Starting phenix.real_space_refine on Tue Aug 26 06:20:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw0_39618/08_2025/8yw0_39618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw0_39618/08_2025/8yw0_39618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw0_39618/08_2025/8yw0_39618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw0_39618/08_2025/8yw0_39618.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw0_39618/08_2025/8yw0_39618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw0_39618/08_2025/8yw0_39618.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.072 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 3 9.91 5 S 286 5.16 5 C 21544 2.51 5 N 5884 2.21 5 O 6547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34264 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "B" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "C" 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: "D" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "F" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "G" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "H" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3330 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "I" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "J" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 386} Chain: "K" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3260 Classifications: {'peptide': 418} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "L" 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: "M" 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: "N" 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: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "P" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "Q" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1245 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "E" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 292 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "R" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 292 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "T" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 292 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} 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: "U" 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: "V" 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: "W" 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: "X" 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: "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: 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: "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: "d" 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: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 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} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.25, per 1000 atoms: 0.21 Number of scatterers: 34264 At special positions: 0 Unit cell: (217.3, 173.84, 218.36, 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 3 19.99 S 286 16.00 O 6547 8.00 N 5884 7.00 C 21544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=65, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.05 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 105 " 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.02 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.05 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.03 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.05 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 114 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 259 " - pdb=" SG CYS H 271 " distance=2.04 Simple disulfide: pdb=" SG CYS H 301 " - pdb=" SG CYS H 376 " distance=2.03 Simple disulfide: pdb=" SG CYS H 306 " - pdb=" SG CYS H 380 " distance=2.03 Simple disulfide: pdb=" SG CYS H 328 " - pdb=" SG CYS H 370 " distance=2.03 Simple disulfide: pdb=" SG CYS I 19 " - pdb=" SG CYS I 125 " distance=2.03 Simple disulfide: pdb=" SG CYS I 91 " - pdb=" SG CYS I 105 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 225 " distance=2.03 Simple disulfide: pdb=" SG CYS I 203 " - pdb=" SG CYS I 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 125 " distance=2.03 Simple disulfide: pdb=" SG CYS J 91 " - pdb=" SG CYS J 105 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 225 " distance=2.04 Simple disulfide: pdb=" SG CYS J 203 " - pdb=" SG CYS J 220 " distance=2.04 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 125 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 225 " distance=2.03 Simple disulfide: pdb=" SG CYS K 203 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS L 9 " - pdb=" SG CYS L 18 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 27 " distance=2.03 Simple disulfide: pdb=" SG CYS L 26 " - pdb=" SG CYS L 58 " distance=2.03 Simple disulfide: pdb=" SG CYS M 9 " - pdb=" SG CYS M 18 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 27 " distance=2.03 Simple disulfide: pdb=" SG CYS M 26 " - pdb=" SG CYS M 58 " distance=2.03 Simple disulfide: pdb=" SG CYS N 9 " - pdb=" SG CYS N 18 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 26 " - pdb=" SG CYS N 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 193 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 200 " - pdb=" SG CYS E 218 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 193 " - pdb=" SG CYS R 205 " distance=2.03 Simple disulfide: pdb=" SG CYS R 200 " - pdb=" SG CYS R 218 " distance=2.03 Simple disulfide: pdb=" SG CYS R 212 " - pdb=" SG CYS R 229 " distance=2.03 Simple disulfide: pdb=" SG CYS T 193 " - pdb=" SG CYS T 205 " distance=2.03 Simple disulfide: pdb=" SG CYS T 200 " - pdb=" SG CYS T 218 " distance=2.03 Simple disulfide: pdb=" SG CYS T 212 " - pdb=" SG CYS T 229 " 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 S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " 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 a 2 " - " BMA a 3 " " 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 d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG S 1 " - " ASN A 141 " " NAG U 1 " - " ASN B 262 " " NAG V 1 " - " ASN B 200 " " NAG W 1 " - " ASN F 141 " " NAG X 1 " - " ASN H 141 " " NAG Y 1 " - " ASN I 262 " " NAG Z 1 " - " ASN I 200 " " NAG a 1 " - " ASN J 262 " " NAG b 1 " - " ASN J 200 " " NAG c 1 " - " ASN K 262 " " NAG d 1 " - " ASN K 200 " Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8172 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 94 sheets defined 15.6% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 removed outlier: 3.552A pdb=" N TYR A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 4.221A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS A 259 " --> pdb=" O PRO A 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 255 through 259' Processing helix chain 'A' and resid 404 through 438 Processing helix chain 'B' and resid 7 through 12 removed outlier: 3.543A pdb=" N ALA B 11 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR B 12 " --> pdb=" O TYR B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 361 removed outlier: 3.569A pdb=" N VAL B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLN B 356 " --> pdb=" O HIS B 352 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 397 Processing helix chain 'B' and resid 398 through 402 removed outlier: 3.883A pdb=" N THR B 402 " --> pdb=" O TYR B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.588A pdb=" N ILE B 413 " --> pdb=" O TRP B 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 31 through 40 Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.526A pdb=" N LEU C 56 " --> pdb=" O LEU C 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 152 through 157 Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.679A pdb=" N MET D 177 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 246 removed outlier: 3.836A pdb=" N TYR F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 4.091A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N CYS F 259 " --> pdb=" O PRO F 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 255 through 259' Processing helix chain 'F' and resid 404 through 438 removed outlier: 3.583A pdb=" N ARG F 438 " --> pdb=" O ILE F 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 removed outlier: 3.600A pdb=" N TYR G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.205A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 255 through 259' Processing helix chain 'G' and resid 283 through 287 removed outlier: 3.658A pdb=" N ALA G 286 " --> pdb=" O PRO G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 438 Processing helix chain 'H' and resid 238 through 247 removed outlier: 3.599A pdb=" N TYR H 242 " --> pdb=" O SER H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.989A pdb=" N GLY H 258 " --> pdb=" O ALA H 255 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N CYS H 259 " --> pdb=" O PRO H 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 255 through 259' Processing helix chain 'H' and resid 404 through 438 Processing helix chain 'I' and resid 350 through 361 removed outlier: 3.724A pdb=" N VAL I 355 " --> pdb=" O PRO I 351 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN I 356 " --> pdb=" O HIS I 352 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU I 361 " --> pdb=" O TYR I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 397 Processing helix chain 'I' and resid 398 through 401 removed outlier: 3.980A pdb=" N LEU I 401 " --> pdb=" O PRO I 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 398 through 401' Processing helix chain 'I' and resid 407 through 414 Processing helix chain 'J' and resid 7 through 12 removed outlier: 3.799A pdb=" N ALA J 11 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR J 12 " --> pdb=" O TYR J 9 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 361 removed outlier: 3.779A pdb=" N VAL J 355 " --> pdb=" O PRO J 351 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN J 356 " --> pdb=" O HIS J 352 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU J 361 " --> pdb=" O TYR J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 397 Processing helix chain 'J' and resid 398 through 402 removed outlier: 3.870A pdb=" N THR J 402 " --> pdb=" O TYR J 399 " (cutoff:3.500A) Processing helix chain 'J' and resid 407 through 414 removed outlier: 3.715A pdb=" N ILE J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 11 removed outlier: 3.512A pdb=" N ALA K 11 " --> pdb=" O VAL K 8 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 361 removed outlier: 3.875A pdb=" N VAL K 355 " --> pdb=" O PRO K 351 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLN K 356 " --> pdb=" O HIS K 352 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU K 361 " --> pdb=" O TYR K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 397 Processing helix chain 'K' and resid 398 through 402 removed outlier: 3.567A pdb=" N LEU K 401 " --> pdb=" O PRO K 398 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR K 402 " --> pdb=" O TYR K 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 398 through 402' Processing helix chain 'K' and resid 407 through 414 Processing helix chain 'L' and resid 26 through 31 Processing helix chain 'L' and resid 31 through 41 removed outlier: 3.516A pdb=" N GLU L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP L 41 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 56 removed outlier: 3.680A pdb=" N LEU L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU L 56 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 31 Processing helix chain 'M' and resid 31 through 42 removed outlier: 3.668A pdb=" N ASN M 42 " --> pdb=" O MET M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 56 removed outlier: 3.540A pdb=" N LEU M 56 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 31 Processing helix chain 'N' and resid 31 through 41 removed outlier: 3.805A pdb=" N ASP N 41 " --> pdb=" O ARG N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 56 removed outlier: 3.561A pdb=" N LEU N 56 " --> pdb=" O LEU N 52 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 119 Processing helix chain 'O' and resid 152 through 157 removed outlier: 3.981A pdb=" N LYS O 157 " --> pdb=" O ALA O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 181 removed outlier: 4.626A pdb=" N SER O 179 " --> pdb=" O HIS O 176 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA O 181 " --> pdb=" O ARG O 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 119 Processing helix chain 'P' and resid 152 through 157 removed outlier: 4.067A pdb=" N LYS P 157 " --> pdb=" O ALA P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 181 removed outlier: 5.169A pdb=" N SER P 179 " --> pdb=" O HIS P 176 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA P 181 " --> pdb=" O ARG P 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 119 Processing helix chain 'Q' and resid 152 through 157 removed outlier: 3.541A pdb=" N LYS Q 157 " --> pdb=" O ALA Q 153 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 181 removed outlier: 4.904A pdb=" N SER Q 179 " --> pdb=" O HIS Q 176 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA Q 181 " --> pdb=" O ARG Q 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'R' and resid 209 through 211 No H-bonds generated for 'chain 'R' and resid 209 through 211' Processing helix chain 'R' and resid 225 through 230 Processing helix chain 'T' and resid 209 through 211 No H-bonds generated for 'chain 'T' and resid 209 through 211' Processing helix chain 'T' and resid 225 through 230 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.516A pdb=" N THR A 159 " --> pdb=" O ILE A 156 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.397A pdb=" N MET A 31 " --> pdb=" O MET A 136 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N MET A 136 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR A 126 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASN A 43 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU A 45 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 47 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER A 120 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 15 through 19 removed outlier: 5.397A pdb=" N MET A 31 " --> pdb=" O MET A 136 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N MET A 136 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL A 33 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG A 134 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR A 41 " --> pdb=" O THR A 126 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR A 126 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ASN A 43 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA A 124 " --> pdb=" O ASN A 43 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N GLU A 45 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR A 122 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 47 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N SER A 120 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.541A pdb=" N TYR A 59 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA7, first strand: chain 'A' and resid 220 through 221 Processing sheet with id=AA8, first strand: chain 'A' and resid 260 through 262 removed outlier: 3.522A pdb=" N GLN A 260 " --> pdb=" O MET A 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 296 through 306 removed outlier: 5.578A pdb=" N ASP A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS A 321 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AB2, first strand: chain 'A' and resid 387 through 388 Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.810A pdb=" N ALA B 17 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 75 through 79 removed outlier: 6.238A pdb=" N LYS B 66 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 55 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN B 53 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA B 70 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N SER B 51 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N ILE B 48 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 10.841A pdb=" N LYS B 104 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N PHE B 50 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 11.638A pdb=" N LEU B 102 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N ALA B 52 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N PHE B 100 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ILE B 56 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 13.036A pdb=" N THR B 96 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 84 through 86 removed outlier: 4.152A pdb=" N GLU B 109 " --> pdb=" O TYR B 129 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR B 129 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 149 through 156 Processing sheet with id=AB7, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.500A pdb=" N VAL B 227 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY B 209 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 182 through 183 removed outlier: 3.526A pdb=" N SER B 182 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 274 through 277 Processing sheet with id=AC1, first strand: chain 'D' and resid 149 through 150 removed outlier: 3.679A pdb=" N VAL D 149 " --> pdb=" O LYS D 124 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE D 121 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TYR D 132 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL D 123 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N TYR D 132 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 256 through 258 removed outlier: 3.718A pdb=" N THR D 244 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE D 207 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY D 191 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 223 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 256 through 258 removed outlier: 6.590A pdb=" N VAL D 249 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL D 234 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N TRP D 251 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA D 232 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 2 through 8 removed outlier: 3.507A pdb=" N THR F 159 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 15 through 19 removed outlier: 5.292A pdb=" N MET F 31 " --> pdb=" O MET F 136 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N MET F 136 " --> pdb=" O MET F 31 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL F 33 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG F 134 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR F 41 " --> pdb=" O THR F 126 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N THR F 126 " --> pdb=" O THR F 41 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 46 through 48 removed outlier: 3.928A pdb=" N TYR F 46 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AC8, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AC9, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AD1, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AD2, first strand: chain 'F' and resid 260 through 262 removed outlier: 3.503A pdb=" N GLN F 260 " --> pdb=" O MET F 269 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 296 through 306 removed outlier: 5.552A pdb=" N ASP F 298 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS F 321 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL F 315 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 326 through 328 Processing sheet with id=AD5, first strand: chain 'F' and resid 331 through 332 Processing sheet with id=AD6, first strand: chain 'F' and resid 387 through 388 removed outlier: 3.514A pdb=" N HIS I 306 " --> pdb=" O TYR I 296 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AD8, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.411A pdb=" N MET G 31 " --> pdb=" O MET G 136 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N MET G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE G 47 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N SER G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 140 through 147 removed outlier: 6.765A pdb=" N SER G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE G 47 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N MET G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N MET G 31 " --> pdb=" O MET G 136 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN G 260 " --> pdb=" O MET G 269 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.591A pdb=" N TYR G 59 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AE3, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AE4, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AE5, first strand: chain 'G' and resid 297 through 306 removed outlier: 5.591A pdb=" N ASP G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS G 321 " --> pdb=" O ASP G 298 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL G 315 " --> pdb=" O ALA G 304 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 326 through 329 Processing sheet with id=AE7, first strand: chain 'G' and resid 331 through 332 Processing sheet with id=AE8, first strand: chain 'G' and resid 387 through 388 removed outlier: 3.508A pdb=" N TYR J 296 " --> pdb=" O HIS J 306 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 2 through 8 Processing sheet with id=AF1, first strand: chain 'H' and resid 15 through 19 removed outlier: 5.277A pdb=" N MET H 31 " --> pdb=" O MET H 136 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N MET H 136 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL H 33 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG H 134 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU H 35 " --> pdb=" O LYS H 132 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR H 41 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR H 126 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASN H 43 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ALA H 124 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU H 45 " --> pdb=" O TYR H 122 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N TYR H 122 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE H 47 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER H 120 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 15 through 19 removed outlier: 5.277A pdb=" N MET H 31 " --> pdb=" O MET H 136 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N MET H 136 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL H 33 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARG H 134 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU H 35 " --> pdb=" O LYS H 132 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR H 41 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N THR H 126 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ASN H 43 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ALA H 124 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLU H 45 " --> pdb=" O TYR H 122 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N TYR H 122 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE H 47 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SER H 120 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.588A pdb=" N TYR H 59 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AF5, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AF6, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AF7, first strand: chain 'H' and resid 260 through 262 Processing sheet with id=AF8, first strand: chain 'H' and resid 296 through 306 removed outlier: 5.494A pdb=" N ASP H 298 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LYS H 321 " --> pdb=" O ASP H 298 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL H 315 " --> pdb=" O ALA H 304 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 326 through 328 removed outlier: 3.680A pdb=" N ALA H 344 " --> pdb=" O CYS H 328 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 331 through 332 Processing sheet with id=AG2, first strand: chain 'H' and resid 387 through 388 removed outlier: 3.515A pdb=" N HIS K 306 " --> pdb=" O TYR K 296 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 17 through 18 removed outlier: 3.537A pdb=" N ALA I 17 " --> pdb=" O SER I 30 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 46 through 54 removed outlier: 6.357A pdb=" N HIS I 99 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N ALA I 52 " --> pdb=" O MET I 97 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N MET I 97 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N ILE I 54 " --> pdb=" O GLY I 95 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N GLY I 95 " --> pdb=" O ILE I 54 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 66 through 70 Processing sheet with id=AG6, first strand: chain 'I' and resid 84 through 86 removed outlier: 4.236A pdb=" N GLU I 109 " --> pdb=" O TYR I 129 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 149 through 156 removed outlier: 3.595A pdb=" N VAL I 267 " --> pdb=" O LYS I 149 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 175 through 177 removed outlier: 3.747A pdb=" N VAL I 227 " --> pdb=" O ASP I 177 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY I 209 " --> pdb=" O TYR I 199 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AH1, first strand: chain 'I' and resid 274 through 277 Processing sheet with id=AH2, first strand: chain 'J' and resid 17 through 19 removed outlier: 3.515A pdb=" N ALA J 17 " --> pdb=" O SER J 30 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS J 19 " --> pdb=" O CYS J 28 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS J 28 " --> pdb=" O CYS J 19 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 75 through 79 removed outlier: 4.946A pdb=" N GLY J 55 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 10.745A pdb=" N THR J 65 " --> pdb=" O GLN J 53 " (cutoff:3.500A) removed outlier: 12.442A pdb=" N GLN J 53 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N ILE J 67 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 11.793A pdb=" N SER J 51 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 13.164A pdb=" N TYR J 69 " --> pdb=" O GLN J 49 " (cutoff:3.500A) removed outlier: 16.669A pdb=" N GLN J 49 " --> pdb=" O TYR J 69 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA J 103 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS J 99 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N ALA J 52 " --> pdb=" O MET J 97 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N MET J 97 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N ILE J 54 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 10.955A pdb=" N GLY J 95 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 15.472A pdb=" N ILE J 56 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 18.617A pdb=" N VAL J 93 " --> pdb=" O ILE J 56 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 84 through 86 removed outlier: 4.229A pdb=" N GLU J 109 " --> pdb=" O TYR J 129 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 149 through 152 Processing sheet with id=AH6, first strand: chain 'J' and resid 155 through 156 Processing sheet with id=AH7, first strand: chain 'J' and resid 167 through 169 Processing sheet with id=AH8, first strand: chain 'J' and resid 175 through 176 Processing sheet with id=AH9, first strand: chain 'J' and resid 181 through 183 Processing sheet with id=AI1, first strand: chain 'J' and resid 274 through 277 Processing sheet with id=AI2, first strand: chain 'K' and resid 17 through 18 Processing sheet with id=AI3, first strand: chain 'K' and resid 46 through 54 removed outlier: 11.310A pdb=" N PHE K 50 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 11.771A pdb=" N LEU K 102 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N ALA K 52 " --> pdb=" O PHE K 100 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE K 100 " --> pdb=" O ALA K 52 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 66 through 69 Processing sheet with id=AI5, first strand: chain 'K' and resid 84 through 86 removed outlier: 4.200A pdb=" N GLU K 109 " --> pdb=" O TYR K 129 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 148 through 152 removed outlier: 3.611A pdb=" N VAL K 267 " --> pdb=" O LYS K 149 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'K' and resid 155 through 156 Processing sheet with id=AI8, first strand: chain 'K' and resid 175 through 176 Processing sheet with id=AI9, first strand: chain 'K' and resid 197 through 199 removed outlier: 3.571A pdb=" N GLY K 209 " --> pdb=" O TYR K 199 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 274 through 277 Processing sheet with id=AJ2, first strand: chain 'O' and resid 149 through 150 removed outlier: 6.367A pdb=" N PHE O 121 " --> pdb=" O TYR O 132 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR O 132 " --> pdb=" O PHE O 121 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL O 123 " --> pdb=" O THR O 130 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 256 through 259 removed outlier: 4.672A pdb=" N PHE O 207 " --> pdb=" O LEU O 246 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY O 191 " --> pdb=" O TYR O 202 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE O 223 " --> pdb=" O VAL O 231 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'O' and resid 256 through 259 removed outlier: 6.345A pdb=" N VAL O 249 " --> pdb=" O VAL O 234 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL O 234 " --> pdb=" O VAL O 249 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N TRP O 251 " --> pdb=" O ALA O 232 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ALA O 232 " --> pdb=" O TRP O 251 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'P' and resid 149 through 150 removed outlier: 6.397A pdb=" N PHE P 121 " --> pdb=" O TYR P 132 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR P 132 " --> pdb=" O PHE P 121 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL P 123 " --> pdb=" O THR P 130 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'P' and resid 256 through 259 removed outlier: 5.000A pdb=" N PHE P 207 " --> pdb=" O LEU P 246 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY P 191 " --> pdb=" O TYR P 202 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA P 232 " --> pdb=" O ILE P 223 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'P' and resid 256 through 259 removed outlier: 6.118A pdb=" N VAL P 249 " --> pdb=" O VAL P 234 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL P 234 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N TRP P 251 " --> pdb=" O ALA P 232 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ALA P 232 " --> pdb=" O TRP P 251 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.593A pdb=" N VAL Q 149 " --> pdb=" O LYS Q 124 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE Q 121 " --> pdb=" O TYR Q 132 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR Q 132 " --> pdb=" O PHE Q 121 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL Q 123 " --> pdb=" O THR Q 130 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR Q 132 " --> pdb=" O PRO Q 143 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER Q 163 " --> pdb=" O LEU Q 168 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS Q 170 " --> pdb=" O LYS Q 161 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Q' and resid 256 through 259 removed outlier: 3.565A pdb=" N THR Q 257 " --> pdb=" O THR Q 250 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR Q 244 " --> pdb=" O ILE Q 209 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N PHE Q 207 " --> pdb=" O LEU Q 246 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY Q 191 " --> pdb=" O TYR Q 202 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE Q 223 " --> pdb=" O VAL Q 231 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Q' and resid 256 through 259 removed outlier: 3.565A pdb=" N THR Q 257 " --> pdb=" O THR Q 250 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL Q 249 " --> pdb=" O VAL Q 234 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL Q 234 " --> pdb=" O VAL Q 249 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N TRP Q 251 " --> pdb=" O ALA Q 232 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA Q 232 " --> pdb=" O TRP Q 251 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'E' and resid 197 through 199 Processing sheet with id=AK3, first strand: chain 'R' and resid 197 through 199 Processing sheet with id=AK4, first strand: chain 'T' and resid 197 through 199 1217 hydrogen bonds defined for protein. 3195 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.04 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11142 1.35 - 1.47: 8655 1.47 - 1.59: 14963 1.59 - 1.72: 2 1.72 - 1.84: 382 Bond restraints: 35144 Sorted by residual: bond pdb=" CB PRO B 363 " pdb=" CG PRO B 363 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.81e+00 bond pdb=" CB PRO J 363 " pdb=" CG PRO J 363 " ideal model delta sigma weight residual 1.492 1.606 -0.114 5.00e-02 4.00e+02 5.20e+00 bond pdb=" CB PRO A 22 " pdb=" CG PRO A 22 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.55e+00 bond pdb=" C1 BMA S 3 " pdb=" C2 BMA S 3 " ideal model delta sigma weight residual 1.519 1.553 -0.034 2.00e-02 2.50e+03 2.92e+00 bond pdb=" C1 BMA W 3 " pdb=" C2 BMA W 3 " ideal model delta sigma weight residual 1.519 1.552 -0.033 2.00e-02 2.50e+03 2.72e+00 ... (remaining 35139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 47040 2.13 - 4.27: 698 4.27 - 6.40: 104 6.40 - 8.54: 14 8.54 - 10.67: 4 Bond angle restraints: 47860 Sorted by residual: angle pdb=" CA PRO B 363 " pdb=" N PRO B 363 " pdb=" CD PRO B 363 " ideal model delta sigma weight residual 112.00 103.49 8.51 1.40e+00 5.10e-01 3.69e+01 angle pdb=" N ILE J 217 " pdb=" CA ILE J 217 " pdb=" C ILE J 217 " ideal model delta sigma weight residual 112.96 107.10 5.86 1.00e+00 1.00e+00 3.43e+01 angle pdb=" CA PRO Q 143 " pdb=" N PRO Q 143 " pdb=" CD PRO Q 143 " ideal model delta sigma weight residual 112.00 104.46 7.54 1.40e+00 5.10e-01 2.90e+01 angle pdb=" CA PRO J 363 " pdb=" N PRO J 363 " pdb=" CD PRO J 363 " ideal model delta sigma weight residual 112.00 104.66 7.34 1.40e+00 5.10e-01 2.75e+01 angle pdb=" CA PRO K 398 " pdb=" N PRO K 398 " pdb=" CD PRO K 398 " ideal model delta sigma weight residual 112.00 105.10 6.90 1.40e+00 5.10e-01 2.43e+01 ... (remaining 47855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.08: 20191 22.08 - 44.17: 1155 44.17 - 66.25: 110 66.25 - 88.33: 85 88.33 - 110.41: 46 Dihedral angle restraints: 21587 sinusoidal: 8850 harmonic: 12737 Sorted by residual: dihedral pdb=" CA GLU K 247 " pdb=" C GLU K 247 " pdb=" N PRO K 248 " pdb=" CA PRO K 248 " ideal model delta harmonic sigma weight residual 180.00 137.76 42.24 0 5.00e+00 4.00e-02 7.14e+01 dihedral pdb=" CB CYS I 203 " pdb=" SG CYS I 203 " pdb=" SG CYS I 220 " pdb=" CB CYS I 220 " ideal model delta sinusoidal sigma weight residual -86.00 -20.90 -65.10 1 1.00e+01 1.00e-02 5.56e+01 dihedral pdb=" CB CYS J 19 " pdb=" SG CYS J 19 " pdb=" SG CYS J 125 " pdb=" CB CYS J 125 " ideal model delta sinusoidal sigma weight residual 93.00 154.96 -61.96 1 1.00e+01 1.00e-02 5.09e+01 ... (remaining 21584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4794 0.073 - 0.146: 588 0.146 - 0.219: 19 0.219 - 0.292: 11 0.292 - 0.365: 1 Chirality restraints: 5413 Sorted by residual: chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN J 262 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C5 BMA d 3 " pdb=" C4 BMA d 3 " pdb=" C6 BMA d 3 " pdb=" O5 BMA d 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.93e+00 ... (remaining 5410 not shown) Planarity restraints: 6166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR K 397 " -0.087 5.00e-02 4.00e+02 1.29e-01 2.64e+01 pdb=" N PRO K 398 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO K 398 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO K 398 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 142 " 0.084 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO Q 143 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO Q 143 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO Q 143 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 362 " 0.069 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO B 363 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO B 363 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 363 " 0.054 5.00e-02 4.00e+02 ... (remaining 6163 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 298 2.63 - 3.20: 29075 3.20 - 3.76: 46951 3.76 - 4.33: 63630 4.33 - 4.90: 110100 Nonbonded interactions: 250054 Sorted by model distance: nonbonded pdb=" OG SER R 201 " pdb=" OD2 ASP R 220 " model vdw 2.059 3.040 nonbonded pdb=" OG SER E 201 " pdb=" OD2 ASP E 220 " model vdw 2.085 3.040 nonbonded pdb=" OG SER T 201 " pdb=" OD2 ASP T 220 " model vdw 2.126 3.040 nonbonded pdb=" OE1 GLU I 166 " pdb=" OH TYR L 49 " model vdw 2.173 3.040 nonbonded pdb=" OG1 THR H 300 " pdb=" OG1 THR H 319 " model vdw 2.190 3.040 ... (remaining 250049 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'D' selection = chain 'O' selection = chain 'P' selection = chain 'Q' } ncs_group { reference = chain 'E' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.260 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4514 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 : 0.003 0.121 35242 Z= 0.155 Angle : 0.650 10.669 48089 Z= 0.340 Chirality : 0.046 0.365 5413 Planarity : 0.006 0.129 6155 Dihedral : 15.024 110.413 13220 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.20 % Favored : 93.58 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.13), residues: 4358 helix: 2.17 (0.23), residues: 575 sheet: -0.43 (0.16), residues: 1092 loop : -1.39 (0.12), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 115 TYR 0.027 0.001 TYR F 93 PHE 0.027 0.001 PHE K 50 TRP 0.014 0.001 TRP P 195 HIS 0.016 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00343 (35144) covalent geometry : angle 0.64107 (47860) SS BOND : bond 0.00420 ( 65) SS BOND : angle 1.49954 ( 130) hydrogen bonds : bond 0.23712 ( 1151) hydrogen bonds : angle 7.93909 ( 3195) link_BETA1-4 : bond 0.00785 ( 22) link_BETA1-4 : angle 2.06708 ( 66) link_NAG-ASN : bond 0.00356 ( 11) link_NAG-ASN : angle 1.68598 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 846 time to evaluate : 1.158 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 252 ASN cc_start: 0.5404 (m110) cc_final: 0.5135 (m110) REVERT: D 142 LYS cc_start: 0.6563 (ptmm) cc_final: 0.5917 (ptmm) REVERT: D 177 MET cc_start: 0.6995 (mtm) cc_final: 0.6349 (mtp) REVERT: H 370 CYS cc_start: 0.3706 (m) cc_final: 0.3428 (m) REVERT: I 50 PHE cc_start: 0.5838 (m-80) cc_final: 0.5563 (m-80) REVERT: K 286 LEU cc_start: 0.4393 (mt) cc_final: 0.3572 (mp) REVERT: O 221 ARG cc_start: 0.6207 (tpp-160) cc_final: 0.5405 (ttm-80) REVERT: O 240 GLU cc_start: 0.6492 (tm-30) cc_final: 0.5914 (pm20) REVERT: P 139 LYS cc_start: 0.6050 (mttm) cc_final: 0.5840 (mtmt) REVERT: P 161 LYS cc_start: 0.6584 (ttmm) cc_final: 0.5735 (tttt) REVERT: Q 193 TYR cc_start: 0.6368 (m-80) cc_final: 0.6082 (m-80) outliers start: 1 outliers final: 0 residues processed: 847 average time/residue: 0.1706 time to fit residues: 235.6631 Evaluate side-chains 587 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.4980 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 30.0000 chunk 155 optimal weight: 0.0040 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN F 32 GLN ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 ASN G 235 GLN H 30 GLN J 120 ASN J 131 HIS J 352 HIS K 53 GLN K 157 GLN K 306 HIS K 340 GLN O 197 HIS P 176 HIS Q 201 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.133789 restraints weight = 47371.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.138116 restraints weight = 23007.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139613 restraints weight = 14217.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140817 restraints weight = 11991.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141315 restraints weight = 9670.116| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5310 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 35242 Z= 0.159 Angle : 0.697 14.075 48089 Z= 0.348 Chirality : 0.047 0.275 5413 Planarity : 0.005 0.080 6155 Dihedral : 8.612 67.176 5420 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.51 % Favored : 94.29 % Rotamer: Outliers : 2.31 % Allowed : 10.22 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.13), residues: 4358 helix: 2.04 (0.22), residues: 575 sheet: -0.51 (0.14), residues: 1376 loop : -1.27 (0.13), residues: 2407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 68 TYR 0.020 0.002 TYR F 93 PHE 0.021 0.002 PHE B 6 TRP 0.025 0.002 TRP K 235 HIS 0.013 0.001 HIS H 394 Details of bonding type rmsd covalent geometry : bond 0.00353 (35144) covalent geometry : angle 0.68724 (47860) SS BOND : bond 0.00480 ( 65) SS BOND : angle 1.05937 ( 130) hydrogen bonds : bond 0.04033 ( 1151) hydrogen bonds : angle 5.53623 ( 3195) link_BETA1-4 : bond 0.00836 ( 22) link_BETA1-4 : angle 2.78402 ( 66) link_NAG-ASN : bond 0.00400 ( 11) link_NAG-ASN : angle 1.59197 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 644 time to evaluate : 1.278 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: A 75 ASP cc_start: 0.5881 (t70) cc_final: 0.4981 (t0) REVERT: F 27 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6668 (pt) REVERT: F 88 MET cc_start: 0.6240 (mmm) cc_final: 0.5891 (mmm) REVERT: G 7 MET cc_start: 0.6903 (ppp) cc_final: 0.6344 (ppp) REVERT: H 370 CYS cc_start: 0.4310 (m) cc_final: 0.3996 (m) REVERT: I 50 PHE cc_start: 0.6035 (m-80) cc_final: 0.5703 (m-80) REVERT: I 169 MET cc_start: 0.5734 (mmm) cc_final: 0.5133 (mmm) REVERT: J 373 MET cc_start: 0.5185 (mmt) cc_final: 0.4911 (mmt) REVERT: K 169 MET cc_start: 0.7291 (mmt) cc_final: 0.6986 (mmm) REVERT: K 358 TYR cc_start: 0.6714 (OUTLIER) cc_final: 0.6232 (t80) REVERT: M 39 LEU cc_start: 0.6693 (mt) cc_final: 0.5953 (mt) REVERT: O 221 ARG cc_start: 0.6517 (tpp-160) cc_final: 0.6218 (ttm110) REVERT: P 128 LYS cc_start: 0.7032 (mmmt) cc_final: 0.6771 (mmmm) REVERT: P 139 LYS cc_start: 0.6070 (mttm) cc_final: 0.5303 (pttm) REVERT: P 161 LYS cc_start: 0.7147 (ttmm) cc_final: 0.6345 (ttpt) REVERT: P 180 ASP cc_start: 0.6711 (OUTLIER) cc_final: 0.6439 (t0) REVERT: P 202 TYR cc_start: 0.7436 (t80) cc_final: 0.7119 (t80) REVERT: P 224 PHE cc_start: 0.4980 (m-80) cc_final: 0.4664 (m-80) outliers start: 86 outliers final: 43 residues processed: 684 average time/residue: 0.1741 time to fit residues: 199.3903 Evaluate side-chains 592 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 546 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 254 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 301 CYS Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain G residue 142 GLN Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain K residue 215 MET Chi-restraints excluded: chain K residue 251 LYS Chi-restraints excluded: chain K residue 358 TYR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 401 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain P residue 176 HIS Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 247 SER Chi-restraints excluded: chain Q residue 251 TRP Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 107 optimal weight: 0.8980 chunk 250 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 363 optimal weight: 50.0000 chunk 217 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 chunk 253 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN B 131 HIS B 255 HIS D 176 HIS D 186 HIS F 116 HIS ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 HIS G 235 GLN H 18 HIS H 270 ASN I 53 GLN I 77 ASN I 340 GLN ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 120 ASN J 218 ASN ** J 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 348 HIS O 197 HIS ** P 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 192 HIS E 199 GLN T 199 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.182315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139405 restraints weight = 47749.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.143718 restraints weight = 22636.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.144172 restraints weight = 13482.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.144871 restraints weight = 12255.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144946 restraints weight = 10944.031| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.6798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.164 35242 Z= 0.275 Angle : 0.866 14.846 48089 Z= 0.445 Chirality : 0.053 0.721 5413 Planarity : 0.007 0.094 6155 Dihedral : 6.689 58.193 5420 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.40 % Favored : 93.35 % Rotamer: Outliers : 4.24 % Allowed : 13.28 % Favored : 82.48 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.12), residues: 4358 helix: 1.94 (0.22), residues: 551 sheet: -0.53 (0.14), residues: 1252 loop : -1.42 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG K 38 TYR 0.038 0.003 TYR A 76 PHE 0.035 0.003 PHE I 258 TRP 0.024 0.002 TRP B 235 HIS 0.106 0.002 HIS P 176 Details of bonding type rmsd covalent geometry : bond 0.00593 (35144) covalent geometry : angle 0.85334 (47860) SS BOND : bond 0.00517 ( 65) SS BOND : angle 1.43704 ( 130) hydrogen bonds : bond 0.05133 ( 1151) hydrogen bonds : angle 5.50633 ( 3195) link_BETA1-4 : bond 0.01117 ( 22) link_BETA1-4 : angle 2.97032 ( 66) link_NAG-ASN : bond 0.00556 ( 11) link_NAG-ASN : angle 3.15702 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 743 time to evaluate : 1.261 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: D 141 MET cc_start: 0.7717 (mtt) cc_final: 0.7516 (mpp) REVERT: F 122 TYR cc_start: 0.8294 (m-80) cc_final: 0.8071 (m-10) REVERT: F 301 CYS cc_start: 0.6779 (OUTLIER) cc_final: 0.6290 (m) REVERT: F 302 THR cc_start: 0.6378 (OUTLIER) cc_final: 0.6064 (p) REVERT: G 2 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7400 (mm-30) REVERT: G 393 SER cc_start: 0.7916 (m) cc_final: 0.7123 (t) REVERT: H 393 SER cc_start: 0.7906 (m) cc_final: 0.7686 (t) REVERT: I 169 MET cc_start: 0.7164 (mmm) cc_final: 0.6455 (mmm) REVERT: I 373 MET cc_start: 0.7312 (tpp) cc_final: 0.6512 (mtt) REVERT: J 132 ASP cc_start: 0.7722 (t0) cc_final: 0.7153 (p0) REVERT: J 168 ASP cc_start: 0.6496 (p0) cc_final: 0.6285 (m-30) REVERT: J 261 ASP cc_start: 0.5821 (t70) cc_final: 0.5307 (t70) REVERT: J 284 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7613 (mp) REVERT: K 71 ASP cc_start: 0.7008 (t0) cc_final: 0.6215 (t0) REVERT: K 130 HIS cc_start: 0.6352 (p-80) cc_final: 0.6038 (t-90) REVERT: K 299 LEU cc_start: 0.9051 (pp) cc_final: 0.8721 (pp) REVERT: L 20 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: O 218 ASP cc_start: 0.5115 (t70) cc_final: 0.4818 (t0) REVERT: P 161 LYS cc_start: 0.7157 (ttmm) cc_final: 0.5980 (tttt) REVERT: P 180 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6898 (t0) REVERT: Q 111 MET cc_start: 0.8115 (pmm) cc_final: 0.7814 (pmm) outliers start: 158 outliers final: 76 residues processed: 836 average time/residue: 0.1773 time to fit residues: 248.8496 Evaluate side-chains 655 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 574 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 78 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 171 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 301 CYS Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 348 THR Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 85 TYR Chi-restraints excluded: chain G residue 120 SER Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 338 THR Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 282 VAL Chi-restraints excluded: chain I residue 337 LEU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 56 ILE Chi-restraints excluded: chain J residue 99 HIS Chi-restraints excluded: chain J residue 284 LEU Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain K residue 21 ASP Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 274 THR Chi-restraints excluded: chain K residue 342 THR Chi-restraints excluded: chain K residue 346 LYS Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain L residue 20 GLN Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 120 ILE Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 257 THR Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 271 optimal weight: 4.9990 chunk 412 optimal weight: 0.0050 chunk 312 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 53 GLN B 236 GLN B 238 ASN F 118 HIS ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 270 ASN G 211 ASN G 270 ASN G 355 HIS H 264 ASN H 270 ASN I 26 HIS I 73 HIS J 73 HIS J 94 HIS J 120 ASN J 218 ASN J 352 HIS K 53 GLN K 226 HIS O 197 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.184686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141963 restraints weight = 47141.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.143564 restraints weight = 22933.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.144455 restraints weight = 16160.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145199 restraints weight = 13178.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.145201 restraints weight = 11627.359| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.7878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 35242 Z= 0.143 Angle : 0.654 10.601 48089 Z= 0.328 Chirality : 0.045 0.289 5413 Planarity : 0.005 0.068 6155 Dihedral : 6.002 59.534 5420 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.37 % Favored : 94.45 % Rotamer: Outliers : 3.46 % Allowed : 16.20 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.13), residues: 4358 helix: 2.55 (0.22), residues: 527 sheet: -0.43 (0.14), residues: 1280 loop : -1.29 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 134 TYR 0.032 0.001 TYR H 93 PHE 0.017 0.001 PHE I 50 TRP 0.019 0.001 TRP B 235 HIS 0.024 0.001 HIS P 176 Details of bonding type rmsd covalent geometry : bond 0.00320 (35144) covalent geometry : angle 0.64345 (47860) SS BOND : bond 0.00890 ( 65) SS BOND : angle 1.18920 ( 130) hydrogen bonds : bond 0.03410 ( 1151) hydrogen bonds : angle 4.97135 ( 3195) link_BETA1-4 : bond 0.00887 ( 22) link_BETA1-4 : angle 2.23009 ( 66) link_NAG-ASN : bond 0.00593 ( 11) link_NAG-ASN : angle 2.81147 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 601 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8815 (m-80) cc_final: 0.8561 (m-80) REVERT: B 45 MET cc_start: 0.8323 (mtp) cc_final: 0.8105 (mtp) REVERT: B 292 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8130 (t) REVERT: B 325 MET cc_start: 0.8172 (pmm) cc_final: 0.7524 (pmm) REVERT: D 141 MET cc_start: 0.7741 (mtt) cc_final: 0.7466 (mpp) REVERT: F 245 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7436 (mmtt) REVERT: F 301 CYS cc_start: 0.7145 (OUTLIER) cc_final: 0.6882 (m) REVERT: G 228 MET cc_start: 0.7917 (mtp) cc_final: 0.7601 (mtp) REVERT: G 393 SER cc_start: 0.8343 (m) cc_final: 0.7594 (t) REVERT: H 95 PHE cc_start: 0.8362 (t80) cc_final: 0.8059 (t80) REVERT: H 370 CYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5718 (m) REVERT: H 386 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.7095 (t-90) REVERT: H 393 SER cc_start: 0.8440 (m) cc_final: 0.8046 (t) REVERT: I 45 MET cc_start: 0.8530 (mmm) cc_final: 0.8193 (mtt) REVERT: I 76 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: I 128 GLN cc_start: 0.7181 (pp30) cc_final: 0.6763 (tt0) REVERT: I 169 MET cc_start: 0.7200 (mmm) cc_final: 0.6206 (mmm) REVERT: I 325 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7846 (ppp) REVERT: I 373 MET cc_start: 0.7432 (tpp) cc_final: 0.6771 (mtt) REVERT: J 115 ILE cc_start: 0.4176 (tt) cc_final: 0.3878 (tt) REVERT: K 45 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7977 (mmt) REVERT: K 84 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7652 (mtmm) REVERT: K 299 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8767 (pp) REVERT: M 18 CYS cc_start: 0.5217 (m) cc_final: 0.4763 (m) REVERT: N 36 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5849 (mp) REVERT: N 40 GLU cc_start: 0.6413 (mm-30) cc_final: 0.6084 (mt-10) REVERT: O 251 TRP cc_start: 0.8523 (p90) cc_final: 0.8291 (p90) REVERT: Q 139 LYS cc_start: 0.5354 (mtmt) cc_final: 0.3893 (mttp) REVERT: Q 224 PHE cc_start: 0.7750 (m-80) cc_final: 0.7473 (m-80) outliers start: 129 outliers final: 80 residues processed: 677 average time/residue: 0.1680 time to fit residues: 193.0416 Evaluate side-chains 616 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 526 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 301 CYS Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 275 ASN Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 62 CYS Chi-restraints excluded: chain H residue 78 CYS Chi-restraints excluded: chain H residue 171 THR Chi-restraints excluded: chain H residue 297 ILE Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain H residue 386 HIS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 274 THR Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 325 MET Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 8 VAL Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 215 MET Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 333 ASP Chi-restraints excluded: chain K residue 45 MET Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain K residue 276 ILE Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 379 ILE Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 242 SER Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 173 optimal weight: 6.9990 chunk 371 optimal weight: 0.6980 chunk 430 optimal weight: 50.0000 chunk 260 optimal weight: 0.0670 chunk 310 optimal weight: 4.9990 chunk 367 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 327 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 346 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 116 HIS B 53 GLN ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 ASN F 270 ASN H 230 HIS H 270 ASN I 26 HIS J 62 HIS ** J 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 352 HIS L 31 ASN Q 197 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.176506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.130076 restraints weight = 47403.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.132985 restraints weight = 22623.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.133799 restraints weight = 14649.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.134356 restraints weight = 13013.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.134378 restraints weight = 11536.421| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.9295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 35242 Z= 0.157 Angle : 0.655 9.570 48089 Z= 0.333 Chirality : 0.046 0.318 5413 Planarity : 0.005 0.063 6155 Dihedral : 5.836 59.298 5420 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.42 % Favored : 93.41 % Rotamer: Outliers : 4.32 % Allowed : 16.93 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.13), residues: 4358 helix: 2.40 (0.23), residues: 531 sheet: -0.45 (0.14), residues: 1284 loop : -1.18 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG Q 110 TYR 0.018 0.001 TYR A 320 PHE 0.020 0.002 PHE G 420 TRP 0.020 0.001 TRP A 89 HIS 0.011 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00361 (35144) covalent geometry : angle 0.64646 (47860) SS BOND : bond 0.00272 ( 65) SS BOND : angle 1.07641 ( 130) hydrogen bonds : bond 0.03551 ( 1151) hydrogen bonds : angle 4.86712 ( 3195) link_BETA1-4 : bond 0.00647 ( 22) link_BETA1-4 : angle 1.85804 ( 66) link_NAG-ASN : bond 0.01002 ( 11) link_NAG-ASN : angle 2.60524 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 553 time to evaluate : 1.214 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: A 24 TYR cc_start: 0.8108 (m-80) cc_final: 0.7858 (m-80) REVERT: B 7 ASN cc_start: 0.7407 (t0) cc_final: 0.6957 (t0) REVERT: B 45 MET cc_start: 0.8552 (mtp) cc_final: 0.8273 (mtp) REVERT: B 251 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7583 (tptp) REVERT: B 299 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8330 (pp) REVERT: B 373 MET cc_start: 0.7983 (ttp) cc_final: 0.7753 (mtm) REVERT: D 183 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7876 (tttt) REVERT: F 302 THR cc_start: 0.7071 (OUTLIER) cc_final: 0.6808 (p) REVERT: G 129 LEU cc_start: 0.7407 (tt) cc_final: 0.7205 (tt) REVERT: G 161 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.6635 (t80) REVERT: G 182 ASP cc_start: 0.7286 (t70) cc_final: 0.7056 (t0) REVERT: H 95 PHE cc_start: 0.8401 (t80) cc_final: 0.8071 (t80) REVERT: H 136 MET cc_start: 0.8097 (ptp) cc_final: 0.7897 (ptp) REVERT: H 177 ILE cc_start: 0.8707 (mm) cc_final: 0.8495 (mm) REVERT: H 386 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7528 (t-90) REVERT: I 45 MET cc_start: 0.8646 (mmm) cc_final: 0.8265 (mtp) REVERT: I 166 GLU cc_start: 0.8084 (mp0) cc_final: 0.7850 (mp0) REVERT: I 373 MET cc_start: 0.7355 (tpp) cc_final: 0.6787 (mtt) REVERT: J 168 ASP cc_start: 0.6690 (OUTLIER) cc_final: 0.6163 (p0) REVERT: J 337 LEU cc_start: 0.7947 (pp) cc_final: 0.7713 (pp) REVERT: K 84 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7938 (mtmm) REVERT: K 128 GLN cc_start: 0.7417 (pp30) cc_final: 0.6594 (pt0) REVERT: K 174 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7203 (p0) REVERT: K 299 LEU cc_start: 0.9254 (pp) cc_final: 0.8943 (pp) REVERT: M 18 CYS cc_start: 0.5174 (m) cc_final: 0.4812 (m) REVERT: O 253 LYS cc_start: 0.7859 (tptp) cc_final: 0.7579 (mtmm) REVERT: P 128 LYS cc_start: 0.7473 (mmmm) cc_final: 0.7253 (mmmt) REVERT: P 215 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7802 (ptmt) REVERT: Q 111 MET cc_start: 0.8135 (pmm) cc_final: 0.7694 (pmm) REVERT: Q 139 LYS cc_start: 0.5379 (mtmt) cc_final: 0.5037 (pttp) REVERT: Q 161 LYS cc_start: 0.8556 (mttm) cc_final: 0.8112 (ttmm) REVERT: Q 224 PHE cc_start: 0.8131 (m-80) cc_final: 0.7758 (m-80) REVERT: Q 256 VAL cc_start: 0.6176 (OUTLIER) cc_final: 0.5858 (t) outliers start: 161 outliers final: 86 residues processed: 664 average time/residue: 0.1824 time to fit residues: 202.4121 Evaluate side-chains 592 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 495 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 37 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 161 PHE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 386 HIS Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 210 THR Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 42 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 132 ASP Chi-restraints excluded: chain J residue 168 ASP Chi-restraints excluded: chain J residue 171 MET Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 333 ASP Chi-restraints excluded: chain J residue 387 MET Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 150 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 292 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 215 LYS Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 256 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 302 optimal weight: 6.9990 chunk 301 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 357 optimal weight: 0.0770 chunk 350 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 241 optimal weight: 0.0770 overall best weight: 1.0298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 GLN B 255 HIS ** F 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 HIS I 255 HIS J 73 HIS J 352 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.181258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136230 restraints weight = 46593.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138089 restraints weight = 21964.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137972 restraints weight = 16126.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.138677 restraints weight = 14657.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140834 restraints weight = 12557.669| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.9831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 35242 Z= 0.114 Angle : 0.611 11.225 48089 Z= 0.306 Chirality : 0.044 0.259 5413 Planarity : 0.005 0.060 6155 Dihedral : 5.570 58.678 5420 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.07 % Favored : 94.75 % Rotamer: Outliers : 3.38 % Allowed : 18.62 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.13), residues: 4358 helix: 2.55 (0.23), residues: 531 sheet: -0.31 (0.14), residues: 1240 loop : -1.12 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 126 TYR 0.019 0.001 TYR A 320 PHE 0.021 0.001 PHE B 110 TRP 0.029 0.001 TRP G 89 HIS 0.011 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00266 (35144) covalent geometry : angle 0.60325 (47860) SS BOND : bond 0.00253 ( 65) SS BOND : angle 0.96565 ( 130) hydrogen bonds : bond 0.03037 ( 1151) hydrogen bonds : angle 4.67348 ( 3195) link_BETA1-4 : bond 0.00602 ( 22) link_BETA1-4 : angle 1.83384 ( 66) link_NAG-ASN : bond 0.00519 ( 11) link_NAG-ASN : angle 2.37667 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 530 time to evaluate : 1.283 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: A 88 MET cc_start: 0.7901 (mmm) cc_final: 0.7690 (mmm) REVERT: B 7 ASN cc_start: 0.7628 (t0) cc_final: 0.7289 (t0) REVERT: B 251 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7621 (tptp) REVERT: B 387 MET cc_start: 0.6546 (ttm) cc_final: 0.6339 (ttm) REVERT: D 183 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7916 (tttt) REVERT: F 302 THR cc_start: 0.7290 (OUTLIER) cc_final: 0.6943 (p) REVERT: G 161 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7763 (m-80) REVERT: G 182 ASP cc_start: 0.7452 (t70) cc_final: 0.7204 (t0) REVERT: H 95 PHE cc_start: 0.8373 (t80) cc_final: 0.8146 (t80) REVERT: H 109 ASP cc_start: 0.7735 (t0) cc_final: 0.7476 (t0) REVERT: H 297 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7561 (mt) REVERT: H 402 MET cc_start: 0.8326 (tpp) cc_final: 0.7851 (mmt) REVERT: H 432 THR cc_start: 0.5690 (t) cc_final: 0.5397 (t) REVERT: I 45 MET cc_start: 0.8565 (mmm) cc_final: 0.8195 (mtp) REVERT: I 76 GLU cc_start: 0.7421 (pm20) cc_final: 0.6896 (mp0) REVERT: I 157 GLN cc_start: 0.7213 (pm20) cc_final: 0.6865 (mm-40) REVERT: I 166 GLU cc_start: 0.7965 (mp0) cc_final: 0.7759 (mp0) REVERT: I 304 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.6807 (mp10) REVERT: I 320 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.9062 (m) REVERT: I 373 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6927 (mtt) REVERT: J 325 MET cc_start: 0.8455 (ptm) cc_final: 0.7882 (ptt) REVERT: J 337 LEU cc_start: 0.8092 (pp) cc_final: 0.7788 (pp) REVERT: K 128 GLN cc_start: 0.7447 (pp30) cc_final: 0.6801 (pt0) REVERT: K 299 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8941 (pp) REVERT: M 18 CYS cc_start: 0.5292 (m) cc_final: 0.4875 (m) REVERT: P 215 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7501 (ptmt) REVERT: Q 111 MET cc_start: 0.8233 (pmm) cc_final: 0.7598 (pmm) REVERT: Q 139 LYS cc_start: 0.5577 (mtmt) cc_final: 0.5254 (pttm) REVERT: Q 161 LYS cc_start: 0.8439 (mttm) cc_final: 0.8106 (ttmm) REVERT: Q 224 PHE cc_start: 0.8260 (m-80) cc_final: 0.7880 (m-80) outliers start: 126 outliers final: 73 residues processed: 608 average time/residue: 0.1715 time to fit residues: 175.2889 Evaluate side-chains 574 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 491 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 259 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 73 HIS Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 251 LYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 332 SER Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 161 PHE Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 259 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 297 ILE Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 12 THR Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 320 VAL Chi-restraints excluded: chain I residue 373 MET Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain I residue 397 THR Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 105 CYS Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 333 ASP Chi-restraints excluded: chain J residue 387 MET Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain P residue 185 THR Chi-restraints excluded: chain P residue 215 LYS Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 257 THR Chi-restraints excluded: chain T residue 200 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 157 optimal weight: 5.9990 chunk 268 optimal weight: 9.9990 chunk 380 optimal weight: 5.9990 chunk 396 optimal weight: 9.9990 chunk 411 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 305 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 421 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN B 226 HIS B 238 ASN B 255 HIS F 32 GLN F 230 HIS F 333 HIS G 118 HIS I 26 HIS I 120 ASN I 255 HIS I 352 HIS J 352 HIS K 340 GLN M 42 ASN Q 196 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.168555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121715 restraints weight = 46390.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.121785 restraints weight = 23699.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.122478 restraints weight = 18044.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.122935 restraints weight = 16887.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.123310 restraints weight = 14458.392| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 1.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 35242 Z= 0.295 Angle : 0.858 13.032 48089 Z= 0.438 Chirality : 0.052 0.332 5413 Planarity : 0.006 0.129 6155 Dihedral : 6.538 59.657 5420 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.62 % Favored : 92.22 % Rotamer: Outliers : 4.59 % Allowed : 18.00 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.13), residues: 4358 helix: 2.04 (0.22), residues: 531 sheet: -0.69 (0.14), residues: 1304 loop : -1.34 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 68 TYR 0.026 0.002 TYR A 93 PHE 0.051 0.002 PHE I 50 TRP 0.037 0.002 TRP G 89 HIS 0.012 0.002 HIS I 130 Details of bonding type rmsd covalent geometry : bond 0.00710 (35144) covalent geometry : angle 0.84689 (47860) SS BOND : bond 0.00470 ( 65) SS BOND : angle 2.03022 ( 130) hydrogen bonds : bond 0.04585 ( 1151) hydrogen bonds : angle 5.24965 ( 3195) link_BETA1-4 : bond 0.01144 ( 22) link_BETA1-4 : angle 1.99288 ( 66) link_NAG-ASN : bond 0.00687 ( 11) link_NAG-ASN : angle 3.06976 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 497 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 SER cc_start: 0.9116 (OUTLIER) cc_final: 0.8914 (t) REVERT: A 320 TYR cc_start: 0.9191 (p90) cc_final: 0.8861 (p90) REVERT: A 325 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8766 (m-40) REVERT: A 364 SER cc_start: 0.9369 (t) cc_final: 0.9061 (p) REVERT: B 134 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8362 (mm-40) REVERT: B 302 ASP cc_start: 0.7811 (p0) cc_final: 0.7567 (p0) REVERT: B 387 MET cc_start: 0.6869 (ttm) cc_final: 0.6435 (ttm) REVERT: F 168 SER cc_start: 0.9239 (t) cc_final: 0.8980 (t) REVERT: F 174 ASP cc_start: 0.8200 (t0) cc_final: 0.7841 (t0) REVERT: F 302 THR cc_start: 0.7599 (OUTLIER) cc_final: 0.7258 (p) REVERT: F 345 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8385 (ttmm) REVERT: F 384 LYS cc_start: 0.4940 (mptt) cc_final: 0.2545 (mmtm) REVERT: G 16 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7771 (ptpp) REVERT: G 105 GLU cc_start: 0.7306 (tt0) cc_final: 0.7048 (mt-10) REVERT: G 147 TYR cc_start: 0.7741 (m-10) cc_final: 0.7279 (m-10) REVERT: G 182 ASP cc_start: 0.7779 (t70) cc_final: 0.7578 (t70) REVERT: G 397 VAL cc_start: 0.9139 (t) cc_final: 0.8898 (p) REVERT: H 42 LEU cc_start: 0.9217 (mm) cc_final: 0.8936 (mt) REVERT: H 182 ASP cc_start: 0.8149 (p0) cc_final: 0.7898 (p0) REVERT: I 76 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: I 97 MET cc_start: 0.7635 (ppp) cc_final: 0.7431 (tmm) REVERT: I 304 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7070 (mp10) REVERT: I 373 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7165 (mtt) REVERT: J 7 ASN cc_start: 0.8186 (t0) cc_final: 0.7805 (t0) REVERT: J 10 LYS cc_start: 0.8396 (ptpt) cc_final: 0.8000 (ptpt) REVERT: J 337 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7986 (pp) REVERT: K 57 ASP cc_start: 0.7680 (t0) cc_final: 0.7022 (t0) REVERT: K 120 ASN cc_start: 0.8277 (m110) cc_final: 0.7983 (m-40) REVERT: K 174 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7765 (p0) REVERT: N 36 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5610 (mp) REVERT: O 165 LYS cc_start: 0.8991 (tttp) cc_final: 0.8714 (tttm) REVERT: O 251 TRP cc_start: 0.9054 (OUTLIER) cc_final: 0.8783 (p90) REVERT: P 183 LYS cc_start: 0.8693 (ptpt) cc_final: 0.8429 (ptpp) REVERT: Q 111 MET cc_start: 0.8211 (pmm) cc_final: 0.7447 (pmm) REVERT: Q 139 LYS cc_start: 0.5305 (mtmt) cc_final: 0.4848 (pttp) REVERT: Q 161 LYS cc_start: 0.8479 (mttm) cc_final: 0.8192 (ttmm) REVERT: Q 183 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7895 (mtpt) REVERT: Q 224 PHE cc_start: 0.8850 (m-80) cc_final: 0.8154 (m-80) REVERT: Q 229 ARG cc_start: 0.7009 (mtm180) cc_final: 0.6793 (mtm180) outliers start: 171 outliers final: 98 residues processed: 633 average time/residue: 0.1839 time to fit residues: 192.7160 Evaluate side-chains 536 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 426 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 4 SER Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 325 ASN Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 27 SER Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 302 THR Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 16 LYS Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 410 VAL Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 330 VAL Chi-restraints excluded: chain H residue 358 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 373 MET Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 79 VAL Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 105 CYS Chi-restraints excluded: chain J residue 132 ASP Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 333 ASP Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 371 VAL Chi-restraints excluded: chain J residue 389 VAL Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 371 VAL Chi-restraints excluded: chain K residue 376 LEU Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 251 TRP Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 130 THR Chi-restraints excluded: chain P residue 185 THR Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 257 THR Chi-restraints excluded: chain T residue 200 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 397 optimal weight: 10.0000 chunk 83 optimal weight: 0.0770 chunk 5 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 346 optimal weight: 0.8980 chunk 354 optimal weight: 10.0000 chunk 407 optimal weight: 9.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN B 255 HIS ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 ASN I 348 HIS J 255 HIS J 352 HIS M 42 ASN O 197 HIS ** Q 145 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 = 0.3980 r_free = 0.3980 target = 0.168302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122269 restraints weight = 45941.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122268 restraints weight = 23085.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123541 restraints weight = 17140.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.124253 restraints weight = 14289.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124772 restraints weight = 12650.231| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 1.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35242 Z= 0.121 Angle : 0.651 12.454 48089 Z= 0.329 Chirality : 0.045 0.289 5413 Planarity : 0.005 0.058 6155 Dihedral : 5.893 59.004 5420 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.09 % Favored : 94.77 % Rotamer: Outliers : 2.60 % Allowed : 20.41 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.13), residues: 4358 helix: 2.39 (0.23), residues: 531 sheet: -0.55 (0.14), residues: 1240 loop : -1.18 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 373 TYR 0.022 0.001 TYR A 320 PHE 0.022 0.001 PHE K 100 TRP 0.021 0.001 TRP G 89 HIS 0.010 0.001 HIS K 328 Details of bonding type rmsd covalent geometry : bond 0.00276 (35144) covalent geometry : angle 0.63955 (47860) SS BOND : bond 0.00362 ( 65) SS BOND : angle 1.42846 ( 130) hydrogen bonds : bond 0.03405 ( 1151) hydrogen bonds : angle 4.87675 ( 3195) link_BETA1-4 : bond 0.00780 ( 22) link_BETA1-4 : angle 1.77511 ( 66) link_NAG-ASN : bond 0.00760 ( 11) link_NAG-ASN : angle 3.30944 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 483 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8390 (mmtp) REVERT: A 88 MET cc_start: 0.8515 (mmm) cc_final: 0.8046 (mtp) REVERT: A 298 ASP cc_start: 0.6753 (t0) cc_final: 0.6460 (t0) REVERT: A 321 LYS cc_start: 0.8697 (mtmm) cc_final: 0.8407 (mtmm) REVERT: B 126 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.8187 (ptm160) REVERT: B 174 ASP cc_start: 0.8507 (p0) cc_final: 0.8183 (p0) REVERT: B 251 LYS cc_start: 0.8137 (tptm) cc_final: 0.7688 (tptp) REVERT: B 301 GLU cc_start: 0.7925 (tp30) cc_final: 0.7668 (tt0) REVERT: B 302 ASP cc_start: 0.7639 (p0) cc_final: 0.7328 (p0) REVERT: B 387 MET cc_start: 0.6737 (ttm) cc_final: 0.6164 (ttp) REVERT: F 168 SER cc_start: 0.9191 (t) cc_final: 0.8921 (t) REVERT: F 174 ASP cc_start: 0.8167 (t0) cc_final: 0.7703 (t0) REVERT: F 384 LYS cc_start: 0.5005 (mptt) cc_final: 0.2592 (mmtm) REVERT: G 147 TYR cc_start: 0.7773 (m-10) cc_final: 0.7269 (m-10) REVERT: G 397 VAL cc_start: 0.9025 (t) cc_final: 0.8782 (p) REVERT: H 42 LEU cc_start: 0.9183 (mm) cc_final: 0.8940 (mt) REVERT: H 88 MET cc_start: 0.8556 (mtp) cc_final: 0.7822 (mtt) REVERT: I 96 THR cc_start: 0.6791 (m) cc_final: 0.6506 (p) REVERT: I 304 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7073 (mp10) REVERT: I 373 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7167 (mtt) REVERT: J 7 ASN cc_start: 0.8195 (t0) cc_final: 0.7837 (t0) REVERT: J 10 LYS cc_start: 0.8278 (ptpt) cc_final: 0.7861 (ptpp) REVERT: J 166 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: J 253 LYS cc_start: 0.8916 (mttp) cc_final: 0.8504 (mtmt) REVERT: J 325 MET cc_start: 0.8626 (ptm) cc_final: 0.8186 (ptt) REVERT: J 356 GLN cc_start: 0.8372 (mm110) cc_final: 0.7811 (mt0) REVERT: K 87 THR cc_start: 0.8476 (t) cc_final: 0.7366 (p) REVERT: K 120 ASN cc_start: 0.8255 (m110) cc_final: 0.7948 (m-40) REVERT: K 174 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7680 (p0) REVERT: O 165 LYS cc_start: 0.8991 (tttp) cc_final: 0.8695 (tttm) REVERT: O 251 TRP cc_start: 0.9015 (OUTLIER) cc_final: 0.8702 (p90) REVERT: P 183 LYS cc_start: 0.8640 (ptpt) cc_final: 0.8370 (ptpp) REVERT: Q 111 MET cc_start: 0.8150 (pmm) cc_final: 0.7361 (pmm) REVERT: Q 139 LYS cc_start: 0.5120 (mtmt) cc_final: 0.4745 (pttm) REVERT: Q 161 LYS cc_start: 0.8338 (mttm) cc_final: 0.8080 (ttmm) REVERT: Q 183 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7932 (mtpt) outliers start: 97 outliers final: 64 residues processed: 555 average time/residue: 0.1904 time to fit residues: 175.9637 Evaluate side-chains 504 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 432 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 373 MET Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 105 CYS Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 232 HIS Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain K residue 276 ILE Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 251 TRP Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 215 LYS Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain T residue 200 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 339 optimal weight: 4.9990 chunk 308 optimal weight: 5.9990 chunk 328 optimal weight: 3.9990 chunk 294 optimal weight: 0.9980 chunk 346 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 124 optimal weight: 0.0040 chunk 50 optimal weight: 0.0270 chunk 383 optimal weight: 1.9990 chunk 249 optimal weight: 6.9990 overall best weight: 1.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 HIS ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 348 HIS J 255 HIS M 42 ASN O 196 HIS Q 196 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.171722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125759 restraints weight = 45515.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126603 restraints weight = 22079.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126440 restraints weight = 17990.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.127445 restraints weight = 14773.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.130367 restraints weight = 12827.437| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 1.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 35242 Z= 0.128 Angle : 0.646 14.642 48089 Z= 0.326 Chirality : 0.045 0.385 5413 Planarity : 0.005 0.073 6155 Dihedral : 5.715 59.036 5420 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.97 % Favored : 93.90 % Rotamer: Outliers : 2.79 % Allowed : 20.76 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.13), residues: 4358 helix: 2.34 (0.23), residues: 539 sheet: -0.45 (0.14), residues: 1260 loop : -1.12 (0.12), residues: 2559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 373 TYR 0.020 0.001 TYR A 320 PHE 0.022 0.001 PHE A 95 TRP 0.044 0.001 TRP G 89 HIS 0.010 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00302 (35144) covalent geometry : angle 0.63357 (47860) SS BOND : bond 0.00227 ( 65) SS BOND : angle 1.34709 ( 130) hydrogen bonds : bond 0.03262 ( 1151) hydrogen bonds : angle 4.73234 ( 3195) link_BETA1-4 : bond 0.00631 ( 22) link_BETA1-4 : angle 1.73265 ( 66) link_NAG-ASN : bond 0.00397 ( 11) link_NAG-ASN : angle 3.56700 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 461 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8396 (mmtp) REVERT: A 88 MET cc_start: 0.8440 (mmm) cc_final: 0.8063 (mtp) REVERT: A 298 ASP cc_start: 0.6752 (t0) cc_final: 0.6551 (t0) REVERT: B 126 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8231 (ptp-170) REVERT: B 174 ASP cc_start: 0.8559 (p0) cc_final: 0.8226 (p0) REVERT: B 224 GLN cc_start: 0.7607 (mt0) cc_final: 0.7356 (tt0) REVERT: B 234 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8172 (mtpp) REVERT: B 251 LYS cc_start: 0.8293 (tptm) cc_final: 0.7811 (tptp) REVERT: B 301 GLU cc_start: 0.7966 (tp30) cc_final: 0.7575 (tt0) REVERT: B 302 ASP cc_start: 0.7590 (p0) cc_final: 0.7274 (p0) REVERT: B 387 MET cc_start: 0.6770 (ttm) cc_final: 0.6356 (ttm) REVERT: D 193 TYR cc_start: 0.7936 (m-80) cc_final: 0.7579 (m-80) REVERT: F 168 SER cc_start: 0.9191 (t) cc_final: 0.8933 (t) REVERT: F 174 ASP cc_start: 0.8302 (t0) cc_final: 0.7850 (t0) REVERT: F 345 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8197 (ttmt) REVERT: F 384 LYS cc_start: 0.5019 (mptt) cc_final: 0.2580 (mptt) REVERT: G 145 ASP cc_start: 0.8201 (t0) cc_final: 0.7907 (p0) REVERT: G 147 TYR cc_start: 0.7693 (m-10) cc_final: 0.7261 (m-10) REVERT: H 42 LEU cc_start: 0.9183 (mm) cc_final: 0.8807 (mt) REVERT: I 53 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7973 (mt0) REVERT: I 76 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: I 96 THR cc_start: 0.6740 (m) cc_final: 0.6430 (p) REVERT: I 304 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7293 (mp10) REVERT: J 7 ASN cc_start: 0.8150 (t0) cc_final: 0.7761 (t0) REVERT: J 10 LYS cc_start: 0.8300 (ptpt) cc_final: 0.7853 (ptpp) REVERT: J 166 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7901 (mm-30) REVERT: J 253 LYS cc_start: 0.9037 (mttp) cc_final: 0.8479 (mtmt) REVERT: J 337 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7912 (pp) REVERT: J 356 GLN cc_start: 0.8329 (mm110) cc_final: 0.7853 (mt0) REVERT: K 76 GLU cc_start: 0.7610 (mp0) cc_final: 0.7402 (mp0) REVERT: K 87 THR cc_start: 0.8396 (t) cc_final: 0.7347 (p) REVERT: K 174 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7655 (p0) REVERT: O 165 LYS cc_start: 0.8999 (tttp) cc_final: 0.8624 (tttm) REVERT: O 251 TRP cc_start: 0.9012 (p90) cc_final: 0.8714 (p90) REVERT: P 183 LYS cc_start: 0.8639 (ptpt) cc_final: 0.8328 (ptpp) REVERT: Q 111 MET cc_start: 0.8119 (pmm) cc_final: 0.7307 (pmm) REVERT: Q 139 LYS cc_start: 0.5098 (mtmt) cc_final: 0.4432 (pttp) REVERT: Q 161 LYS cc_start: 0.8433 (mttm) cc_final: 0.8195 (ttmm) REVERT: Q 183 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7965 (mtpt) REVERT: Q 224 PHE cc_start: 0.8778 (m-80) cc_final: 0.8522 (m-80) outliers start: 104 outliers final: 74 residues processed: 541 average time/residue: 0.1924 time to fit residues: 173.2497 Evaluate side-chains 525 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 441 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 105 CYS Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 174 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 255 MET Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 257 THR Chi-restraints excluded: chain T residue 200 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 330 optimal weight: 5.9990 chunk 1 optimal weight: 0.1980 chunk 202 optimal weight: 10.0000 chunk 336 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 395 optimal weight: 30.0000 chunk 196 optimal weight: 0.8980 chunk 177 optimal weight: 0.9980 chunk 316 optimal weight: 6.9990 chunk 368 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 HIS ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 ASN I 348 HIS J 255 HIS M 42 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.164367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117460 restraints weight = 45998.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118401 restraints weight = 23277.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119117 restraints weight = 16706.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120209 restraints weight = 14033.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.120225 restraints weight = 12553.449| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 1.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 35242 Z= 0.185 Angle : 0.686 12.319 48089 Z= 0.348 Chirality : 0.047 0.253 5413 Planarity : 0.005 0.066 6155 Dihedral : 5.843 58.974 5420 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.17 % Favored : 93.69 % Rotamer: Outliers : 2.82 % Allowed : 20.98 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.13), residues: 4358 helix: 2.32 (0.23), residues: 539 sheet: -0.47 (0.14), residues: 1264 loop : -1.18 (0.12), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 115 TYR 0.021 0.002 TYR A 93 PHE 0.021 0.001 PHE A 95 TRP 0.040 0.001 TRP G 89 HIS 0.011 0.001 HIS B 255 Details of bonding type rmsd covalent geometry : bond 0.00456 (35144) covalent geometry : angle 0.67342 (47860) SS BOND : bond 0.00295 ( 65) SS BOND : angle 1.78486 ( 130) hydrogen bonds : bond 0.03570 ( 1151) hydrogen bonds : angle 4.80323 ( 3195) link_BETA1-4 : bond 0.00711 ( 22) link_BETA1-4 : angle 1.68708 ( 66) link_NAG-ASN : bond 0.00344 ( 11) link_NAG-ASN : angle 3.27828 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8716 Ramachandran restraints generated. 4358 Oldfield, 0 Emsley, 4358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 448 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8502 (mmtp) REVERT: B 126 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (ptp-170) REVERT: B 224 GLN cc_start: 0.7523 (mt0) cc_final: 0.7207 (tt0) REVERT: B 234 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8425 (mtpp) REVERT: B 251 LYS cc_start: 0.8406 (tptm) cc_final: 0.7925 (tptp) REVERT: B 302 ASP cc_start: 0.7625 (p0) cc_final: 0.7385 (p0) REVERT: B 387 MET cc_start: 0.6780 (ttm) cc_final: 0.6372 (ttm) REVERT: D 193 TYR cc_start: 0.8060 (m-80) cc_final: 0.7626 (m-80) REVERT: F 168 SER cc_start: 0.9259 (t) cc_final: 0.9018 (t) REVERT: F 174 ASP cc_start: 0.8294 (t0) cc_final: 0.7857 (t0) REVERT: F 345 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8293 (ttmm) REVERT: F 384 LYS cc_start: 0.5207 (mptt) cc_final: 0.2622 (mmtm) REVERT: G 147 TYR cc_start: 0.7777 (m-10) cc_final: 0.7311 (m-10) REVERT: G 321 LYS cc_start: 0.8941 (mttm) cc_final: 0.8619 (mtmm) REVERT: H 42 LEU cc_start: 0.9111 (mm) cc_final: 0.8851 (mt) REVERT: I 53 GLN cc_start: 0.8558 (pt0) cc_final: 0.7946 (mt0) REVERT: I 76 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: I 96 THR cc_start: 0.6921 (m) cc_final: 0.6618 (p) REVERT: I 199 TYR cc_start: 0.7332 (p90) cc_final: 0.6990 (p90) REVERT: I 304 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: J 7 ASN cc_start: 0.8296 (t0) cc_final: 0.7926 (t0) REVERT: J 10 LYS cc_start: 0.8489 (ptpt) cc_final: 0.7971 (ptpp) REVERT: J 166 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8031 (mm-30) REVERT: J 253 LYS cc_start: 0.9108 (mttp) cc_final: 0.8375 (mtmt) REVERT: J 337 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8018 (pp) REVERT: J 356 GLN cc_start: 0.8271 (mm110) cc_final: 0.7805 (mt0) REVERT: O 165 LYS cc_start: 0.9018 (tttp) cc_final: 0.8759 (tttm) REVERT: O 262 GLU cc_start: 0.8495 (pm20) cc_final: 0.8279 (pm20) REVERT: Q 111 MET cc_start: 0.8084 (pmm) cc_final: 0.7241 (pmm) REVERT: Q 139 LYS cc_start: 0.4988 (mtmt) cc_final: 0.3410 (mmtt) REVERT: Q 161 LYS cc_start: 0.8527 (mttm) cc_final: 0.8292 (ttmm) REVERT: Q 183 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.8001 (mtpt) outliers start: 105 outliers final: 87 residues processed: 524 average time/residue: 0.2061 time to fit residues: 178.8088 Evaluate side-chains 530 residues out of total 3728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 435 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 GLU Chi-restraints excluded: chain A residue 73 LYS Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 216 ASN Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain C residue 8 MET Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 259 VAL Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain G residue 301 CYS Chi-restraints excluded: chain G residue 315 VAL Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain H residue 410 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 76 GLU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 105 CYS Chi-restraints excluded: chain J residue 166 GLU Chi-restraints excluded: chain J residue 167 ILE Chi-restraints excluded: chain J residue 256 ILE Chi-restraints excluded: chain J residue 337 LEU Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 99 HIS Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 305 TYR Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain K residue 366 THR Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain M residue 8 MET Chi-restraints excluded: chain N residue 8 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain O residue 183 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 209 ILE Chi-restraints excluded: chain O residue 249 VAL Chi-restraints excluded: chain O residue 253 LYS Chi-restraints excluded: chain O residue 265 GLU Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 242 SER Chi-restraints excluded: chain P residue 255 MET Chi-restraints excluded: chain P residue 259 VAL Chi-restraints excluded: chain Q residue 183 LYS Chi-restraints excluded: chain Q residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 362 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 234 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 8.9990 chunk 349 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 236 GLN B 255 HIS B 356 GLN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 GLN ** H 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 ASN I 348 HIS J 255 HIS M 42 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.162003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115341 restraints weight = 45599.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117083 restraints weight = 22320.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.117665 restraints weight = 15347.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118067 restraints weight = 13098.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118104 restraints weight = 12006.701| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 1.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35242 Z= 0.190 Angle : 0.705 12.373 48089 Z= 0.357 Chirality : 0.047 0.316 5413 Planarity : 0.005 0.071 6155 Dihedral : 5.940 58.990 5420 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.72 % Favored : 93.16 % Rotamer: Outliers : 2.95 % Allowed : 21.11 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.14 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.13), residues: 4358 helix: 2.13 (0.22), residues: 563 sheet: -0.43 (0.15), residues: 1140 loop : -1.26 (0.12), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 115 TYR 0.020 0.002 TYR A 93 PHE 0.028 0.002 PHE I 50 TRP 0.039 0.001 TRP G 89 HIS 0.008 0.001 HIS K 328 Details of bonding type rmsd covalent geometry : bond 0.00463 (35144) covalent geometry : angle 0.69234 (47860) SS BOND : bond 0.00308 ( 65) SS BOND : angle 1.80354 ( 130) hydrogen bonds : bond 0.03752 ( 1151) hydrogen bonds : angle 4.91574 ( 3195) link_BETA1-4 : bond 0.00669 ( 22) link_BETA1-4 : angle 1.69735 ( 66) link_NAG-ASN : bond 0.00364 ( 11) link_NAG-ASN : angle 3.12167 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6457.15 seconds wall clock time: 111 minutes 58.83 seconds (6718.83 seconds total)