm170) cc_final: 0.8256 (ttm170) REVERT: I 2 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7342 (mm-30) REVERT: I 139 ASN cc_start: 0.8495 (p0) cc_final: 0.8224 (p0) REVERT: I 146 VAL cc_start: 0.8580 (t) cc_final: 0.8279 (m) REVERT: I 220 LYS cc_start: 0.8264 (ttmt) cc_final: 0.8041 (ttmt) REVERT: I 237 PRO cc_start: 0.8740 (Cg_exo) cc_final: 0.8478 (Cg_endo) REVERT: I 356 PHE cc_start: 0.8542 (p90) cc_final: 0.8285 (p90) REVERT: I 371 SER cc_start: 0.8831 (t) cc_final: 0.8492 (p) REVERT: I 381 GLU cc_start: 0.7308 (pm20) cc_final: 0.6939 (pm20) REVERT: J 10 LYS cc_start: 0.8808 (tttm) cc_final: 0.8386 (tttm) REVERT: J 97 MET cc_start: 0.7380 (tmm) cc_final: 0.7134 (tmm) REVERT: J 129 TYR cc_start: 0.7774 (t80) cc_final: 0.7192 (t80) REVERT: J 235 TRP cc_start: 0.7790 (OUTLIER) cc_final: 0.7376 (m-10) REVERT: J 304 GLN cc_start: 0.8447 (tt0) cc_final: 0.8240 (tt0) REVERT: J 331 ASN cc_start: 0.8890 (m110) cc_final: 0.8562 (m110) REVERT: L 188 LYS cc_start: 0.9169 (ptpp) cc_final: 0.8590 (ptpp) REVERT: L 218 ASP cc_start: 0.8334 (p0) cc_final: 0.6921 (p0) REVERT: L 221 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6448 (ptp-110) REVERT: L 258 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7771 (ttm110) REVERT: M 5 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8315 (t) REVERT: M 15 TYR cc_start: 0.7722 (t80) cc_final: 0.6902 (t80) REVERT: M 16 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8293 (mmmt) REVERT: M 30 GLN cc_start: 0.8420 (pt0) cc_final: 0.7755 (pt0) REVERT: M 32 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: M 35 GLU cc_start: 0.7872 (pm20) cc_final: 0.7432 (pm20) REVERT: M 50 GLU cc_start: 0.6960 (tp30) cc_final: 0.6730 (tp30) REVERT: M 94 CYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6837 (m) REVERT: M 100 ASN cc_start: 0.7710 (m110) cc_final: 0.6778 (m-40) REVERT: M 105 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: M 174 ASP cc_start: 0.7583 (m-30) cc_final: 0.7224 (m-30) REVERT: M 186 ASN cc_start: 0.8658 (p0) cc_final: 0.8106 (p0) REVERT: M 204 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7138 (mm-40) REVERT: M 216 ASN cc_start: 0.8164 (p0) cc_final: 0.7892 (p0) REVERT: M 292 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7578 (mm-30) REVERT: M 321 LYS cc_start: 0.8267 (mtmm) cc_final: 0.7772 (mtmm) REVERT: M 351 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7866 (mmmt) REVERT: M 411 GLN cc_start: 0.7820 (tp40) cc_final: 0.7202 (tp40) REVERT: N 40 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7131 (mp0) REVERT: N 49 GLN cc_start: 0.8161 (tt0) cc_final: 0.7469 (tp-100) REVERT: N 53 GLN cc_start: 0.8282 (mp10) cc_final: 0.8011 (mp10) REVERT: N 104 LYS cc_start: 0.8545 (mtmm) cc_final: 0.7990 (mtmm) REVERT: N 140 LYS cc_start: 0.8714 (mmtp) cc_final: 0.8428 (mttp) REVERT: N 166 GLU cc_start: 0.7922 (pm20) cc_final: 0.7577 (pm20) REVERT: N 215 MET cc_start: 0.6169 (ppp) cc_final: 0.5737 (ppp) REVERT: N 224 GLN cc_start: 0.8088 (tp40) cc_final: 0.7420 (tp40) REVERT: N 234 LYS cc_start: 0.8438 (mmmm) cc_final: 0.8035 (mmmm) REVERT: N 250 ARG cc_start: 0.7027 (mmm-85) cc_final: 0.6662 (mmm-85) REVERT: N 272 GLU cc_start: 0.8039 (mp0) cc_final: 0.7554 (mp0) REVERT: N 282 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8393 (t) REVERT: N 318 ILE cc_start: 0.8774 (pp) cc_final: 0.8403 (pp) REVERT: N 329 TRP cc_start: 0.8957 (t-100) cc_final: 0.8741 (t-100) REVERT: N 356 GLN cc_start: 0.8340 (tt0) cc_final: 0.7653 (tm-30) REVERT: N 394 LYS cc_start: 0.8857 (mmtm) cc_final: 0.8320 (mmtm) REVERT: O 8 MET cc_start: 0.7522 (ttp) cc_final: 0.6877 (ttp) REVERT: P 142 LYS cc_start: 0.9027 (tmtt) cc_final: 0.8512 (tmtt) REVERT: P 166 TYR cc_start: 0.7819 (m-10) cc_final: 0.7432 (m-10) REVERT: P 195 TRP cc_start: 0.8146 (t60) cc_final: 0.7914 (t60) REVERT: P 197 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7733 (m90) REVERT: P 256 VAL cc_start: 0.8841 (t) cc_final: 0.8592 (t) REVERT: P 258 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8130 (ttm110) outliers start: 288 outliers final: 194 residues processed: 1593 average time/residue: 0.4370 time to fit residues: 1111.8551 Evaluate side-chains 1657 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 1446 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 113 VAL 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 260 GLN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 354 LEU 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 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 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 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 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 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 207 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 221 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 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 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 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 229 VAL 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 310 VAL 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 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 136 MET 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 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 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 81 SER Chi-restraints excluded: chain J residue 88 SER 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 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 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 32 GLN 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 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 263 THR 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 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 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 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 O residue 24 VAL 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 195 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 38 optimal weight: 0.0040 chunk 140 optimal weight: 9.9990 chunk 262 optimal weight: 6.9990 chunk 357 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 418 optimal weight: 0.0010 chunk 228 optimal weight: 1.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- 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 ** 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 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** I 235 GLN ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 212 ASN N 255 HIS P 186 HIS ** P 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.100854 restraints weight = 56617.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.104364 restraints weight = 23406.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.106571 restraints weight = 12399.781| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34178 Z= 0.175 Angle : 0.746 9.421 46677 Z= 0.370 Chirality : 0.048 0.285 5266 Planarity : 0.006 0.115 5972 Dihedral : 7.149 62.671 5277 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.81 % Favored : 93.93 % Rotamer: Outliers : 7.85 % Allowed : 30.74 % Favored : 61.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 4233 helix: 1.21 (0.23), residues: 493 sheet: -0.86 (0.14), residues: 1295 loop : -1.36 (0.13), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 409 HIS 0.013 0.001 HIS H 176 PHE 0.037 0.002 PHE F 237 TYR 0.029 0.002 TYR N 296 ARG 0.009 0.001 ARG N 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 14) link_NAG-ASN : angle 2.31347 ( 42) link_BETA1-4 : bond 0.00840 ( 18) link_BETA1-4 : angle 3.62172 ( 54) hydrogen bonds : bond 0.03531 ( 1205) hydrogen bonds : angle 5.46141 ( 3159) SS BOND : bond 0.00388 ( 68) SS BOND : angle 1.54018 ( 136) covalent geometry : bond 0.00389 (34078) covalent geometry : angle 0.72988 (46445) *********************** 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 1740 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 283 poor density : 1457 time to evaluate : 3.558 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: A 24 TYR cc_start: 0.8259 (m-80) cc_final: 0.8004 (m-80) REVERT: A 31 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8019 (mtm) REVERT: A 44 LEU cc_start: 0.8812 (tp) cc_final: 0.8484 (tt) REVERT: A 51 TYR cc_start: 0.7962 (p90) cc_final: 0.7314 (p90) REVERT: A 170 TRP cc_start: 0.9003 (t60) cc_final: 0.8559 (t60) REVERT: A 230 HIS cc_start: 0.8261 (p-80) cc_final: 0.7635 (p-80) REVERT: A 246 GLU cc_start: 0.7521 (tp30) cc_final: 0.7179 (tt0) REVERT: A 257 PHE cc_start: 0.8628 (m-10) cc_final: 0.8328 (m-10) REVERT: A 287 PHE cc_start: 0.8665 (m-80) cc_final: 0.8393 (m-10) REVERT: A 292 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: A 317 THR cc_start: 0.8785 (t) cc_final: 0.8475 (p) REVERT: A 354 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8212 (mt) REVERT: B 9 TYR cc_start: 0.8124 (m-80) cc_final: 0.7679 (m-80) REVERT: B 40 GLU cc_start: 0.7539 (mp0) cc_final: 0.7278 (mp0) REVERT: B 49 GLN cc_start: 0.8393 (tt0) cc_final: 0.8130 (tt0) REVERT: B 60 ASP cc_start: 0.8699 (m-30) cc_final: 0.7545 (m-30) REVERT: B 75 ILE cc_start: 0.8693 (mp) cc_final: 0.8303 (mt) REVERT: B 97 MET cc_start: 0.7494 (tmm) cc_final: 0.6905 (tmm) REVERT: B 109 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7052 (mm-30) REVERT: B 129 TYR cc_start: 0.8200 (t80) cc_final: 0.7783 (t80) REVERT: B 153 CYS cc_start: 0.5168 (m) cc_final: 0.4821 (m) REVERT: B 156 TYR cc_start: 0.8541 (m-10) cc_final: 0.8247 (m-10) REVERT: B 169 MET cc_start: 0.7330 (mmm) cc_final: 0.6528 (mmm) REVERT: B 254 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7451 (m) REVERT: B 280 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.7076 (mpp80) REVERT: B 326 GLU cc_start: 0.7303 (tt0) cc_final: 0.6960 (tt0) REVERT: B 327 TYR cc_start: 0.8657 (p90) cc_final: 0.8444 (p90) REVERT: B 357 TYR cc_start: 0.8538 (t80) cc_final: 0.8161 (t80) REVERT: B 362 TYR cc_start: 0.8456 (m-80) cc_final: 0.7956 (m-80) REVERT: B 387 MET cc_start: 0.8085 (mmt) cc_final: 0.7726 (mmt) REVERT: D 141 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7004 (mtp) REVERT: D 265 GLU cc_start: 0.7511 (pp20) cc_final: 0.7126 (pp20) REVERT: E 79 LYS cc_start: 0.7947 (ttpt) cc_final: 0.7546 (mtpt) REVERT: E 100 ASN cc_start: 0.7668 (m-40) cc_final: 0.7409 (m-40) REVERT: E 140 VAL cc_start: 0.8220 (t) cc_final: 0.7829 (p) REVERT: E 186 ASN cc_start: 0.8108 (m-40) cc_final: 0.7641 (m-40) REVERT: E 199 ARG cc_start: 0.7812 (mmt180) cc_final: 0.7353 (mmt180) REVERT: E 202 ASP cc_start: 0.7151 (m-30) cc_final: 0.6894 (m-30) REVERT: E 204 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7846 (mm-40) REVERT: E 216 ASN cc_start: 0.8194 (p0) cc_final: 0.7859 (p0) REVERT: E 228 MET cc_start: 0.7449 (tpt) cc_final: 0.7225 (tpt) REVERT: E 246 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6697 (tm-30) REVERT: E 324 LYS cc_start: 0.8598 (pttm) cc_final: 0.8274 (pttm) REVERT: E 336 VAL cc_start: 0.8736 (t) cc_final: 0.8411 (p) REVERT: E 407 LEU cc_start: 0.8649 (tp) cc_final: 0.8096 (tp) REVERT: F 7 ASN cc_start: 0.8321 (t0) cc_final: 0.7446 (t0) REVERT: F 10 LYS cc_start: 0.8611 (mtmp) cc_final: 0.7683 (mtmp) REVERT: F 38 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7565 (mtm-85) REVERT: F 40 GLU cc_start: 0.7146 (mp0) cc_final: 0.6885 (mp0) REVERT: F 64 TYR cc_start: 0.8175 (p90) cc_final: 0.7798 (p90) REVERT: F 97 MET cc_start: 0.7894 (tpp) cc_final: 0.7324 (tpp) REVERT: F 112 GLN cc_start: 0.8597 (tt0) cc_final: 0.8344 (tt0) REVERT: F 196 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8287 (ttpt) REVERT: F 215 MET cc_start: 0.7989 (pmm) cc_final: 0.7506 (pmm) REVERT: F 234 LYS cc_start: 0.8539 (mmmt) cc_final: 0.7830 (mmmm) REVERT: F 272 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7456 (mm-30) REVERT: F 274 THR cc_start: 0.8616 (m) cc_final: 0.8284 (t) REVERT: F 362 TYR cc_start: 0.8497 (m-80) cc_final: 0.8157 (m-80) REVERT: F 407 VAL cc_start: 0.7075 (t) cc_final: 0.6842 (p) REVERT: H 258 ARG cc_start: 0.8756 (ttm170) cc_final: 0.8291 (ttm170) REVERT: I 2 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7328 (mm-30) REVERT: I 61 LYS cc_start: 0.8397 (tttt) cc_final: 0.8008 (tttt) REVERT: I 76 TYR cc_start: 0.8285 (t80) cc_final: 0.7961 (t80) REVERT: I 146 VAL cc_start: 0.8592 (t) cc_final: 0.8297 (m) REVERT: I 220 LYS cc_start: 0.8250 (ttmt) cc_final: 0.8008 (ttmt) REVERT: I 237 PRO cc_start: 0.8757 (Cg_exo) cc_final: 0.8501 (Cg_endo) REVERT: I 323 ASP cc_start: 0.7952 (p0) cc_final: 0.7661 (p0) REVERT: I 356 PHE cc_start: 0.8568 (p90) cc_final: 0.8292 (p90) REVERT: I 371 SER cc_start: 0.8827 (t) cc_final: 0.8501 (p) REVERT: I 381 GLU cc_start: 0.7281 (pm20) cc_final: 0.6945 (pm20) REVERT: J 10 LYS cc_start: 0.8787 (tttm) cc_final: 0.8356 (tttm) REVERT: J 129 TYR cc_start: 0.7765 (t80) cc_final: 0.7191 (t80) REVERT: J 235 TRP cc_start: 0.7820 (OUTLIER) cc_final: 0.7460 (m-10) REVERT: J 331 ASN cc_start: 0.8864 (m110) cc_final: 0.8539 (m110) REVERT: J 362 TYR cc_start: 0.8057 (m-80) cc_final: 0.7579 (m-80) REVERT: L 121 PHE cc_start: 0.8205 (m-10) cc_final: 0.7961 (m-10) REVERT: L 188 LYS cc_start: 0.9190 (ptpp) cc_final: 0.8578 (ptpp) REVERT: L 227 LYS cc_start: 0.8804 (tppt) cc_final: 0.8409 (tppt) REVERT: L 258 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7831 (ttm110) REVERT: M 5 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8280 (t) REVERT: M 15 TYR cc_start: 0.7726 (t80) cc_final: 0.6874 (t80) REVERT: M 35 GLU cc_start: 0.7872 (pm20) cc_final: 0.7470 (pm20) REVERT: M 94 CYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6869 (m) REVERT: M 100 ASN cc_start: 0.7629 (m110) cc_final: 0.6677 (m-40) REVERT: M 174 ASP cc_start: 0.7607 (m-30) cc_final: 0.7231 (m-30) REVERT: M 183 GLU cc_start: 0.7312 (pm20) cc_final: 0.6731 (pm20) REVERT: M 186 ASN cc_start: 0.8646 (p0) cc_final: 0.8062 (p0) REVERT: M 216 ASN cc_start: 0.8124 (p0) cc_final: 0.7886 (p0) REVERT: M 246 GLU cc_start: 0.7695 (mm-30) cc_final: 0.6960 (tm-30) REVERT: M 292 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7530 (mm-30) REVERT: M 305 THR cc_start: 0.8540 (t) cc_final: 0.8155 (p) REVERT: M 321 LYS cc_start: 0.8244 (mtmm) cc_final: 0.7764 (mtmm) REVERT: M 351 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7821 (mmmt) REVERT: M 381 GLU cc_start: 0.7653 (pm20) cc_final: 0.7386 (pm20) REVERT: M 411 GLN cc_start: 0.7809 (tp40) cc_final: 0.7176 (tp40) REVERT: N 40 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7171 (mp0) REVERT: N 49 GLN cc_start: 0.8156 (tt0) cc_final: 0.7758 (tp-100) REVERT: N 104 LYS cc_start: 0.8529 (mtmm) cc_final: 0.7970 (mtmm) REVERT: N 140 LYS cc_start: 0.8728 (mmtp) cc_final: 0.8417 (mttp) REVERT: N 166 GLU cc_start: 0.7875 (pm20) cc_final: 0.7551 (pm20) REVERT: N 177 ASP cc_start: 0.7954 (p0) cc_final: 0.7268 (p0) REVERT: N 215 MET cc_start: 0.6026 (ppp) cc_final: 0.5635 (ppp) REVERT: N 223 GLU cc_start: 0.7655 (mp0) cc_final: 0.7436 (mp0) REVERT: N 224 GLN cc_start: 0.8112 (tp40) cc_final: 0.7531 (tp40) REVERT: N 234 LYS cc_start: 0.8453 (mmmm) cc_final: 0.8074 (mmmm) REVERT: N 250 ARG cc_start: 0.7025 (mmm-85) cc_final: 0.6653 (mmm-85) REVERT: N 272 GLU cc_start: 0.8013 (mp0) cc_final: 0.7540 (mp0) REVERT: N 282 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8390 (t) REVERT: N 318 ILE cc_start: 0.8786 (pp) cc_final: 0.8460 (pp) REVERT: N 356 GLN cc_start: 0.8337 (tt0) cc_final: 0.7648 (tm-30) REVERT: N 394 LYS cc_start: 0.8859 (mmtm) cc_final: 0.8341 (mmtm) REVERT: O 8 MET cc_start: 0.7496 (ttp) cc_final: 0.7192 (ttp) REVERT: P 142 LYS cc_start: 0.9041 (tmtt) cc_final: 0.8536 (tmtt) REVERT: P 166 TYR cc_start: 0.7800 (m-10) cc_final: 0.7479 (m-80) REVERT: P 195 TRP cc_start: 0.8128 (t60) cc_final: 0.7922 (t60) REVERT: P 196 HIS cc_start: 0.8948 (t-90) cc_final: 0.8696 (t70) REVERT: P 197 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7678 (m90) REVERT: P 215 LYS cc_start: 0.8433 (pmtt) cc_final: 0.8145 (pmtt) REVERT: P 256 VAL cc_start: 0.8868 (t) cc_final: 0.8537 (t) REVERT: P 258 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8108 (ttm110) outliers start: 283 outliers final: 213 residues processed: 1580 average time/residue: 0.4472 time to fit residues: 1131.8869 Evaluate side-chains 1663 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1436 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 167 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 260 GLN 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 354 LEU Chi-restraints excluded: chain A residue 381 GLU 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 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 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 388 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 141 MET 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 7 MET 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 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 221 LEU 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 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 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 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 378 LEU 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 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 135 VAL 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 260 GLN 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 341 GLU Chi-restraints excluded: chain I residue 347 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 81 SER 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 228 SER Chi-restraints excluded: chain J residue 235 TRP 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 352 HIS 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 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 197 HIS 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 57 SER Chi-restraints excluded: chain M residue 72 GLU Chi-restraints excluded: chain M residue 94 CYS Chi-restraints excluded: chain M residue 156 ILE 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 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 348 THR Chi-restraints excluded: chain M residue 353 THR 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 M residue 436 LEU 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 88 SER Chi-restraints excluded: chain N residue 101 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 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 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 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 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 255 MET 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 315 optimal weight: 9.9990 chunk 416 optimal weight: 40.0000 chunk 134 optimal weight: 20.0000 chunk 400 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 412 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 401 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 overall best weight: 4.0986 ------------------------------------------------------------------------------- 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 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN F 207 ASN ** 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 252 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097766 restraints weight = 57675.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.101229 restraints weight = 23970.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103436 restraints weight = 12766.022| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 34178 Z= 0.250 Angle : 0.769 14.408 46677 Z= 0.383 Chirality : 0.049 0.278 5266 Planarity : 0.006 0.111 5972 Dihedral : 7.030 64.021 5274 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.50 % Favored : 93.24 % Rotamer: Outliers : 8.52 % Allowed : 30.97 % Favored : 60.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 4233 helix: 1.23 (0.23), residues: 493 sheet: -0.86 (0.14), residues: 1295 loop : -1.39 (0.13), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 170 HIS 0.013 0.001 HIS F 287 PHE 0.034 0.002 PHE F 237 TYR 0.029 0.002 TYR N 296 ARG 0.011 0.001 ARG N 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 14) link_NAG-ASN : angle 2.33869 ( 42) link_BETA1-4 : bond 0.00774 ( 18) link_BETA1-4 : angle 3.57434 ( 54) hydrogen bonds : bond 0.03735 ( 1205) hydrogen bonds : angle 5.45394 ( 3159) SS BOND : bond 0.00497 ( 68) SS BOND : angle 1.73080 ( 136) covalent geometry : bond 0.00530 (34078) covalent geometry : angle 0.75228 (46445) *********************** 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 1779 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 307 poor density : 1472 time to evaluate : 4.004 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 51 TYR cc_start: 0.7889 (p90) cc_final: 0.7285 (p90) REVERT: A 115 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.7880 (mtm110) REVERT: A 170 TRP cc_start: 0.9026 (t60) cc_final: 0.8643 (t60) REVERT: A 230 HIS cc_start: 0.8276 (p-80) cc_final: 0.7689 (p-80) REVERT: A 246 GLU cc_start: 0.7605 (tp30) cc_final: 0.7233 (tt0) REVERT: A 257 PHE cc_start: 0.8670 (m-10) cc_final: 0.8377 (m-10) REVERT: A 287 PHE cc_start: 0.8679 (m-80) cc_final: 0.8380 (m-10) REVERT: A 292 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: A 317 THR cc_start: 0.8773 (t) cc_final: 0.8474 (p) REVERT: A 354 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8212 (mt) REVERT: B 9 TYR cc_start: 0.8195 (m-80) cc_final: 0.7807 (m-80) REVERT: B 40 GLU cc_start: 0.7574 (mp0) cc_final: 0.7323 (mp0) REVERT: B 49 GLN cc_start: 0.8433 (tt0) cc_final: 0.8137 (tt0) REVERT: B 60 ASP cc_start: 0.8698 (m-30) cc_final: 0.7525 (m-30) REVERT: B 75 ILE cc_start: 0.8686 (mp) cc_final: 0.8327 (mt) REVERT: B 96 THR cc_start: 0.8207 (m) cc_final: 0.7609 (p) REVERT: B 97 MET cc_start: 0.7503 (tmm) cc_final: 0.7125 (tmm) REVERT: B 109 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7084 (mm-30) REVERT: B 129 TYR cc_start: 0.8241 (t80) cc_final: 0.7828 (t80) REVERT: B 156 TYR cc_start: 0.8636 (m-10) cc_final: 0.8261 (m-10) REVERT: B 169 MET cc_start: 0.7385 (mmm) cc_final: 0.6581 (mmm) REVERT: B 265 CYS cc_start: 0.5201 (OUTLIER) cc_final: 0.4745 (t) REVERT: B 280 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.7129 (mpp80) REVERT: B 326 GLU cc_start: 0.7396 (tt0) cc_final: 0.7082 (tt0) REVERT: B 327 TYR cc_start: 0.8686 (p90) cc_final: 0.8459 (p90) REVERT: B 362 TYR cc_start: 0.8475 (m-80) cc_final: 0.7916 (m-80) REVERT: D 116 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7190 (pt0) REVERT: D 141 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.7090 (mtp) REVERT: D 265 GLU cc_start: 0.7590 (pp20) cc_final: 0.7187 (pp20) REVERT: E 100 ASN cc_start: 0.7750 (m-40) cc_final: 0.7466 (m-40) REVERT: E 140 VAL cc_start: 0.8193 (t) cc_final: 0.7769 (p) REVERT: E 176 LYS cc_start: 0.8496 (mmtp) cc_final: 0.7879 (mmtp) REVERT: E 186 ASN cc_start: 0.8149 (m-40) cc_final: 0.7712 (m-40) REVERT: E 199 ARG cc_start: 0.7817 (mmt180) cc_final: 0.7357 (mmt180) REVERT: E 202 ASP cc_start: 0.7159 (m-30) cc_final: 0.6894 (m-30) REVERT: E 216 ASN cc_start: 0.8263 (p0) cc_final: 0.7918 (p0) REVERT: E 246 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6771 (tm-30) REVERT: E 324 LYS cc_start: 0.8613 (pttm) cc_final: 0.8298 (pttm) REVERT: E 336 VAL cc_start: 0.8721 (t) cc_final: 0.8401 (p) REVERT: E 340 GLN cc_start: 0.8845 (tp40) cc_final: 0.8542 (tp40) REVERT: E 407 LEU cc_start: 0.8666 (tp) cc_final: 0.8159 (tp) REVERT: F 7 ASN cc_start: 0.8379 (t0) cc_final: 0.7614 (t0) REVERT: F 10 LYS cc_start: 0.8617 (mtmp) cc_final: 0.7773 (mtmp) REVERT: F 13 ARG cc_start: 0.8524 (ptm160) cc_final: 0.8122 (ptm-80) REVERT: F 35 GLU cc_start: 0.7080 (tt0) cc_final: 0.6870 (tt0) REVERT: F 38 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7650 (mtm-85) REVERT: F 40 GLU cc_start: 0.7170 (mp0) cc_final: 0.6911 (mp0) REVERT: F 64 TYR cc_start: 0.8190 (p90) cc_final: 0.7829 (p90) REVERT: F 97 MET cc_start: 0.7928 (tpp) cc_final: 0.7324 (tpp) REVERT: F 111 LEU cc_start: 0.8392 (tp) cc_final: 0.8185 (tt) REVERT: F 112 GLN cc_start: 0.8598 (tt0) cc_final: 0.8365 (tt0) REVERT: F 166 GLU cc_start: 0.7989 (pm20) cc_final: 0.7680 (pm20) REVERT: F 196 LYS cc_start: 0.8551 (ttpt) cc_final: 0.8340 (ttpt) REVERT: F 215 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7531 (pmm) REVERT: F 234 LYS cc_start: 0.8545 (mmmt) cc_final: 0.7591 (mmmm) REVERT: F 272 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7452 (mm-30) REVERT: F 274 THR cc_start: 0.8638 (m) cc_final: 0.8315 (t) REVERT: F 399 TYR cc_start: 0.8258 (m-10) cc_final: 0.7992 (m-10) REVERT: H 258 ARG cc_start: 0.8777 (ttm170) cc_final: 0.8280 (ttm170) REVERT: I 2 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7320 (mm-30) REVERT: I 61 LYS cc_start: 0.8399 (tttt) cc_final: 0.7969 (tttt) REVERT: I 73 LYS cc_start: 0.7647 (ttmm) cc_final: 0.7407 (mtpp) REVERT: I 76 TYR cc_start: 0.8262 (t80) cc_final: 0.8047 (t80) REVERT: I 137 TYR cc_start: 0.8597 (p90) cc_final: 0.8307 (p90) REVERT: I 139 ASN cc_start: 0.8429 (p0) cc_final: 0.8164 (p0) REVERT: I 146 VAL cc_start: 0.8599 (t) cc_final: 0.8271 (m) REVERT: I 220 LYS cc_start: 0.8255 (ttmt) cc_final: 0.8006 (ttmt) REVERT: I 356 PHE cc_start: 0.8551 (p90) cc_final: 0.8262 (p90) REVERT: I 371 SER cc_start: 0.8873 (t) cc_final: 0.8570 (p) REVERT: I 381 GLU cc_start: 0.7296 (pm20) cc_final: 0.6888 (pm20) REVERT: J 10 LYS cc_start: 0.8827 (tttm) cc_final: 0.8417 (tttm) REVERT: J 129 TYR cc_start: 0.7803 (t80) cc_final: 0.7228 (t80) REVERT: J 153 CYS cc_start: 0.5670 (m) cc_final: 0.5123 (m) REVERT: J 169 MET cc_start: 0.7339 (mmt) cc_final: 0.7096 (mmt) REVERT: J 235 TRP cc_start: 0.7769 (OUTLIER) cc_final: 0.7420 (m-10) REVERT: J 320 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8503 (t) REVERT: J 331 ASN cc_start: 0.8863 (m110) cc_final: 0.8465 (m110) REVERT: J 362 TYR cc_start: 0.8108 (m-80) cc_final: 0.7701 (m-80) REVERT: L 188 LYS cc_start: 0.9182 (ptpp) cc_final: 0.8586 (ptpp) REVERT: L 215 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7759 (mmtt) REVERT: L 218 ASP cc_start: 0.8464 (p0) cc_final: 0.8195 (p0) REVERT: L 227 LYS cc_start: 0.8882 (tppt) cc_final: 0.8400 (tppt) REVERT: L 258 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7867 (ttm110) REVERT: M 15 TYR cc_start: 0.7815 (t80) cc_final: 0.7305 (t80) REVERT: M 16 LYS cc_start: 0.8603 (mmmt) cc_final: 0.8390 (mmtt) REVERT: M 35 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7457 (pm20) REVERT: M 50 GLU cc_start: 0.7057 (tp30) cc_final: 0.6810 (tp30) REVERT: M 94 CYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7121 (m) REVERT: M 100 ASN cc_start: 0.7609 (m110) cc_final: 0.6924 (m-40) REVERT: M 174 ASP cc_start: 0.7656 (m-30) cc_final: 0.7238 (m-30) REVERT: M 186 ASN cc_start: 0.8651 (p0) cc_final: 0.8118 (p0) REVERT: M 216 ASN cc_start: 0.8191 (p0) cc_final: 0.7898 (p0) REVERT: M 246 GLU cc_start: 0.7694 (mm-30) cc_final: 0.6974 (tm-30) REVERT: M 292 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7573 (mm-30) REVERT: M 305 THR cc_start: 0.8587 (t) cc_final: 0.8239 (p) REVERT: M 321 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7741 (mtmm) REVERT: M 351 LYS cc_start: 0.8313 (mmmt) cc_final: 0.7860 (mmmt) REVERT: M 381 GLU cc_start: 0.7688 (pm20) cc_final: 0.7407 (pm20) REVERT: M 411 GLN cc_start: 0.7842 (tp40) cc_final: 0.7207 (tp40) REVERT: N 40 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7244 (mp0) REVERT: N 53 GLN cc_start: 0.8309 (mp10) cc_final: 0.8100 (mp10) REVERT: N 104 LYS cc_start: 0.8535 (mtmm) cc_final: 0.7972 (mtmm) REVERT: N 140 LYS cc_start: 0.8756 (mmtp) cc_final: 0.8432 (mttp) REVERT: N 166 GLU cc_start: 0.7837 (pm20) cc_final: 0.7487 (pm20) REVERT: N 177 ASP cc_start: 0.7894 (p0) cc_final: 0.7339 (p0) REVERT: N 215 MET cc_start: 0.6066 (ppp) cc_final: 0.5657 (ppp) REVERT: N 223 GLU cc_start: 0.7682 (mp0) cc_final: 0.7464 (mp0) REVERT: N 234 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8027 (mmmm) REVERT: N 250 ARG cc_start: 0.7070 (mmm-85) cc_final: 0.6736 (mmm-85) REVERT: N 272 GLU cc_start: 0.8056 (mp0) cc_final: 0.7595 (mp0) REVERT: N 282 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8423 (t) REVERT: N 318 ILE cc_start: 0.8783 (pp) cc_final: 0.8505 (pp) REVERT: N 356 GLN cc_start: 0.8361 (tt0) cc_final: 0.7683 (tm-30) REVERT: N 394 LYS cc_start: 0.8891 (mmtm) cc_final: 0.8344 (mmtm) REVERT: O 8 MET cc_start: 0.7536 (ttp) cc_final: 0.6912 (ttp) REVERT: P 142 LYS cc_start: 0.9083 (tmtt) cc_final: 0.8562 (tmtt) REVERT: P 196 HIS cc_start: 0.8997 (t-90) cc_final: 0.8728 (t70) REVERT: P 197 HIS cc_start: 0.7953 (OUTLIER) cc_final: 0.7593 (m90) REVERT: P 215 LYS cc_start: 0.8537 (pmtt) cc_final: 0.8289 (pmtt) REVERT: P 258 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7755 (ttm110) outliers start: 307 outliers final: 231 residues processed: 1595 average time/residue: 0.4479 time to fit residues: 1140.6442 Evaluate side-chains 1699 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 1453 time to evaluate : 3.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 136 MET Chi-restraints excluded: chain A residue 160 GLN 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 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 260 GLN 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 354 LEU Chi-restraints excluded: chain A residue 381 GLU 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 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 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 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 265 CYS 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 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 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 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 166 LEU 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 221 LEU Chi-restraints excluded: chain E residue 244 LEU 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 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 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 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 378 LEU Chi-restraints excluded: chain F residue 387 MET 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 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 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 53 THR 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 244 LEU 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 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 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 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 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 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 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 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 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 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 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 231 VAL Chi-restraints excluded: chain M residue 252 ASN Chi-restraints excluded: chain M residue 263 THR 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 353 THR Chi-restraints excluded: chain M residue 358 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 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 235 TRP 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 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 252 ASN Chi-restraints excluded: chain P residue 255 MET Chi-restraints excluded: chain P residue 257 THR 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 13 optimal weight: 9.9990 chunk 362 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 chunk 64 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 chunk 302 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 315 optimal weight: 0.9980 chunk 297 optimal weight: 20.0000 chunk 357 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 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 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 340 GLN H 252 ASN I 77 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 187 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.100535 restraints weight = 56626.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.104064 restraints weight = 23353.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106238 restraints weight = 12371.899| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34178 Z= 0.182 Angle : 0.751 13.156 46677 Z= 0.373 Chirality : 0.049 0.274 5266 Planarity : 0.006 0.108 5972 Dihedral : 6.898 64.566 5274 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.86 % Favored : 93.91 % Rotamer: Outliers : 8.05 % Allowed : 31.44 % Favored : 60.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 4233 helix: 1.26 (0.23), residues: 493 sheet: -0.85 (0.13), residues: 1310 loop : -1.37 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP I 170 HIS 0.012 0.001 HIS F 287 PHE 0.025 0.002 PHE F 237 TYR 0.039 0.002 TYR N 305 ARG 0.011 0.001 ARG N 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 14) link_NAG-ASN : angle 2.36018 ( 42) link_BETA1-4 : bond 0.00781 ( 18) link_BETA1-4 : angle 3.38588 ( 54) hydrogen bonds : bond 0.03496 ( 1205) hydrogen bonds : angle 5.39995 ( 3159) SS BOND : bond 0.00456 ( 68) SS BOND : angle 1.76587 ( 136) covalent geometry : bond 0.00402 (34078) covalent geometry : angle 0.73400 (46445) *********************** 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 1758 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 290 poor density : 1468 time to evaluate : 3.549 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: A 51 TYR cc_start: 0.7863 (p90) cc_final: 0.7224 (p90) REVERT: A 115 ARG cc_start: 0.8320 (ttp-110) cc_final: 0.7813 (mtm110) REVERT: A 170 TRP cc_start: 0.8995 (t60) cc_final: 0.8627 (t60) REVERT: A 230 HIS cc_start: 0.8314 (p-80) cc_final: 0.7781 (p-80) REVERT: A 246 GLU cc_start: 0.7564 (tp30) cc_final: 0.7237 (tt0) REVERT: A 257 PHE cc_start: 0.8673 (m-10) cc_final: 0.8397 (m-10) REVERT: A 287 PHE cc_start: 0.8641 (m-80) cc_final: 0.8382 (m-10) REVERT: A 292 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: A 317 THR cc_start: 0.8760 (t) cc_final: 0.8468 (p) REVERT: A 354 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8213 (mt) REVERT: B 9 TYR cc_start: 0.8127 (m-80) cc_final: 0.7740 (m-80) REVERT: B 40 GLU cc_start: 0.7528 (mp0) cc_final: 0.7260 (mp0) REVERT: B 49 GLN cc_start: 0.8426 (tt0) cc_final: 0.8165 (tt0) REVERT: B 60 ASP cc_start: 0.8697 (m-30) cc_final: 0.7560 (m-30) REVERT: B 85 VAL cc_start: 0.8896 (m) cc_final: 0.8574 (p) REVERT: B 97 MET cc_start: 0.7403 (tmm) cc_final: 0.7083 (tmm) REVERT: B 109 GLU cc_start: 0.7290 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 129 TYR cc_start: 0.8193 (t80) cc_final: 0.7783 (t80) REVERT: B 156 TYR cc_start: 0.8583 (m-10) cc_final: 0.8208 (m-10) REVERT: B 254 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7519 (m) REVERT: B 280 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7099 (mpp80) REVERT: B 320 VAL cc_start: 0.8682 (t) cc_final: 0.8348 (m) REVERT: B 326 GLU cc_start: 0.7329 (tt0) cc_final: 0.6973 (tt0) REVERT: B 327 TYR cc_start: 0.8659 (p90) cc_final: 0.8417 (p90) REVERT: B 331 ASN cc_start: 0.8512 (m-40) cc_final: 0.8273 (m-40) REVERT: B 357 TYR cc_start: 0.8527 (t80) cc_final: 0.8158 (t80) REVERT: B 362 TYR cc_start: 0.8444 (m-80) cc_final: 0.7929 (m-80) REVERT: D 116 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7102 (pt0) REVERT: D 206 ARG cc_start: 0.7509 (mtt180) cc_final: 0.7074 (mtt180) REVERT: D 265 GLU cc_start: 0.7598 (pp20) cc_final: 0.7187 (pp20) REVERT: E 38 LEU cc_start: 0.8494 (tp) cc_final: 0.8273 (tt) REVERT: E 49 CYS cc_start: 0.6435 (p) cc_final: 0.5971 (p) REVERT: E 100 ASN cc_start: 0.7737 (m-40) cc_final: 0.7484 (m-40) REVERT: E 140 VAL cc_start: 0.8183 (t) cc_final: 0.7809 (p) REVERT: E 176 LYS cc_start: 0.8497 (mmtp) cc_final: 0.7819 (mmtp) REVERT: E 186 ASN cc_start: 0.8124 (m-40) cc_final: 0.7705 (m-40) REVERT: E 199 ARG cc_start: 0.7793 (mmt180) cc_final: 0.7309 (mmt180) REVERT: E 202 ASP cc_start: 0.7171 (m-30) cc_final: 0.6923 (m-30) REVERT: E 204 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7903 (mm-40) REVERT: E 216 ASN cc_start: 0.8217 (p0) cc_final: 0.7885 (p0) REVERT: E 246 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6751 (tm-30) REVERT: E 324 LYS cc_start: 0.8602 (pttm) cc_final: 0.8270 (pttm) REVERT: E 336 VAL cc_start: 0.8690 (t) cc_final: 0.8376 (p) REVERT: E 364 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.7912 (p) REVERT: E 407 LEU cc_start: 0.8653 (tp) cc_final: 0.8188 (tp) REVERT: F 7 ASN cc_start: 0.8343 (t0) cc_final: 0.7612 (t0) REVERT: F 10 LYS cc_start: 0.8699 (mtmp) cc_final: 0.7736 (mtmp) REVERT: F 35 GLU cc_start: 0.7079 (tt0) cc_final: 0.6717 (tt0) REVERT: F 40 GLU cc_start: 0.7120 (mp0) cc_final: 0.6851 (mp0) REVERT: F 64 TYR cc_start: 0.8109 (p90) cc_final: 0.7741 (p90) REVERT: F 97 MET cc_start: 0.7856 (tpp) cc_final: 0.7217 (tpp) REVERT: F 112 GLN cc_start: 0.8564 (tt0) cc_final: 0.8286 (tt0) REVERT: F 166 GLU cc_start: 0.8000 (pm20) cc_final: 0.7691 (pm20) REVERT: F 195 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7674 (tptp) REVERT: F 215 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7543 (pmm) REVERT: F 234 LYS cc_start: 0.8543 (mmmt) cc_final: 0.7801 (mmmm) REVERT: F 272 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7447 (mm-30) REVERT: F 274 THR cc_start: 0.8627 (m) cc_final: 0.8296 (t) REVERT: F 326 GLU cc_start: 0.7548 (tt0) cc_final: 0.7311 (tt0) REVERT: F 399 TYR cc_start: 0.8198 (m-10) cc_final: 0.7966 (m-10) REVERT: H 170 CYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7443 (p) REVERT: H 177 MET cc_start: 0.8355 (mtt) cc_final: 0.8003 (mtt) REVERT: H 258 ARG cc_start: 0.8760 (ttm170) cc_final: 0.8319 (ttm170) REVERT: I 2 GLU cc_start: 0.7619 (mm-30) cc_final: 0.7307 (mm-30) REVERT: I 61 LYS cc_start: 0.8400 (tttt) cc_final: 0.7973 (tttt) REVERT: I 139 ASN cc_start: 0.8433 (p0) cc_final: 0.8178 (p0) REVERT: I 146 VAL cc_start: 0.8593 (t) cc_final: 0.8295 (m) REVERT: I 356 PHE cc_start: 0.8556 (p90) cc_final: 0.8273 (p90) REVERT: I 371 SER cc_start: 0.8769 (t) cc_final: 0.8508 (p) REVERT: I 381 GLU cc_start: 0.7283 (pm20) cc_final: 0.6884 (pm20) REVERT: I 390 TYR cc_start: 0.8745 (p90) cc_final: 0.8525 (p90) REVERT: J 10 LYS cc_start: 0.8799 (tttm) cc_final: 0.8390 (tttm) REVERT: J 40 GLU cc_start: 0.7350 (mp0) cc_final: 0.6969 (mp0) REVERT: J 61 ASN cc_start: 0.7899 (t0) cc_final: 0.7550 (t0) REVERT: J 129 TYR cc_start: 0.7754 (t80) cc_final: 0.7190 (t80) REVERT: J 169 MET cc_start: 0.7337 (mmt) cc_final: 0.7045 (mmt) REVERT: J 235 TRP cc_start: 0.7759 (OUTLIER) cc_final: 0.7441 (m-10) REVERT: J 320 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8490 (t) REVERT: J 329 TRP cc_start: 0.8953 (t-100) cc_final: 0.8730 (t-100) REVERT: J 331 ASN cc_start: 0.8836 (m110) cc_final: 0.8498 (m110) REVERT: J 362 TYR cc_start: 0.8053 (m-80) cc_final: 0.7752 (m-80) REVERT: L 188 LYS cc_start: 0.9189 (ptpp) cc_final: 0.8600 (ptpp) REVERT: L 215 LYS cc_start: 0.8128 (mmtt) cc_final: 0.7782 (mmtt) REVERT: L 218 ASP cc_start: 0.8357 (p0) cc_final: 0.8093 (p0) REVERT: L 227 LYS cc_start: 0.8858 (tppt) cc_final: 0.8352 (tppt) REVERT: L 258 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7853 (ttm110) REVERT: M 5 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8243 (t) REVERT: M 15 TYR cc_start: 0.7813 (t80) cc_final: 0.6853 (t80) REVERT: M 35 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: M 94 CYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7157 (m) REVERT: M 100 ASN cc_start: 0.7647 (m110) cc_final: 0.6957 (m-40) REVERT: M 174 ASP cc_start: 0.7634 (m-30) cc_final: 0.7274 (m-30) REVERT: M 181 LYS cc_start: 0.8401 (mtmm) cc_final: 0.7947 (mtmm) REVERT: M 183 GLU cc_start: 0.7375 (pm20) cc_final: 0.7033 (pm20) REVERT: M 186 ASN cc_start: 0.8604 (p0) cc_final: 0.8077 (p0) REVERT: M 216 ASN cc_start: 0.8113 (p0) cc_final: 0.7852 (p0) REVERT: M 246 GLU cc_start: 0.7658 (mm-30) cc_final: 0.6941 (tm-30) REVERT: M 292 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7542 (mm-30) REVERT: M 305 THR cc_start: 0.8580 (t) cc_final: 0.8236 (p) REVERT: M 321 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7726 (mtmm) REVERT: M 351 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7820 (mmmt) REVERT: M 381 GLU cc_start: 0.7669 (pm20) cc_final: 0.7386 (pm20) REVERT: M 411 GLN cc_start: 0.7834 (tp40) cc_final: 0.7198 (tp40) REVERT: N 40 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7226 (mp0) REVERT: N 47 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8361 (mtpp) REVERT: N 49 GLN cc_start: 0.8149 (tt0) cc_final: 0.7776 (tp-100) REVERT: N 53 GLN cc_start: 0.8295 (mp10) cc_final: 0.8062 (mp10) REVERT: N 96 THR cc_start: 0.8088 (p) cc_final: 0.7768 (p) REVERT: N 104 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8013 (mtmm) REVERT: N 140 LYS cc_start: 0.8747 (mmtp) cc_final: 0.8416 (mttp) REVERT: N 166 GLU cc_start: 0.7741 (pm20) cc_final: 0.7395 (pm20) REVERT: N 177 ASP cc_start: 0.7823 (p0) cc_final: 0.7286 (p0) REVERT: N 215 MET cc_start: 0.6046 (ppp) cc_final: 0.5636 (ppp) REVERT: N 234 LYS cc_start: 0.8485 (mmmm) cc_final: 0.8111 (mmmm) REVERT: N 250 ARG cc_start: 0.7078 (mmm-85) cc_final: 0.6717 (mmm-85) REVERT: N 272 GLU cc_start: 0.8042 (mp0) cc_final: 0.7595 (mp0) REVERT: N 356 GLN cc_start: 0.8343 (tt0) cc_final: 0.7651 (tm-30) REVERT: N 394 LYS cc_start: 0.8882 (mmtm) cc_final: 0.8270 (mmtm) REVERT: O 8 MET cc_start: 0.7568 (ttp) cc_final: 0.6945 (ttp) REVERT: P 142 LYS cc_start: 0.9052 (tmtt) cc_final: 0.8528 (tmtt) REVERT: P 166 TYR cc_start: 0.7799 (m-10) cc_final: 0.7344 (m-10) REVERT: P 196 HIS cc_start: 0.8967 (t-90) cc_final: 0.8679 (t70) REVERT: P 197 HIS cc_start: 0.7923 (OUTLIER) cc_final: 0.7588 (m90) REVERT: P 215 LYS cc_start: 0.8519 (pmtt) cc_final: 0.8147 (pmtt) REVERT: P 258 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7693 (ttm110) outliers start: 290 outliers final: 226 residues processed: 1589 average time/residue: 0.4332 time to fit residues: 1092.7320 Evaluate side-chains 1701 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 246 poor density : 1455 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 136 MET Chi-restraints excluded: chain A residue 160 GLN 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 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 260 GLN 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 354 LEU Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 GLU 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 139 GLU 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 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 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 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 204 GLN Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 LEU 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 E residue 417 LEU 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 96 THR 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 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 141 MET 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 35 GLU Chi-restraints excluded: chain I residue 53 THR 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 219 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 249 THR Chi-restraints excluded: chain I residue 260 GLN 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 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 426 LEU 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 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 130 HIS 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 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 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 197 HIS 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 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 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 231 VAL 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 348 THR Chi-restraints excluded: chain M residue 353 THR Chi-restraints excluded: chain M residue 358 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 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 104 LYS Chi-restraints excluded: chain N residue 115 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 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 158 LEU 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 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 255 MET 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 88 optimal weight: 9.9990 chunk 405 optimal weight: 20.0000 chunk 251 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 302 optimal weight: 20.0000 chunk 316 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- 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 332 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 340 GLN H 252 ASN I 77 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 187 GLN ** N 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 255 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.100417 restraints weight = 56592.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.103937 restraints weight = 23410.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106106 restraints weight = 12430.599| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 34178 Z= 0.207 Angle : 0.766 13.822 46677 Z= 0.381 Chirality : 0.049 0.277 5266 Planarity : 0.006 0.117 5972 Dihedral : 6.822 65.172 5274 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.43 % Favored : 93.34 % Rotamer: Outliers : 7.63 % Allowed : 32.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 4233 helix: 1.28 (0.23), residues: 494 sheet: -0.80 (0.14), residues: 1282 loop : -1.41 (0.13), residues: 2457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 170 HIS 0.011 0.001 HIS F 287 PHE 0.024 0.002 PHE M 95 TYR 0.036 0.002 TYR N 305 ARG 0.012 0.001 ARG N 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00450 ( 14) link_NAG-ASN : angle 2.70185 ( 42) link_BETA1-4 : bond 0.00736 ( 18) link_BETA1-4 : angle 3.30644 ( 54) hydrogen bonds : bond 0.03573 ( 1205) hydrogen bonds : angle 5.36732 ( 3159) SS BOND : bond 0.00464 ( 68) SS BOND : angle 1.90117 ( 136) covalent geometry : bond 0.00451 (34078) covalent geometry : angle 0.74785 (46445) *********************** 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 1745 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 275 poor density : 1470 time to evaluate : 3.941 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: symmetry clash REVERT: A 51 TYR cc_start: 0.7831 (p90) cc_final: 0.7237 (p90) REVERT: A 115 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.7870 (mtm110) REVERT: A 155 THR cc_start: 0.8596 (m) cc_final: 0.8360 (t) REVERT: A 170 TRP cc_start: 0.8994 (t60) cc_final: 0.8638 (t60) REVERT: A 186 ASN cc_start: 0.8361 (p0) cc_final: 0.7805 (p0) REVERT: A 230 HIS cc_start: 0.8395 (p-80) cc_final: 0.7995 (p-80) REVERT: A 246 GLU cc_start: 0.7529 (tp30) cc_final: 0.7192 (tt0) REVERT: A 257 PHE cc_start: 0.8711 (m-10) cc_final: 0.8433 (m-10) REVERT: A 287 PHE cc_start: 0.8636 (m-80) cc_final: 0.8387 (m-10) REVERT: A 292 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7700 (mp0) REVERT: A 317 THR cc_start: 0.8768 (t) cc_final: 0.8492 (p) REVERT: A 354 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8214 (mt) REVERT: B 9 TYR cc_start: 0.8141 (m-80) cc_final: 0.7750 (m-80) REVERT: B 40 GLU cc_start: 0.7536 (mp0) cc_final: 0.7262 (mp0) REVERT: B 49 GLN cc_start: 0.8408 (tt0) cc_final: 0.8145 (tt0) REVERT: B 69 TYR cc_start: 0.7836 (p90) cc_final: 0.7632 (p90) REVERT: B 85 VAL cc_start: 0.8897 (m) cc_final: 0.8593 (p) REVERT: B 97 MET cc_start: 0.7384 (tmm) cc_final: 0.7093 (tmm) REVERT: B 109 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7091 (mm-30) REVERT: B 129 TYR cc_start: 0.8195 (t80) cc_final: 0.7798 (t80) REVERT: B 156 TYR cc_start: 0.8596 (m-10) cc_final: 0.8246 (m-10) REVERT: B 254 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7563 (m) REVERT: B 280 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.7122 (mpp80) REVERT: B 320 VAL cc_start: 0.8677 (t) cc_final: 0.8362 (m) REVERT: B 327 TYR cc_start: 0.8690 (p90) cc_final: 0.8431 (p90) REVERT: B 331 ASN cc_start: 0.8550 (m-40) cc_final: 0.8245 (m-40) REVERT: B 357 TYR cc_start: 0.8523 (t80) cc_final: 0.8144 (t80) REVERT: B 362 TYR cc_start: 0.8456 (m-80) cc_final: 0.7964 (m-80) REVERT: D 116 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7131 (pt0) REVERT: D 141 MET cc_start: 0.7373 (mtp) cc_final: 0.7079 (mtp) REVERT: D 215 LYS cc_start: 0.8501 (mttt) cc_final: 0.7956 (mttt) REVERT: D 265 GLU cc_start: 0.7636 (pp20) cc_final: 0.7240 (pp20) REVERT: E 38 LEU cc_start: 0.8495 (tp) cc_final: 0.8284 (tt) REVERT: E 49 CYS cc_start: 0.6420 (p) cc_final: 0.6044 (p) REVERT: E 100 ASN cc_start: 0.7793 (m-40) cc_final: 0.7565 (m-40) REVERT: E 140 VAL cc_start: 0.8186 (t) cc_final: 0.7812 (p) REVERT: E 186 ASN cc_start: 0.8156 (m-40) cc_final: 0.7710 (m-40) REVERT: E 199 ARG cc_start: 0.7830 (mmt180) cc_final: 0.7339 (mmt180) REVERT: E 202 ASP cc_start: 0.7191 (m-30) cc_final: 0.6917 (m-30) REVERT: E 216 ASN cc_start: 0.8241 (p0) cc_final: 0.7894 (p0) REVERT: E 246 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: E 324 LYS cc_start: 0.8600 (pttm) cc_final: 0.8275 (pttm) REVERT: E 364 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7951 (p) REVERT: E 407 LEU cc_start: 0.8653 (tp) cc_final: 0.8122 (tp) REVERT: F 10 LYS cc_start: 0.8700 (mtmp) cc_final: 0.8356 (mtmp) REVERT: F 13 ARG cc_start: 0.8505 (ptm160) cc_final: 0.8171 (ptm-80) REVERT: F 40 GLU cc_start: 0.7113 (mp0) cc_final: 0.6890 (mp0) REVERT: F 64 TYR cc_start: 0.8101 (p90) cc_final: 0.7783 (p90) REVERT: F 97 MET cc_start: 0.7834 (tpp) cc_final: 0.7207 (tpp) REVERT: F 111 LEU cc_start: 0.8383 (tp) cc_final: 0.8169 (tt) REVERT: F 112 GLN cc_start: 0.8584 (tt0) cc_final: 0.8337 (tt0) REVERT: F 166 GLU cc_start: 0.7983 (pm20) cc_final: 0.7692 (pm20) REVERT: F 195 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7701 (tptp) REVERT: F 215 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7579 (pmm) REVERT: F 272 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7450 (mm-30) REVERT: F 274 THR cc_start: 0.8628 (m) cc_final: 0.8309 (t) REVERT: F 286 LEU cc_start: 0.8567 (mp) cc_final: 0.8337 (mt) REVERT: F 326 GLU cc_start: 0.7543 (tt0) cc_final: 0.7306 (tt0) REVERT: F 346 LYS cc_start: 0.8406 (mptt) cc_final: 0.8022 (mptt) REVERT: F 399 TYR cc_start: 0.8225 (m-10) cc_final: 0.8016 (m-10) REVERT: H 170 CYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7439 (p) REVERT: H 258 ARG cc_start: 0.8759 (ttm170) cc_final: 0.8326 (ttm170) REVERT: I 2 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7302 (mm-30) REVERT: I 61 LYS cc_start: 0.8423 (tttt) cc_final: 0.8004 (tttt) REVERT: I 146 VAL cc_start: 0.8631 (t) cc_final: 0.8329 (m) REVERT: I 298 ASP cc_start: 0.7388 (t0) cc_final: 0.7114 (t0) REVERT: I 356 PHE cc_start: 0.8527 (p90) cc_final: 0.8269 (p90) REVERT: I 371 SER cc_start: 0.8787 (t) cc_final: 0.8517 (p) REVERT: I 381 GLU cc_start: 0.7289 (pm20) cc_final: 0.6887 (pm20) REVERT: I 390 TYR cc_start: 0.8747 (p90) cc_final: 0.8538 (p90) REVERT: J 10 LYS cc_start: 0.8811 (tttm) cc_final: 0.8420 (tttm) REVERT: J 61 ASN cc_start: 0.7945 (t0) cc_final: 0.7590 (t0) REVERT: J 68 ARG cc_start: 0.8407 (ttp-170) cc_final: 0.7915 (ttp80) REVERT: J 129 TYR cc_start: 0.7751 (t80) cc_final: 0.7211 (t80) REVERT: J 169 MET cc_start: 0.7350 (mmt) cc_final: 0.6995 (mmt) REVERT: J 235 TRP cc_start: 0.7789 (OUTLIER) cc_final: 0.7458 (m-10) REVERT: J 320 VAL cc_start: 0.8747 (OUTLIER) cc_final: 0.8434 (t) REVERT: J 331 ASN cc_start: 0.8811 (m110) cc_final: 0.8488 (m110) REVERT: J 362 TYR cc_start: 0.8110 (m-80) cc_final: 0.7751 (m-80) REVERT: L 188 LYS cc_start: 0.9187 (ptpp) cc_final: 0.8630 (ptpp) REVERT: L 215 LYS cc_start: 0.8118 (mmtt) cc_final: 0.7774 (mmtt) REVERT: L 218 ASP cc_start: 0.8334 (p0) cc_final: 0.8052 (p0) REVERT: L 227 LYS cc_start: 0.8855 (tppt) cc_final: 0.8337 (tppt) REVERT: L 258 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7833 (ttm110) REVERT: M 15 TYR cc_start: 0.7868 (t80) cc_final: 0.7438 (t80) REVERT: M 16 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8339 (mmtt) REVERT: M 35 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: M 59 TYR cc_start: 0.8654 (t80) cc_final: 0.8389 (t80) REVERT: M 94 CYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7190 (m) REVERT: M 100 ASN cc_start: 0.7589 (m110) cc_final: 0.6989 (m-40) REVERT: M 174 ASP cc_start: 0.7646 (m-30) cc_final: 0.7276 (m-30) REVERT: M 181 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8023 (mtmm) REVERT: M 183 GLU cc_start: 0.7394 (pm20) cc_final: 0.7007 (pm20) REVERT: M 186 ASN cc_start: 0.8595 (p0) cc_final: 0.8052 (p0) REVERT: M 216 ASN cc_start: 0.8160 (p0) cc_final: 0.7914 (p0) REVERT: M 246 GLU cc_start: 0.7670 (mm-30) cc_final: 0.6953 (tm-30) REVERT: M 292 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7537 (mm-30) REVERT: M 305 THR cc_start: 0.8656 (t) cc_final: 0.8304 (p) REVERT: M 321 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7764 (mtmm) REVERT: M 351 LYS cc_start: 0.8279 (mmmt) cc_final: 0.7840 (mmmt) REVERT: M 381 GLU cc_start: 0.7667 (pm20) cc_final: 0.7378 (pm20) REVERT: M 411 GLN cc_start: 0.7838 (tp40) cc_final: 0.7218 (tp40) REVERT: N 40 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7203 (mp0) REVERT: N 47 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8384 (mtpp) REVERT: N 49 GLN cc_start: 0.8155 (tt0) cc_final: 0.7783 (tp-100) REVERT: N 96 THR cc_start: 0.8139 (p) cc_final: 0.7823 (p) REVERT: N 104 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8016 (mtmm) REVERT: N 140 LYS cc_start: 0.8756 (mmtp) cc_final: 0.8421 (mttp) REVERT: N 166 GLU cc_start: 0.7665 (pm20) cc_final: 0.7313 (pm20) REVERT: N 177 ASP cc_start: 0.7806 (p0) cc_final: 0.7279 (p0) REVERT: N 215 MET cc_start: 0.6046 (ppp) cc_final: 0.5635 (ppp) REVERT: N 234 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8111 (mmmm) REVERT: N 250 ARG cc_start: 0.7096 (mmm-85) cc_final: 0.6740 (mmm-85) REVERT: N 272 GLU cc_start: 0.8002 (mp0) cc_final: 0.7566 (mp0) REVERT: N 356 GLN cc_start: 0.8346 (tt0) cc_final: 0.7665 (tm-30) REVERT: N 394 LYS cc_start: 0.8889 (mmtm) cc_final: 0.8270 (mmtm) REVERT: O 8 MET cc_start: 0.7562 (ttp) cc_final: 0.6955 (ttp) REVERT: P 142 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8541 (tmtt) REVERT: P 166 TYR cc_start: 0.7800 (m-10) cc_final: 0.7277 (m-10) REVERT: P 196 HIS cc_start: 0.8972 (t-90) cc_final: 0.8693 (t70) REVERT: P 197 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7605 (m90) REVERT: P 215 LYS cc_start: 0.8537 (pmtt) cc_final: 0.8169 (pmtt) REVERT: P 255 MET cc_start: 0.5820 (OUTLIER) cc_final: 0.5346 (mpp) REVERT: P 258 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.7723 (ttm110) outliers start: 275 outliers final: 227 residues processed: 1587 average time/residue: 0.4420 time to fit residues: 1113.2130 Evaluate side-chains 1710 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 1463 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 136 MET Chi-restraints excluded: chain A residue 160 GLN 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 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 260 GLN 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 351 LYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 381 GLU 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 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 373 MET 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 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 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 221 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 244 LEU 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 340 GLN 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 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 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 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 141 MET 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 35 GLU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 87 PHE 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 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 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 260 GLN Chi-restraints excluded: chain I residue 290 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 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 293 LEU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 315 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 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 146 VAL Chi-restraints excluded: chain L residue 170 CYS Chi-restraints excluded: chain L residue 190 GLU 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 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 178 VAL Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 203 ILE 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 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 358 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 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 104 LYS Chi-restraints excluded: chain N residue 115 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 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 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 255 MET 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 350 optimal weight: 8.9990 chunk 402 optimal weight: 0.0010 chunk 38 optimal weight: 0.1980 chunk 368 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 412 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 332 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 340 GLN H 197 HIS I 32 GLN 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 187 GLN ** M 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 255 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101578 restraints weight = 56721.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105055 restraints weight = 23473.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107253 restraints weight = 12508.622| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34178 Z= 0.148 Angle : 0.754 14.002 46677 Z= 0.374 Chirality : 0.048 0.281 5266 Planarity : 0.006 0.117 5972 Dihedral : 6.698 65.036 5273 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.76 % Favored : 94.02 % Rotamer: Outliers : 6.91 % Allowed : 33.19 % Favored : 59.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.13), residues: 4233 helix: 1.33 (0.23), residues: 494 sheet: -0.85 (0.14), residues: 1278 loop : -1.32 (0.13), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP I 170 HIS 0.009 0.001 HIS F 287 PHE 0.021 0.001 PHE E 312 TYR 0.035 0.002 TYR A 81 ARG 0.011 0.001 ARG H 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00465 ( 14) link_NAG-ASN : angle 2.53254 ( 42) link_BETA1-4 : bond 0.00783 ( 18) link_BETA1-4 : angle 3.14260 ( 54) hydrogen bonds : bond 0.03376 ( 1205) hydrogen bonds : angle 5.27224 ( 3159) SS BOND : bond 0.00381 ( 68) SS BOND : angle 1.79423 ( 136) covalent geometry : bond 0.00340 (34078) covalent geometry : angle 0.73758 (46445) *********************** 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 1716 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 1467 time to evaluate : 3.805 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: 0.7772 (p90) cc_final: 0.7203 (p90) REVERT: A 78 CYS cc_start: 0.5220 (OUTLIER) cc_final: 0.5007 (p) REVERT: A 139 ASN cc_start: 0.8498 (p0) cc_final: 0.8176 (p0) REVERT: A 155 THR cc_start: 0.8567 (m) cc_final: 0.8326 (t) REVERT: A 170 TRP cc_start: 0.8942 (t60) cc_final: 0.8618 (t60) REVERT: A 186 ASN cc_start: 0.8254 (p0) cc_final: 0.7874 (p0) REVERT: A 228 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.6436 (ppp) REVERT: A 230 HIS cc_start: 0.8410 (p-80) cc_final: 0.7500 (p90) REVERT: A 246 GLU cc_start: 0.7473 (tp30) cc_final: 0.7178 (tt0) REVERT: A 257 PHE cc_start: 0.8699 (m-10) cc_final: 0.8426 (m-10) REVERT: A 287 PHE cc_start: 0.8603 (m-80) cc_final: 0.8344 (m-10) REVERT: A 317 THR cc_start: 0.8769 (t) cc_final: 0.8488 (p) REVERT: A 354 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8194 (mt) REVERT: B 9 TYR cc_start: 0.8102 (m-80) cc_final: 0.7760 (m-80) REVERT: B 40 GLU cc_start: 0.7518 (mp0) cc_final: 0.7220 (mp0) REVERT: B 49 GLN cc_start: 0.8373 (tt0) cc_final: 0.8168 (tt0) REVERT: B 60 ASP cc_start: 0.8692 (m-30) cc_final: 0.7014 (m-30) REVERT: B 85 VAL cc_start: 0.8911 (m) cc_final: 0.8581 (p) REVERT: B 97 MET cc_start: 0.7266 (tmm) cc_final: 0.7061 (tmm) REVERT: B 109 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 129 TYR cc_start: 0.8161 (t80) cc_final: 0.7780 (t80) REVERT: B 156 TYR cc_start: 0.8583 (m-10) cc_final: 0.8225 (m-10) REVERT: B 254 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7519 (m) REVERT: B 280 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7071 (mpp80) REVERT: B 320 VAL cc_start: 0.8668 (t) cc_final: 0.8319 (m) REVERT: B 331 ASN cc_start: 0.8444 (m-40) cc_final: 0.8181 (m-40) REVERT: B 357 TYR cc_start: 0.8508 (t80) cc_final: 0.8138 (t80) REVERT: B 362 TYR cc_start: 0.8378 (m-80) cc_final: 0.7900 (m-80) REVERT: D 116 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7013 (pt0) REVERT: D 141 MET cc_start: 0.7338 (mtp) cc_final: 0.7061 (mtp) REVERT: D 265 GLU cc_start: 0.7623 (pp20) cc_final: 0.7234 (pp20) REVERT: E 100 ASN cc_start: 0.7768 (m-40) cc_final: 0.7544 (m-40) REVERT: E 116 HIS cc_start: 0.8626 (m-70) cc_final: 0.8277 (m-70) REVERT: E 140 VAL cc_start: 0.8165 (t) cc_final: 0.7795 (p) REVERT: E 152 HIS cc_start: 0.8691 (t70) cc_final: 0.8416 (t-90) REVERT: E 186 ASN cc_start: 0.8136 (m-40) cc_final: 0.7700 (m-40) REVERT: E 199 ARG cc_start: 0.7784 (mmt180) cc_final: 0.7299 (mmt180) REVERT: E 202 ASP cc_start: 0.7179 (m-30) cc_final: 0.6908 (m-30) REVERT: E 216 ASN cc_start: 0.8092 (p0) cc_final: 0.7775 (p0) REVERT: E 246 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6753 (tm-30) REVERT: E 262 LYS cc_start: 0.8294 (mttm) cc_final: 0.8070 (mmtp) REVERT: E 324 LYS cc_start: 0.8545 (pttm) cc_final: 0.8201 (pttm) REVERT: E 364 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7992 (p) REVERT: E 394 HIS cc_start: 0.8578 (p90) cc_final: 0.8061 (p90) REVERT: E 407 LEU cc_start: 0.8662 (tp) cc_final: 0.8202 (tp) REVERT: F 10 LYS cc_start: 0.8697 (mtmp) cc_final: 0.8103 (mtmp) REVERT: F 40 GLU cc_start: 0.7072 (mp0) cc_final: 0.6790 (mp0) REVERT: F 64 TYR cc_start: 0.8073 (p90) cc_final: 0.7773 (p90) REVERT: F 97 MET cc_start: 0.7795 (tpp) cc_final: 0.7156 (tpp) REVERT: F 112 GLN cc_start: 0.8562 (tt0) cc_final: 0.8266 (tt0) REVERT: F 166 GLU cc_start: 0.7985 (pm20) cc_final: 0.7630 (pm20) REVERT: F 215 MET cc_start: 0.8033 (pmm) cc_final: 0.7544 (pmm) REVERT: F 234 LYS cc_start: 0.8528 (mmmt) cc_final: 0.7813 (mmmm) REVERT: F 253 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8221 (mtpp) REVERT: F 272 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7443 (mm-30) REVERT: F 274 THR cc_start: 0.8574 (m) cc_final: 0.8053 (p) REVERT: F 326 GLU cc_start: 0.7542 (tt0) cc_final: 0.7299 (tt0) REVERT: F 346 LYS cc_start: 0.8413 (mptt) cc_final: 0.8012 (mptt) REVERT: F 399 TYR cc_start: 0.8157 (m-10) cc_final: 0.7937 (m-10) REVERT: H 170 CYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7230 (p) REVERT: H 258 ARG cc_start: 0.8771 (ttm170) cc_final: 0.8336 (ttm170) REVERT: I 2 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7310 (mm-30) REVERT: I 61 LYS cc_start: 0.8422 (tttt) cc_final: 0.7998 (tttt) REVERT: I 146 VAL cc_start: 0.8644 (t) cc_final: 0.8361 (m) REVERT: I 209 GLU cc_start: 0.8022 (pt0) cc_final: 0.7820 (pt0) REVERT: I 237 PRO cc_start: 0.8737 (Cg_exo) cc_final: 0.8449 (Cg_endo) REVERT: I 298 ASP cc_start: 0.7373 (t0) cc_final: 0.7082 (t0) REVERT: I 371 SER cc_start: 0.8768 (t) cc_final: 0.8539 (p) REVERT: I 381 GLU cc_start: 0.7279 (pm20) cc_final: 0.6872 (pm20) REVERT: I 390 TYR cc_start: 0.8739 (p90) cc_final: 0.8527 (p90) REVERT: J 10 LYS cc_start: 0.8819 (tttm) cc_final: 0.8423 (tttm) REVERT: J 40 GLU cc_start: 0.7355 (mp0) cc_final: 0.7074 (mp0) REVERT: J 43 ASP cc_start: 0.8028 (t0) cc_final: 0.7674 (t0) REVERT: J 61 ASN cc_start: 0.7927 (t0) cc_final: 0.7592 (t0) REVERT: J 68 ARG cc_start: 0.8365 (ttp-170) cc_final: 0.7836 (ttp80) REVERT: J 111 LEU cc_start: 0.8295 (tp) cc_final: 0.8070 (tt) REVERT: J 129 TYR cc_start: 0.7723 (t80) cc_final: 0.7163 (t80) REVERT: J 140 LYS cc_start: 0.8948 (mptt) cc_final: 0.8700 (mttp) REVERT: J 169 MET cc_start: 0.7316 (mmt) cc_final: 0.6966 (mmt) REVERT: J 235 TRP cc_start: 0.7769 (OUTLIER) cc_final: 0.7441 (m-10) REVERT: J 251 LYS cc_start: 0.7883 (mtpp) cc_final: 0.7679 (mtpp) REVERT: J 258 PHE cc_start: 0.8382 (m-80) cc_final: 0.8071 (m-80) REVERT: J 320 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8455 (t) REVERT: J 331 ASN cc_start: 0.8795 (m110) cc_final: 0.8522 (m110) REVERT: J 362 TYR cc_start: 0.8050 (m-80) cc_final: 0.7622 (m-80) REVERT: L 188 LYS cc_start: 0.9210 (ptpp) cc_final: 0.8611 (ptpp) REVERT: L 215 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7660 (mmtt) REVERT: L 227 LYS cc_start: 0.8809 (tppt) cc_final: 0.8279 (tppt) REVERT: L 258 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7812 (ttm110) REVERT: M 5 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8293 (t) REVERT: M 15 TYR cc_start: 0.7842 (t80) cc_final: 0.7042 (t80) REVERT: M 16 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8345 (mmtt) REVERT: M 35 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7452 (pm20) REVERT: M 59 TYR cc_start: 0.8616 (t80) cc_final: 0.8363 (t80) REVERT: M 94 CYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6644 (m) REVERT: M 140 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8045 (t) REVERT: M 143 THR cc_start: 0.8504 (p) cc_final: 0.8287 (p) REVERT: M 174 ASP cc_start: 0.7650 (m-30) cc_final: 0.7287 (m-30) REVERT: M 181 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8017 (mtmm) REVERT: M 183 GLU cc_start: 0.7384 (pm20) cc_final: 0.7025 (pm20) REVERT: M 186 ASN cc_start: 0.8572 (p0) cc_final: 0.8046 (p0) REVERT: M 246 GLU cc_start: 0.7653 (mm-30) cc_final: 0.6968 (tm-30) REVERT: M 292 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7502 (mm-30) REVERT: M 305 THR cc_start: 0.8619 (t) cc_final: 0.8256 (p) REVERT: M 321 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7726 (mtmm) REVERT: M 351 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7811 (mmmt) REVERT: M 381 GLU cc_start: 0.7648 (pm20) cc_final: 0.7358 (pm20) REVERT: M 411 GLN cc_start: 0.7814 (tp40) cc_final: 0.7189 (tp40) REVERT: N 40 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7188 (mp0) REVERT: N 47 LYS cc_start: 0.8653 (mtpp) cc_final: 0.8360 (mtpp) REVERT: N 49 GLN cc_start: 0.8060 (tt0) cc_final: 0.7829 (tp-100) REVERT: N 84 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8283 (mtmt) REVERT: N 96 THR cc_start: 0.8109 (p) cc_final: 0.7779 (p) REVERT: N 104 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8284 (mtmm) REVERT: N 140 LYS cc_start: 0.8751 (mmtp) cc_final: 0.8403 (mttp) REVERT: N 166 GLU cc_start: 0.7611 (pm20) cc_final: 0.7254 (pm20) REVERT: N 177 ASP cc_start: 0.7770 (p0) cc_final: 0.6978 (p0) REVERT: N 215 MET cc_start: 0.6025 (ppp) cc_final: 0.5632 (ppp) REVERT: N 234 LYS cc_start: 0.8463 (mmmm) cc_final: 0.8074 (mmmm) REVERT: N 250 ARG cc_start: 0.7103 (mmm-85) cc_final: 0.6702 (mmm-85) REVERT: N 261 ASP cc_start: 0.7527 (p0) cc_final: 0.7080 (p0) REVERT: N 272 GLU cc_start: 0.7982 (mp0) cc_final: 0.7556 (mp0) REVERT: N 356 GLN cc_start: 0.8337 (tt0) cc_final: 0.7644 (tm-30) REVERT: N 394 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8249 (mmtm) REVERT: O 8 MET cc_start: 0.7567 (ttp) cc_final: 0.6967 (ttp) REVERT: P 142 LYS cc_start: 0.9050 (tmtt) cc_final: 0.8523 (tmtt) REVERT: P 166 TYR cc_start: 0.7732 (m-10) cc_final: 0.7021 (m-10) REVERT: P 196 HIS cc_start: 0.8943 (t-90) cc_final: 0.8649 (t70) REVERT: P 197 HIS cc_start: 0.7883 (OUTLIER) cc_final: 0.7553 (m90) REVERT: P 215 LYS cc_start: 0.8498 (pmtt) cc_final: 0.8142 (pmtt) REVERT: P 255 MET cc_start: 0.5685 (OUTLIER) cc_final: 0.5217 (mpp) REVERT: P 258 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7581 (ttm110) outliers start: 249 outliers final: 198 residues processed: 1580 average time/residue: 0.4645 time to fit residues: 1182.3990 Evaluate side-chains 1666 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 219 poor density : 1447 time to evaluate : 3.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 136 MET Chi-restraints excluded: chain A residue 160 GLN 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 178 VAL Chi-restraints excluded: chain A residue 183 GLU 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 260 GLN Chi-restraints excluded: chain A residue 266 VAL 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 354 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 GLU 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 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 280 ARG 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 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 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 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 166 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 244 LEU 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 338 THR 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 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 101 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 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 H residue 136 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 141 MET 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 35 GLU Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 87 PHE Chi-restraints excluded: chain I residue 135 VAL 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 228 MET Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 244 LEU Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 290 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 387 ILE Chi-restraints excluded: chain I residue 388 VAL 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 101 ILE 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 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 315 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 380 SER 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 170 CYS Chi-restraints excluded: chain L residue 190 GLU 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 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 140 VAL Chi-restraints excluded: chain M residue 144 VAL Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 178 VAL Chi-restraints excluded: chain M residue 181 LYS Chi-restraints excluded: chain M residue 203 ILE Chi-restraints excluded: chain M residue 207 THR Chi-restraints excluded: chain M residue 263 THR 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 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 M residue 436 LEU 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 88 SER Chi-restraints excluded: chain N residue 101 ILE Chi-restraints excluded: chain N residue 104 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 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 197 HIS Chi-restraints excluded: chain P residue 200 VAL 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 255 MET 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 375 optimal weight: 30.0000 chunk 408 optimal weight: 2.9990 chunk 414 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 204 optimal weight: 4.9990 chunk 213 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 340 GLN I 32 GLN I 77 GLN ** I 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 187 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100025 restraints weight = 56515.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.103539 restraints weight = 23365.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.105674 restraints weight = 12408.123| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 34178 Z= 0.237 Angle : 0.800 13.455 46677 Z= 0.399 Chirality : 0.050 0.311 5266 Planarity : 0.006 0.117 5972 Dihedral : 6.767 65.609 5273 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.45 % Favored : 93.34 % Rotamer: Outliers : 6.41 % Allowed : 34.18 % Favored : 59.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.35 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 4233 helix: 1.29 (0.23), residues: 494 sheet: -0.87 (0.14), residues: 1257 loop : -1.43 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 170 HIS 0.011 0.001 HIS F 287 PHE 0.027 0.002 PHE A 95 TYR 0.034 0.002 TYR N 305 ARG 0.013 0.001 ARG N 271 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 14) link_NAG-ASN : angle 2.90913 ( 42) link_BETA1-4 : bond 0.00733 ( 18) link_BETA1-4 : angle 3.16226 ( 54) hydrogen bonds : bond 0.03660 ( 1205) hydrogen bonds : angle 5.35591 ( 3159) SS BOND : bond 0.00488 ( 68) SS BOND : angle 1.98054 ( 136) covalent geometry : bond 0.00512 (34078) covalent geometry : angle 0.78270 (46445) ********************** 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 1707 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 1476 time to evaluate : 3.713 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: 0.7727 (p90) cc_final: 0.7110 (p90) REVERT: A 78 CYS cc_start: 0.5214 (OUTLIER) cc_final: 0.4994 (p) REVERT: A 139 ASN cc_start: 0.8501 (p0) cc_final: 0.8192 (p0) REVERT: A 155 THR cc_start: 0.8598 (m) cc_final: 0.8375 (t) REVERT: A 170 TRP cc_start: 0.8998 (t60) cc_final: 0.8650 (t60) REVERT: A 186 ASN cc_start: 0.8348 (p0) cc_final: 0.7811 (p0) REVERT: A 230 HIS cc_start: 0.8452 (p-80) cc_final: 0.8170 (p-80) REVERT: A 246 GLU cc_start: 0.7577 (tp30) cc_final: 0.7236 (tt0) REVERT: A 257 PHE cc_start: 0.8745 (m-10) cc_final: 0.8501 (m-10) REVERT: A 287 PHE cc_start: 0.8642 (m-80) cc_final: 0.8415 (m-10) REVERT: A 317 THR cc_start: 0.8768 (t) cc_final: 0.8497 (p) REVERT: A 354 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8215 (mt) REVERT: A 401 ASP cc_start: 0.7399 (t0) cc_final: 0.7155 (t0) REVERT: B 9 TYR cc_start: 0.8182 (m-80) cc_final: 0.7828 (m-80) REVERT: B 40 GLU cc_start: 0.7543 (mp0) cc_final: 0.7256 (mp0) REVERT: B 49 GLN cc_start: 0.8406 (tt0) cc_final: 0.8139 (tt0) REVERT: B 85 VAL cc_start: 0.8906 (m) cc_final: 0.8573 (p) REVERT: B 97 MET cc_start: 0.7337 (tmm) cc_final: 0.7126 (tmm) REVERT: B 109 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7109 (mm-30) REVERT: B 129 TYR cc_start: 0.8200 (t80) cc_final: 0.7812 (t80) REVERT: B 156 TYR cc_start: 0.8620 (m-10) cc_final: 0.8284 (m-10) REVERT: B 227 VAL cc_start: 0.8895 (p) cc_final: 0.8669 (m) REVERT: B 254 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7554 (m) REVERT: B 280 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.7192 (mpp80) REVERT: B 320 VAL cc_start: 0.8680 (t) cc_final: 0.8360 (m) REVERT: B 331 ASN cc_start: 0.8548 (m-40) cc_final: 0.8215 (m-40) REVERT: B 357 TYR cc_start: 0.8530 (t80) cc_final: 0.8152 (t80) REVERT: B 362 TYR cc_start: 0.8447 (m-80) cc_final: 0.7930 (m-80) REVERT: B 402 THR cc_start: 0.8625 (t) cc_final: 0.8132 (p) REVERT: D 116 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7141 (pt0) REVERT: D 141 MET cc_start: 0.7406 (mtp) cc_final: 0.7116 (mtp) REVERT: D 162 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8315 (mtpp) REVERT: D 265 GLU cc_start: 0.7638 (pp20) cc_final: 0.7266 (pp20) REVERT: E 100 ASN cc_start: 0.7840 (m-40) cc_final: 0.7598 (m-40) REVERT: E 116 HIS cc_start: 0.8596 (m-70) cc_final: 0.8235 (m-70) REVERT: E 140 VAL cc_start: 0.8162 (t) cc_final: 0.7771 (p) REVERT: E 186 ASN cc_start: 0.8156 (m-40) cc_final: 0.7722 (m-40) REVERT: E 199 ARG cc_start: 0.7819 (mmt180) cc_final: 0.7235 (mmt180) REVERT: E 216 ASN cc_start: 0.8200 (p0) cc_final: 0.7913 (p0) REVERT: E 228 MET cc_start: 0.7400 (tpp) cc_final: 0.6945 (tpt) REVERT: E 246 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: E 262 LYS cc_start: 0.8297 (mttm) cc_final: 0.8091 (mmtp) REVERT: E 324 LYS cc_start: 0.8587 (pttm) cc_final: 0.8248 (pttm) REVERT: E 364 SER cc_start: 0.8232 (OUTLIER) cc_final: 0.7965 (p) REVERT: E 394 HIS cc_start: 0.8583 (p90) cc_final: 0.8074 (p90) REVERT: E 407 LEU cc_start: 0.8672 (tp) cc_final: 0.8196 (tp) REVERT: F 10 LYS cc_start: 0.8696 (mtmp) cc_final: 0.8352 (mtmp) REVERT: F 13 ARG cc_start: 0.8497 (ptm160) cc_final: 0.8180 (ptm-80) REVERT: F 40 GLU cc_start: 0.7150 (mp0) cc_final: 0.6907 (mp0) REVERT: F 64 TYR cc_start: 0.8104 (p90) cc_final: 0.7800 (p90) REVERT: F 97 MET cc_start: 0.7817 (tpp) cc_final: 0.7156 (tpp) REVERT: F 111 LEU cc_start: 0.8394 (tp) cc_final: 0.8183 (tt) REVERT: F 112 GLN cc_start: 0.8583 (tt0) cc_final: 0.8348 (tt0) REVERT: F 129 TYR cc_start: 0.7753 (t80) cc_final: 0.7475 (t80) REVERT: F 166 GLU cc_start: 0.7969 (pm20) cc_final: 0.7702 (pm20) REVERT: F 215 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7559 (pmm) REVERT: F 272 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7441 (mm-30) REVERT: F 274 THR cc_start: 0.8631 (m) cc_final: 0.8311 (t) REVERT: F 326 GLU cc_start: 0.7565 (tt0) cc_final: 0.7318 (tt0) REVERT: F 346 LYS cc_start: 0.8428 (mptt) cc_final: 0.8012 (mptt) REVERT: F 399 TYR cc_start: 0.8203 (m-10) cc_final: 0.7988 (m-10) REVERT: H 258 ARG cc_start: 0.8773 (ttm170) cc_final: 0.8324 (ttm170) REVERT: I 2 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7268 (mm-30) REVERT: I 61 LYS cc_start: 0.8442 (tttt) cc_final: 0.7994 (tttt) REVERT: I 67 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7306 (tm-30) REVERT: I 137 TYR cc_start: 0.8526 (p90) cc_final: 0.8315 (p90) REVERT: I 146 VAL cc_start: 0.8656 (t) cc_final: 0.8345 (m) REVERT: I 298 ASP cc_start: 0.7453 (t0) cc_final: 0.7145 (t0) REVERT: I 356 PHE cc_start: 0.8521 (p90) cc_final: 0.8258 (p90) REVERT: I 371 SER cc_start: 0.8861 (t) cc_final: 0.8560 (p) REVERT: I 381 GLU cc_start: 0.7294 (pm20) cc_final: 0.6894 (pm20) REVERT: J 10 LYS cc_start: 0.8860 (tttm) cc_final: 0.8473 (tttm) REVERT: J 40 GLU cc_start: 0.7353 (mp0) cc_final: 0.7057 (mp0) REVERT: J 43 ASP cc_start: 0.8058 (t0) cc_final: 0.7672 (t0) REVERT: J 61 ASN cc_start: 0.7969 (t0) cc_final: 0.7636 (t0) REVERT: J 68 ARG cc_start: 0.8334 (ttp-170) cc_final: 0.7863 (ttp80) REVERT: J 111 LEU cc_start: 0.8373 (tp) cc_final: 0.8126 (tt) REVERT: J 129 TYR cc_start: 0.7755 (t80) cc_final: 0.7142 (t80) REVERT: J 140 LYS cc_start: 0.8930 (mptt) cc_final: 0.8664 (mttp) REVERT: J 169 MET cc_start: 0.7287 (mmt) cc_final: 0.6982 (mmt) REVERT: J 235 TRP cc_start: 0.7743 (OUTLIER) cc_final: 0.7434 (m-10) REVERT: J 320 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8462 (t) REVERT: J 331 ASN cc_start: 0.8833 (m110) cc_final: 0.8588 (m110) REVERT: J 362 TYR cc_start: 0.8113 (m-80) cc_final: 0.7721 (m-80) REVERT: L 162 LYS cc_start: 0.8542 (mtpp) cc_final: 0.8277 (mtpp) REVERT: L 188 LYS cc_start: 0.9196 (ptpp) cc_final: 0.8656 (ptpp) REVERT: L 215 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7641 (mmtt) REVERT: L 227 LYS cc_start: 0.8856 (tppt) cc_final: 0.8330 (tppt) REVERT: L 258 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7807 (ttm110) REVERT: M 5 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8243 (t) REVERT: M 15 TYR cc_start: 0.7830 (t80) cc_final: 0.7054 (t80) REVERT: M 16 LYS cc_start: 0.8582 (mmtt) cc_final: 0.8374 (mmtt) REVERT: M 35 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: M 59 TYR cc_start: 0.8681 (t80) cc_final: 0.8423 (t80) REVERT: M 94 CYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7046 (m) REVERT: M 100 ASN cc_start: 0.7455 (m110) cc_final: 0.6905 (m-40) REVERT: M 140 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8134 (t) REVERT: M 174 ASP cc_start: 0.7652 (m-30) cc_final: 0.7260 (m-30) REVERT: M 183 GLU cc_start: 0.7417 (pm20) cc_final: 0.7000 (pm20) REVERT: M 186 ASN cc_start: 0.8582 (p0) cc_final: 0.8071 (p0) REVERT: M 246 GLU cc_start: 0.7685 (mm-30) cc_final: 0.6995 (tm-30) REVERT: M 292 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7549 (mm-30) REVERT: M 305 THR cc_start: 0.8696 (t) cc_final: 0.8370 (p) REVERT: M 321 LYS cc_start: 0.8255 (mtmm) cc_final: 0.7748 (mtmm) REVERT: M 333 HIS cc_start: 0.7893 (m90) cc_final: 0.7488 (m-70) REVERT: M 351 LYS cc_start: 0.8329 (mmmt) cc_final: 0.7890 (mmmt) REVERT: M 381 GLU cc_start: 0.7682 (pm20) cc_final: 0.7376 (pm20) REVERT: M 411 GLN cc_start: 0.7839 (tp40) cc_final: 0.7222 (tp40) REVERT: N 40 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7232 (mp0) REVERT: N 61 ASN cc_start: 0.8014 (m-40) cc_final: 0.7747 (m-40) REVERT: N 84 LYS cc_start: 0.8554 (mtmt) cc_final: 0.8281 (mtmt) REVERT: N 96 THR cc_start: 0.8194 (p) cc_final: 0.7879 (p) REVERT: N 104 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8301 (mtmm) REVERT: N 140 LYS cc_start: 0.8781 (mmtp) cc_final: 0.8441 (mttp) REVERT: N 166 GLU cc_start: 0.7631 (pm20) cc_final: 0.7261 (pm20) REVERT: N 177 ASP cc_start: 0.7790 (p0) cc_final: 0.7044 (p0) REVERT: N 215 MET cc_start: 0.6076 (ppp) cc_final: 0.5667 (ppp) REVERT: N 234 LYS cc_start: 0.8470 (mmmm) cc_final: 0.8104 (mmmm) REVERT: N 238 ASN cc_start: 0.8509 (t0) cc_final: 0.8288 (t0) REVERT: N 250 ARG cc_start: 0.7133 (mmm-85) cc_final: 0.6743 (mmm-85) REVERT: N 261 ASP cc_start: 0.7527 (p0) cc_final: 0.7098 (p0) REVERT: N 272 GLU cc_start: 0.7996 (mp0) cc_final: 0.7588 (mp0) REVERT: N 316 ARG cc_start: 0.8304 (mmt-90) cc_final: 0.7980 (mmt90) REVERT: N 394 LYS cc_start: 0.8908 (mmtm) cc_final: 0.8290 (mmtm) REVERT: O 8 MET cc_start: 0.7576 (ttp) cc_final: 0.6988 (ttp) REVERT: P 142 LYS cc_start: 0.9049 (tmtt) cc_final: 0.8513 (tmtt) REVERT: P 166 TYR cc_start: 0.7829 (m-10) cc_final: 0.7168 (m-10) REVERT: P 196 HIS cc_start: 0.8983 (t-90) cc_final: 0.8702 (t70) REVERT: P 197 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7578 (m90) REVERT: P 215 LYS cc_start: 0.8575 (pmtt) cc_final: 0.8232 (pmtt) REVERT: P 255 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.5280 (mpp) REVERT: P 258 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7807 (ttm110) outliers start: 231 outliers final: 197 residues processed: 1574 average time/residue: 0.4391 time to fit residues: 1097.5423 Evaluate side-chains 1678 residues out of total 3609 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1462 time to evaluate : 3.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU 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 136 MET 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 183 GLU 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 260 GLN Chi-restraints excluded: chain A residue 266 VAL 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 354 LEU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 GLU 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 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 280 ARG 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 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 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 219 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 244 LEU 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 340 GLN 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 409 TRP 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 101 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 215 MET 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 H residue 136 VAL Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 141 MET 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 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 53 THR Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 87 PHE Chi-restraints excluded: chain I residue 135 VAL 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 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 249 THR Chi-restraints excluded: chain I residue 290 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 387 ILE Chi-restraints excluded: chain I residue 388 VAL 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 88 SER Chi-restraints excluded: chain J residue 101 ILE 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 287 HIS Chi-restraints excluded: chain J residue 293 LEU Chi-restraints excluded: chain J residue 308 GLU Chi-restraints excluded: chain J residue 315 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 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 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 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 140 VAL Chi-restraints excluded: chain M residue 156 ILE 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 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 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 54 ILE 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 104 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 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 197 HIS Chi-restraints excluded: chain P residue 200 VAL 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 255 MET 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 388 optimal weight: 6.9990 chunk 339 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 313 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 GLN E 340 GLN ** H 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN I 77 GLN ** I 100 ASN ** 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 187 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.098614 restraints weight = 57718.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.102125 restraints weight = 23929.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104304 restraints weight = 12737.191| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 34178 Z= 0.271 Angle : 0.878 59.197 46677 Z= 0.454 Chirality : 0.050 0.286 5266 Planarity : 0.006 0.118 5972 Dihedral : 6.770 65.578 5273 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.45 % Favored : 93.34 % Rotamer: Outliers : 6.44 % Allowed : 34.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.13), residues: 4233 helix: 1.26 (0.23), residues: 494 sheet: -0.90 (0.14), residues: 1296 loop : -1.41 (0.13), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP I 170 HIS 0.013 0.001 HIS B 226 PHE 0.041 0.002 PHE A 95 TYR 0.031 0.002 TYR N 296 ARG 0.011 0.001 ARG H 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00421 ( 14) link_NAG-ASN : angle 2.84838 ( 42) link_BETA1-4 : bond 0.00742 ( 18) link_BETA1-4 : angle 3.18364 ( 54) hydrogen bonds : bond 0.03676 ( 1205) hydrogen bonds : angle 5.35118 ( 3159) SS BOND : bond 0.00525 ( 68) SS BOND : angle 2.09555 ( 136) covalent geometry : bond 0.00581 (34078) covalent geometry : angle 0.86185 (46445) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18418.01 seconds wall clock time: 319 minutes 31.75 seconds (19171.75 seconds total)