Starting phenix.real_space_refine on Tue Aug 26 04:25:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yvy_39616/08_2025/8yvy_39616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yvy_39616/08_2025/8yvy_39616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yvy_39616/08_2025/8yvy_39616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yvy_39616/08_2025/8yvy_39616.map" model { file = "/net/cci-nas-00/data/ceres_data/8yvy_39616/08_2025/8yvy_39616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yvy_39616/08_2025/8yvy_39616.cif" } resolution = 3.02 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= 0.003 sd= 0.049 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: 4 Type Number sf(0) Gaussians S 268 5.16 5 C 21056 2.51 5 N 5748 2.21 5 O 6352 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 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: 33424 Number of models: 1 Model: "" Number of chains: 28 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: 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: "R" 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: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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 Time building chain proxies: 7.29, per 1000 atoms: 0.22 Number of scatterers: 33424 At special positions: 0 Unit cell: (208.44, 157.68, 218.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 268 16.00 O 6352 8.00 N 5748 7.00 C 21056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, 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=2.00 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.06 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.02 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.04 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.02 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=2.02 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.05 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=2.05 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=2.02 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS J 203 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 125 " distance=2.04 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.02 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 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 E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG 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-ASN " NAG E 1 " - " ASN A 141 " " NAG R 1 " - " ASN B 262 " " NAG S 1 " - " ASN B 200 " " NAG T 1 " - " ASN F 141 " " NAG U 1 " - " ASN G 141 " " NAG V 1 " - " ASN H 141 " " NAG W 1 " - " ASN I 262 " " NAG X 1 " - " ASN I 200 " " NAG Y 1 " - " ASN J 262 " " NAG Z 1 " - " ASN J 200 " " NAG a 1 " - " ASN K 262 " " NAG b 1 " - " ASN K 200 " Time building additional restraints: 3.08 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7944 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 91 sheets defined 15.6% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.677A pdb=" N LYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 259 removed outlier: 3.949A pdb=" N GLY A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.961A 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 11 removed outlier: 3.532A pdb=" N LYS B 10 " --> pdb=" O ASN B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 361 removed outlier: 3.534A pdb=" N VAL B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN B 356 " --> pdb=" O HIS B 352 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 401 removed outlier: 3.735A pdb=" N SER B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Proline residue: B 398 - end of helix removed outlier: 3.649A pdb=" N LEU B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.526A 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 41 removed outlier: 3.566A pdb=" N ASP C 41 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 56 removed outlier: 3.694A 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 Processing helix chain 'F' and resid 238 through 246 removed outlier: 3.529A pdb=" N TYR F 242 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.972A pdb=" N GLY F 258 " --> pdb=" O ALA F 255 " (cutoff:3.500A) removed outlier: 3.741A 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 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.573A pdb=" N TYR G 242 " --> pdb=" O SER G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 259 removed outlier: 4.078A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.708A 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 Processing helix chain 'G' and resid 404 through 438 removed outlier: 3.558A pdb=" N ARG G 438 " --> pdb=" O ILE G 434 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 247 removed outlier: 3.649A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.958A pdb=" N GLY H 258 " --> pdb=" O ALA H 255 " (cutoff:3.500A) removed outlier: 3.869A 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 202 through 206 removed outlier: 3.944A pdb=" N THR I 205 " --> pdb=" O THR I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 361 removed outlier: 3.601A pdb=" N VAL I 355 " --> pdb=" O PRO I 351 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN I 356 " --> pdb=" O HIS I 352 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU I 361 " --> pdb=" O TYR I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 397 removed outlier: 4.125A pdb=" N SER I 368 " --> pdb=" O ALA I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 402 removed outlier: 3.829A pdb=" N THR I 402 " --> pdb=" O TYR I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 407 through 414 Processing helix chain 'J' and resid 7 through 12 removed outlier: 3.744A pdb=" N LYS J 10 " --> pdb=" O ASN J 7 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA J 11 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR J 12 " --> pdb=" O TYR J 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 7 through 12' Processing helix chain 'J' and resid 350 through 361 removed outlier: 3.682A pdb=" N VAL J 355 " --> pdb=" O PRO J 351 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN J 356 " --> pdb=" O HIS J 352 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU J 361 " --> pdb=" O TYR J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 397 removed outlier: 4.077A pdb=" N SER J 368 " --> pdb=" O ALA J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 398 through 401 Processing helix chain 'J' and resid 407 through 414 removed outlier: 3.801A pdb=" N ILE J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 11 Processing helix chain 'K' and resid 350 through 361 removed outlier: 3.694A pdb=" N VAL K 355 " --> pdb=" O PRO K 351 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN K 356 " --> pdb=" O HIS K 352 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU K 361 " --> pdb=" O TYR K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 397 removed outlier: 4.104A pdb=" N SER K 368 " --> pdb=" O ALA K 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 398 through 402 removed outlier: 3.537A pdb=" N LEU K 401 " --> pdb=" O PRO K 398 " (cutoff:3.500A) removed outlier: 3.722A 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 removed outlier: 3.507A pdb=" N ILE K 413 " --> pdb=" O TRP K 409 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 31 Processing helix chain 'L' and resid 31 through 41 removed outlier: 3.853A pdb=" N ASP L 41 " --> pdb=" O ARG L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 47 through 56 removed outlier: 3.583A pdb=" N LEU L 51 " --> pdb=" O GLY L 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 31 Processing helix chain 'M' and resid 31 through 42 removed outlier: 3.717A pdb=" N THR M 35 " --> pdb=" O ASN M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 56 removed outlier: 3.523A 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 Processing helix chain 'N' and resid 47 through 55 Processing helix chain 'O' and resid 108 through 119 Processing helix chain 'O' and resid 152 through 157 removed outlier: 3.597A pdb=" N LYS O 157 " --> pdb=" O ALA O 153 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 181 removed outlier: 4.911A pdb=" N SER O 179 " --> pdb=" O HIS O 176 " (cutoff:3.500A) removed outlier: 4.126A 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: 3.551A pdb=" N LYS P 157 " --> pdb=" O ALA P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 181 removed outlier: 5.335A pdb=" N SER P 179 " --> pdb=" O HIS P 176 " (cutoff:3.500A) removed outlier: 3.703A 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 Processing helix chain 'Q' and resid 174 through 181 removed outlier: 4.896A pdb=" N SER Q 179 " --> pdb=" O HIS Q 176 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA Q 181 " --> pdb=" O ARG Q 178 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.851A pdb=" N GLN A 160 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 6.933A pdb=" N MET A 31 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 135 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 33 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 133 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA A 131 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 37 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 129 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA A 127 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA A 119 " --> pdb=" O ILE A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 147 removed outlier: 6.448A pdb=" N ALA A 119 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ILE A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA A 127 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 129 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N SER A 37 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA A 131 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 133 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 33 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL A 135 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET A 31 " --> pdb=" O VAL A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 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 296 through 305 removed outlier: 5.680A pdb=" N ASP A 298 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N LYS A 321 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 315 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AB1, first strand: chain 'A' and resid 331 through 332 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 19 removed outlier: 3.543A pdb=" N CYS B 28 " --> pdb=" O CYS B 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 37 through 38 removed outlier: 10.057A pdb=" N SER B 51 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA B 70 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS B 66 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 37 through 38 removed outlier: 6.299A pdb=" N HIS B 99 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 9.567A pdb=" N ALA B 52 " --> pdb=" O MET B 97 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N MET B 97 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N ILE B 54 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N GLY B 95 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 15.890A pdb=" N ILE B 56 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 18.625A pdb=" N VAL B 93 " --> pdb=" O ILE B 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 84 through 86 removed outlier: 4.169A pdb=" N GLU B 109 " --> pdb=" O TYR B 129 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 149 through 156 Processing sheet with id=AB8, first strand: chain 'B' and resid 175 through 177 removed outlier: 3.757A pdb=" N VAL B 227 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AC1, first strand: chain 'B' and resid 274 through 278 removed outlier: 3.961A pdb=" N GLU B 281 " --> pdb=" O GLY B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 149 through 150 removed outlier: 6.566A pdb=" N PHE D 121 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR D 132 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL D 123 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR D 132 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 256 through 259 removed outlier: 3.549A pdb=" N THR D 244 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE D 207 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY D 191 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE D 223 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 256 through 259 removed outlier: 6.528A pdb=" N VAL D 249 " --> pdb=" O VAL D 234 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL D 234 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N TRP D 251 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA D 232 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 2 through 8 Processing sheet with id=AC6, first strand: chain 'F' and resid 15 through 19 removed outlier: 6.972A pdb=" N MET F 31 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL F 135 " --> pdb=" O MET F 31 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL F 33 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL F 133 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU F 35 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA F 131 " --> pdb=" O GLU F 35 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER F 37 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU F 129 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU F 39 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA F 127 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA F 121 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE F 47 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA F 119 " --> pdb=" O ILE F 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 143 through 147 removed outlier: 6.524A pdb=" N ALA F 119 " --> pdb=" O ILE F 47 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE F 47 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA F 121 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA F 127 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLU F 39 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU F 129 " --> pdb=" O SER F 37 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER F 37 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA F 131 " --> pdb=" O GLU F 35 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU F 35 " --> pdb=" O ALA F 131 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL F 133 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL F 33 " --> pdb=" O VAL F 133 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL F 135 " --> pdb=" O MET F 31 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET F 31 " --> pdb=" O VAL F 135 " (cutoff:3.500A) 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 51 through 54 Processing sheet with id=AD1, first strand: chain 'F' and resid 203 through 204 Processing sheet with id=AD2, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AD3, first strand: chain 'F' and resid 296 through 306 removed outlier: 5.783A pdb=" N ASP F 298 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS F 321 " --> pdb=" O ASP F 298 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL F 315 " --> pdb=" O ALA F 304 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 343 through 344 Processing sheet with id=AD5, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AD6, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AD7, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.460A pdb=" N MET G 31 " --> pdb=" O MET G 136 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU G 35 " --> pdb=" O LYS G 132 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE G 47 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 140 through 147 removed outlier: 3.584A pdb=" N TYR G 137 " --> pdb=" O VAL G 140 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN G 142 " --> pdb=" O VAL G 135 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE G 47 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU G 35 " --> pdb=" O LYS G 132 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG G 134 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL G 33 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET G 136 " --> pdb=" O MET G 31 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N MET G 31 " --> pdb=" O MET G 136 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.618A pdb=" N TYR G 59 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AE2, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AE3, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AE4, first strand: chain 'G' and resid 297 through 306 removed outlier: 7.375A pdb=" N LEU G 299 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N LYS G 321 " --> pdb=" O LEU G 299 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N CYS G 301 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR G 319 " --> pdb=" O CYS G 301 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL G 303 " --> pdb=" O THR G 317 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N THR G 317 " --> pdb=" O VAL G 303 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR G 305 " --> pdb=" O VAL G 315 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AE6, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AE7, first strand: chain 'H' and resid 2 through 8 Processing sheet with id=AE8, first strand: chain 'H' and resid 15 through 19 removed outlier: 7.764A pdb=" N LEU H 29 " --> pdb=" O TYR H 137 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR H 137 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET H 31 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL H 135 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL H 33 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL H 133 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU H 35 " --> pdb=" O ALA H 131 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA H 131 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER H 37 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU H 129 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU H 39 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA H 127 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA H 121 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE H 47 " --> pdb=" O ALA H 119 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA H 119 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 140 through 147 removed outlier: 6.499A pdb=" N ALA H 119 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILE H 47 " --> pdb=" O ALA H 119 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA H 121 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA H 127 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU H 39 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU H 129 " --> pdb=" O SER H 37 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER H 37 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA H 131 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU H 35 " --> pdb=" O ALA H 131 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL H 133 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL H 33 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL H 135 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET H 31 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR H 137 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU H 29 " --> pdb=" O TYR H 137 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AF2, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AF3, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AF4, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AF5, first strand: chain 'H' and resid 296 through 306 removed outlier: 5.675A pdb=" N ASP H 298 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LYS H 321 " --> pdb=" O ASP H 298 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL H 315 " --> pdb=" O ALA H 304 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 326 through 328 Processing sheet with id=AF7, first strand: chain 'H' and resid 330 through 332 Processing sheet with id=AF8, first strand: chain 'H' and resid 387 through 388 Processing sheet with id=AF9, first strand: chain 'I' and resid 17 through 19 Processing sheet with id=AG1, first strand: chain 'I' and resid 37 through 38 removed outlier: 11.793A pdb=" N ILE I 54 " --> pdb=" O ALA I 70 " (cutoff:3.500A) removed outlier: 11.977A pdb=" N ALA I 70 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE I 56 " --> pdb=" O ARG I 68 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 37 through 38 removed outlier: 6.540A pdb=" N HIS I 99 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N ALA I 52 " --> pdb=" O MET I 97 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N MET I 97 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N ILE I 54 " --> pdb=" O GLY I 95 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N GLY I 95 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 15.675A pdb=" N ILE I 56 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 18.620A pdb=" N VAL I 93 " --> pdb=" O ILE I 56 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 84 through 86 removed outlier: 4.141A pdb=" N GLU I 109 " --> pdb=" O TYR I 129 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 151 through 156 Processing sheet with id=AG5, first strand: chain 'I' and resid 175 through 177 removed outlier: 3.644A pdb=" N VAL I 227 " --> pdb=" O ASP I 177 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AG7, first strand: chain 'I' and resid 274 through 277 Processing sheet with id=AG8, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AG9, first strand: chain 'J' and resid 37 through 38 removed outlier: 16.700A pdb=" N GLN J 49 " --> pdb=" O TYR J 69 " (cutoff:3.500A) removed outlier: 13.464A pdb=" N TYR J 69 " --> pdb=" O GLN J 49 " (cutoff:3.500A) removed outlier: 11.338A pdb=" N SER J 51 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 11.632A pdb=" N ILE J 67 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 11.414A pdb=" N GLN J 53 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 9.815A pdb=" N THR J 65 " --> pdb=" O GLN J 53 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY J 55 " --> pdb=" O ASP J 63 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 37 through 38 removed outlier: 6.518A pdb=" N HIS J 99 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N ALA J 52 " --> pdb=" O MET J 97 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N MET J 97 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 9.432A pdb=" N ILE J 54 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N GLY J 95 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 15.778A pdb=" N ILE J 56 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 18.828A pdb=" N VAL J 93 " --> pdb=" O ILE J 56 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 84 through 86 Processing sheet with id=AH3, first strand: chain 'J' and resid 149 through 152 Processing sheet with id=AH4, first strand: chain 'J' and resid 155 through 156 Processing sheet with id=AH5, first strand: chain 'J' and resid 167 through 169 Processing sheet with id=AH6, first strand: chain 'J' and resid 175 through 177 removed outlier: 3.502A pdb=" N THR J 175 " --> pdb=" O VAL J 229 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL J 227 " --> pdb=" O ASP J 177 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 181 through 183 Processing sheet with id=AH8, first strand: chain 'J' and resid 197 through 199 Processing sheet with id=AH9, first strand: chain 'J' and resid 274 through 278 removed outlier: 3.861A pdb=" N GLU J 281 " --> pdb=" O GLY J 278 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AI2, first strand: chain 'K' and resid 46 through 54 removed outlier: 6.565A pdb=" N HIS K 99 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 9.248A pdb=" N ALA K 52 " --> pdb=" O MET K 97 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N MET K 97 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N ILE K 54 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 10.622A pdb=" N GLY K 95 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 66 through 69 Processing sheet with id=AI4, first strand: chain 'K' and resid 84 through 86 removed outlier: 4.193A pdb=" N GLU K 109 " --> pdb=" O TYR K 129 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 149 through 152 Processing sheet with id=AI6, first strand: chain 'K' and resid 155 through 156 Processing sheet with id=AI7, first strand: chain 'K' and resid 175 through 177 removed outlier: 3.690A pdb=" N THR K 175 " --> pdb=" O VAL K 229 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL K 229 " --> pdb=" O THR K 175 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL K 227 " --> pdb=" O ASP K 177 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 182 through 183 Processing sheet with id=AI9, first strand: chain 'K' and resid 198 through 199 removed outlier: 3.643A 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 278 removed outlier: 3.731A pdb=" N GLU K 281 " --> pdb=" O GLY K 278 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'O' and resid 149 through 150 removed outlier: 3.863A pdb=" N GLY O 131 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N HIS O 125 " --> pdb=" O VAL O 129 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N VAL O 129 " --> pdb=" O HIS O 125 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR O 132 " --> pdb=" O PRO O 143 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'O' and resid 256 through 259 removed outlier: 4.936A pdb=" N PHE O 207 " --> pdb=" O LEU O 246 " (cutoff:3.500A) removed outlier: 6.847A 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: 6.593A pdb=" N VAL O 249 " --> pdb=" O VAL O 234 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL O 234 " --> pdb=" O VAL O 249 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N TRP O 251 " --> pdb=" O ALA O 232 " (cutoff:3.500A) removed outlier: 7.909A 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: 4.205A pdb=" N GLY P 131 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N HIS P 125 " --> pdb=" O VAL P 129 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL P 129 " --> pdb=" O HIS P 125 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N TYR P 132 " --> pdb=" O PRO P 143 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N CYS P 134 " --> pdb=" O MET P 141 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'P' and resid 256 through 259 removed outlier: 4.979A pdb=" N PHE P 207 " --> pdb=" O LEU P 246 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA P 232 " --> pdb=" O ILE P 223 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY P 237 " --> pdb=" O GLU P 265 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'P' and resid 256 through 259 removed outlier: 6.021A pdb=" N VAL P 249 " --> pdb=" O VAL P 234 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL P 234 " --> pdb=" O VAL P 249 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N TRP P 251 " --> pdb=" O ALA P 232 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ALA P 232 " --> pdb=" O TRP P 251 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY P 237 " --> pdb=" O GLU P 265 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Q' and resid 149 through 150 removed outlier: 6.406A pdb=" N PHE Q 121 " --> pdb=" O TYR Q 132 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR Q 132 " --> pdb=" O PHE Q 121 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL Q 123 " --> pdb=" O THR Q 130 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N TYR Q 132 " --> pdb=" O PRO Q 143 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Q' and resid 256 through 259 removed outlier: 3.528A pdb=" N THR Q 244 " --> pdb=" O ILE Q 209 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE Q 207 " --> pdb=" O LEU Q 246 " (cutoff:3.500A) removed outlier: 6.952A 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: 6.391A pdb=" N VAL Q 249 " --> pdb=" O VAL Q 234 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL Q 234 " --> pdb=" O VAL Q 249 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N TRP Q 251 " --> pdb=" O ALA Q 232 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA Q 232 " --> pdb=" O TRP Q 251 " (cutoff:3.500A) 1247 hydrogen bonds defined for protein. 3216 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: 7.17 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7874 1.33 - 1.46: 9260 1.46 - 1.58: 16793 1.58 - 1.71: 1 1.71 - 1.84: 364 Bond restraints: 34292 Sorted by residual: bond pdb=" CG1 ILE J 115 " pdb=" CD1 ILE J 115 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.54e+00 bond pdb=" CA CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.64e-02 3.72e+03 6.04e+00 bond pdb=" CA TYR B 9 " pdb=" C TYR B 9 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.80e-02 3.09e+03 5.77e+00 bond pdb=" C1 BMA U 3 " pdb=" C2 BMA U 3 " ideal model delta sigma weight residual 1.519 1.566 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" C1 BMA b 3 " pdb=" C2 BMA b 3 " ideal model delta sigma weight residual 1.519 1.564 -0.045 2.00e-02 2.50e+03 5.09e+00 ... (remaining 34287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 45594 2.71 - 5.41: 982 5.41 - 8.12: 97 8.12 - 10.83: 18 10.83 - 13.54: 13 Bond angle restraints: 46704 Sorted by residual: angle pdb=" C LYS K 104 " pdb=" N CYS K 105 " pdb=" CA CYS K 105 " ideal model delta sigma weight residual 122.90 109.36 13.54 2.07e+00 2.33e-01 4.28e+01 angle pdb=" C THR H 249 " pdb=" CA THR H 249 " pdb=" CB THR H 249 " ideal model delta sigma weight residual 115.79 108.55 7.24 1.19e+00 7.06e-01 3.70e+01 angle pdb=" C PHE K 50 " pdb=" CA PHE K 50 " pdb=" CB PHE K 50 " ideal model delta sigma weight residual 112.99 100.27 12.72 2.10e+00 2.27e-01 3.67e+01 angle pdb=" CA PRO I 363 " pdb=" N PRO I 363 " pdb=" CD PRO I 363 " ideal model delta sigma weight residual 112.00 103.84 8.16 1.40e+00 5.10e-01 3.40e+01 angle pdb=" C THR A 249 " pdb=" CA THR A 249 " pdb=" CB THR A 249 " ideal model delta sigma weight residual 115.79 108.95 6.84 1.19e+00 7.06e-01 3.30e+01 ... (remaining 46699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.05: 19890 23.05 - 46.10: 956 46.10 - 69.15: 101 69.15 - 92.20: 91 92.20 - 115.25: 46 Dihedral angle restraints: 21084 sinusoidal: 8692 harmonic: 12392 Sorted by residual: dihedral pdb=" CB CYS A 306 " pdb=" SG CYS A 306 " pdb=" SG CYS A 380 " pdb=" CB CYS A 380 " ideal model delta sinusoidal sigma weight residual -86.00 -0.89 -85.11 1 1.00e+01 1.00e-02 8.78e+01 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 180.00 135.73 44.27 0 5.00e+00 4.00e-02 7.84e+01 dihedral pdb=" CA VAL A 140 " pdb=" C VAL A 140 " pdb=" N ASN A 141 " pdb=" CA ASN A 141 " ideal model delta harmonic sigma weight residual 180.00 143.01 36.99 0 5.00e+00 4.00e-02 5.47e+01 ... (remaining 21081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 5270 0.216 - 0.432: 24 0.432 - 0.648: 1 0.648 - 0.863: 0 0.863 - 1.079: 1 Chirality restraints: 5296 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.32 -1.08 2.00e-01 2.50e+01 2.91e+01 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN J 262 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" C5 BMA a 3 " pdb=" C4 BMA a 3 " pdb=" C6 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 5293 not shown) Planarity restraints: 6004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 141 " 0.008 2.00e-02 2.50e+03 6.32e-02 4.99e+01 pdb=" CG ASN A 141 " -0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN A 141 " 0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN A 141 " -0.084 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 50 " 0.052 2.00e-02 2.50e+03 4.04e-02 2.85e+01 pdb=" CG PHE K 50 " -0.091 2.00e-02 2.50e+03 pdb=" CD1 PHE K 50 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE K 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE K 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE K 50 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE K 50 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG H 21 " -0.082 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO H 22 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO H 22 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO H 22 " -0.064 5.00e-02 4.00e+02 ... (remaining 6001 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 326 2.63 - 3.20: 28708 3.20 - 3.76: 47306 3.76 - 4.33: 65128 4.33 - 4.90: 112885 Nonbonded interactions: 254353 Sorted by model distance: nonbonded pdb=" OH TYR K 69 " pdb=" OD1 ASP K 117 " model vdw 2.062 3.040 nonbonded pdb=" OG1 THR B 202 " pdb=" OE1 GLN B 224 " model vdw 2.126 3.040 nonbonded pdb=" OG SER J 59 " pdb=" OD1 ASN J 61 " model vdw 2.143 3.040 nonbonded pdb=" OE1 GLU J 166 " pdb=" OH TYR M 49 " model vdw 2.162 3.040 nonbonded pdb=" NZ LYS O 188 " pdb=" OG1 THR O 250 " model vdw 2.171 3.120 ... (remaining 254348 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 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 30.180 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5261 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 : 0.008 0.114 34384 Z= 0.338 Angle : 0.972 18.498 46924 Z= 0.499 Chirality : 0.059 1.079 5296 Planarity : 0.007 0.173 5992 Dihedral : 15.115 115.249 12972 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.95 % Favored : 92.81 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.05 % 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: -1.25 (0.12), residues: 4244 helix: 1.68 (0.22), residues: 564 sheet: -0.72 (0.14), residues: 1296 loop : -1.55 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 199 TYR 0.040 0.003 TYR B 305 PHE 0.091 0.003 PHE K 50 TRP 0.021 0.002 TRP P 195 HIS 0.018 0.003 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00837 (34292) covalent geometry : angle 0.95025 (46704) SS BOND : bond 0.00871 ( 56) SS BOND : angle 2.32267 ( 112) hydrogen bonds : bond 0.14420 ( 1182) hydrogen bonds : angle 6.89039 ( 3216) link_BETA1-4 : bond 0.01245 ( 24) link_BETA1-4 : angle 2.86705 ( 72) link_NAG-ASN : bond 0.00667 ( 12) link_NAG-ASN : angle 5.18391 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 957 time to evaluate : 1.209 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: A 101 THR cc_start: 0.5945 (p) cc_final: 0.5649 (p) REVERT: B 12 THR cc_start: 0.4998 (p) cc_final: 0.4705 (p) REVERT: D 111 MET cc_start: 0.7386 (ptt) cc_final: 0.7163 (ptt) REVERT: D 120 ILE cc_start: 0.8391 (mt) cc_final: 0.8137 (tt) REVERT: D 193 TYR cc_start: 0.6927 (m-80) cc_final: 0.6590 (m-80) REVERT: D 201 GLN cc_start: 0.7281 (mt0) cc_final: 0.6863 (mt0) REVERT: D 207 PHE cc_start: 0.6943 (m-80) cc_final: 0.6687 (m-80) REVERT: D 221 ARG cc_start: 0.7758 (mtt-85) cc_final: 0.7419 (mtp85) REVERT: F 289 ARG cc_start: 0.6866 (mmt180) cc_final: 0.6615 (mtp85) REVERT: G 402 MET cc_start: 0.5185 (ttp) cc_final: 0.4973 (tpt) REVERT: H 287 PHE cc_start: 0.6822 (m-80) cc_final: 0.6542 (m-80) REVERT: H 402 MET cc_start: 0.6786 (mmt) cc_final: 0.6186 (mmt) REVERT: I 199 TYR cc_start: 0.5964 (p90) cc_final: 0.5750 (p90) REVERT: I 210 THR cc_start: 0.8177 (p) cc_final: 0.7902 (m) REVERT: I 340 GLN cc_start: 0.4184 (tt0) cc_final: 0.3518 (tt0) REVERT: K 199 TYR cc_start: 0.5235 (p90) cc_final: 0.5013 (p90) REVERT: L 45 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7540 (mtt-85) REVERT: O 140 VAL cc_start: 0.6918 (t) cc_final: 0.6617 (t) REVERT: O 177 MET cc_start: 0.8294 (mtp) cc_final: 0.7949 (mtt) REVERT: O 183 LYS cc_start: 0.6887 (tppp) cc_final: 0.6648 (mtmt) REVERT: O 258 ARG cc_start: 0.7183 (ttp80) cc_final: 0.6895 (ttp80) REVERT: P 184 TYR cc_start: 0.6320 (p90) cc_final: 0.5872 (p90) REVERT: Q 113 MET cc_start: 0.7416 (tpt) cc_final: 0.6874 (tpt) REVERT: Q 114 LYS cc_start: 0.6828 (pttm) cc_final: 0.6472 (ptpt) REVERT: Q 139 LYS cc_start: 0.3356 (pttm) cc_final: 0.3041 (mtpp) outliers start: 1 outliers final: 0 residues processed: 958 average time/residue: 0.2073 time to fit residues: 316.8723 Evaluate side-chains 560 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS B 49 GLN B 236 GLN B 340 GLN D 176 HIS D 186 HIS F 235 GLN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 ASN H 331 HIS I 53 GLN I 170 HIS I 232 HIS I 255 HIS I 352 HIS J 131 HIS J 287 HIS J 340 GLN ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS K 236 GLN M 53 GLN N 20 GLN Q 125 HIS Q 196 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.185197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124845 restraints weight = 42291.527| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.63 r_work: 0.3371 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 34384 Z= 0.209 Angle : 0.832 12.979 46924 Z= 0.414 Chirality : 0.051 0.416 5296 Planarity : 0.006 0.078 5992 Dihedral : 8.407 56.737 5364 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.23 % Favored : 94.56 % Rotamer: Outliers : 3.34 % Allowed : 10.88 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.99 (0.12), residues: 4244 helix: 2.12 (0.23), residues: 512 sheet: -0.34 (0.14), residues: 1212 loop : -1.46 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 80 TYR 0.031 0.002 TYR J 18 PHE 0.033 0.002 PHE K 50 TRP 0.026 0.002 TRP F 243 HIS 0.012 0.002 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00460 (34292) covalent geometry : angle 0.81069 (46704) SS BOND : bond 0.00847 ( 56) SS BOND : angle 1.43629 ( 112) hydrogen bonds : bond 0.04044 ( 1182) hydrogen bonds : angle 5.55965 ( 3216) link_BETA1-4 : bond 0.01340 ( 24) link_BETA1-4 : angle 4.06849 ( 72) link_NAG-ASN : bond 0.00860 ( 12) link_NAG-ASN : angle 3.22355 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 675 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.6669 (mp0) cc_final: 0.6419 (mt-10) REVERT: A 194 SER cc_start: 0.7852 (t) cc_final: 0.7638 (t) REVERT: A 209 GLU cc_start: 0.6976 (tp30) cc_final: 0.6672 (mm-30) REVERT: D 221 ARG cc_start: 0.7861 (mtt-85) cc_final: 0.7383 (mtp85) REVERT: D 252 ASN cc_start: 0.7400 (m-40) cc_final: 0.7071 (m110) REVERT: F 79 LYS cc_start: 0.7814 (ttmm) cc_final: 0.7460 (tttp) REVERT: F 214 TYR cc_start: 0.7677 (t80) cc_final: 0.7329 (t80) REVERT: F 235 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: F 261 ILE cc_start: 0.7126 (mp) cc_final: 0.6915 (mp) REVERT: G 42 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6315 (mt) REVERT: G 402 MET cc_start: 0.5986 (ttp) cc_final: 0.5511 (tpt) REVERT: H 77 GLN cc_start: 0.7158 (mm-40) cc_final: 0.6759 (mm-40) REVERT: H 99 GLU cc_start: 0.7320 (mp0) cc_final: 0.6866 (tp30) REVERT: H 151 ASP cc_start: 0.6445 (t70) cc_final: 0.6168 (t70) REVERT: H 182 ASP cc_start: 0.6482 (p0) cc_final: 0.6281 (p0) REVERT: H 402 MET cc_start: 0.7112 (mmt) cc_final: 0.6604 (mmt) REVERT: I 61 ASN cc_start: 0.7764 (m-40) cc_final: 0.7526 (m-40) REVERT: I 210 THR cc_start: 0.8325 (p) cc_final: 0.8086 (m) REVERT: I 282 VAL cc_start: 0.7309 (t) cc_final: 0.6986 (t) REVERT: I 344 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: I 399 TYR cc_start: 0.6714 (m-80) cc_final: 0.6508 (t80) REVERT: J 221 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5676 (mp) REVERT: K 97 MET cc_start: 0.5484 (OUTLIER) cc_final: 0.5108 (tpt) REVERT: K 215 MET cc_start: 0.7152 (mmt) cc_final: 0.6759 (mmt) REVERT: K 344 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7441 (pm20) REVERT: L 50 ASP cc_start: 0.7642 (m-30) cc_final: 0.6633 (p0) REVERT: N 8 MET cc_start: 0.5848 (pmm) cc_final: 0.5263 (pmm) REVERT: N 41 ASP cc_start: 0.7955 (m-30) cc_final: 0.7634 (m-30) REVERT: O 111 MET cc_start: 0.7101 (pmm) cc_final: 0.6807 (pmm) REVERT: O 183 LYS cc_start: 0.6923 (tppp) cc_final: 0.6687 (mtpt) REVERT: P 157 LYS cc_start: 0.8423 (ptpp) cc_final: 0.8137 (pttt) REVERT: P 227 LYS cc_start: 0.6535 (mmtm) cc_final: 0.5836 (mtpp) REVERT: Q 113 MET cc_start: 0.7589 (tpt) cc_final: 0.7100 (tpt) REVERT: Q 253 LYS cc_start: 0.7694 (tptp) cc_final: 0.7259 (tppt) REVERT: Q 255 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5300 (mmt) outliers start: 121 outliers final: 67 residues processed: 760 average time/residue: 0.1950 time to fit residues: 242.6826 Evaluate side-chains 575 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 501 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 158 LEU Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 HIS Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 96 CYS Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 358 THR Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 188 ASP Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 353 THR Chi-restraints excluded: chain I residue 170 HIS Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 344 GLU Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 97 MET Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 329 TRP Chi-restraints excluded: chain K residue 333 ASP Chi-restraints excluded: chain K residue 344 GLU Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain Q residue 170 CYS Chi-restraints excluded: chain Q residue 255 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 76 optimal weight: 0.0770 chunk 264 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 154 optimal weight: 8.9990 chunk 208 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 273 optimal weight: 3.9990 chunk 416 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 HIS B 62 HIS B 112 GLN B 232 HIS B 332 ASN D 197 HIS F 275 ASN ** F 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 GLN G 252 ASN H 18 HIS H 43 ASN I 77 ASN I 170 HIS I 226 HIS I 340 GLN J 62 HIS J 77 ASN J 255 HIS ** K 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 131 HIS K 226 HIS K 255 HIS M 42 ASN O 252 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.184232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.122582 restraints weight = 42133.700| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.42 r_work: 0.3364 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 34384 Z= 0.124 Angle : 0.642 13.085 46924 Z= 0.318 Chirality : 0.045 0.343 5296 Planarity : 0.004 0.067 5992 Dihedral : 6.671 55.993 5364 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.07 % Favored : 94.75 % Rotamer: Outliers : 3.43 % Allowed : 13.34 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.73 (0.13), residues: 4244 helix: 2.60 (0.23), residues: 512 sheet: -0.30 (0.14), residues: 1288 loop : -1.30 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 37 TYR 0.020 0.001 TYR A 93 PHE 0.036 0.001 PHE K 50 TRP 0.009 0.001 TRP P 195 HIS 0.038 0.001 HIS D 186 Details of bonding type rmsd covalent geometry : bond 0.00278 (34292) covalent geometry : angle 0.62337 (46704) SS BOND : bond 0.00348 ( 56) SS BOND : angle 1.56387 ( 112) hydrogen bonds : bond 0.03438 ( 1182) hydrogen bonds : angle 4.99556 ( 3216) link_BETA1-4 : bond 0.00919 ( 24) link_BETA1-4 : angle 2.61739 ( 72) link_NAG-ASN : bond 0.00841 ( 12) link_NAG-ASN : angle 3.44521 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 533 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 SER cc_start: 0.8161 (t) cc_final: 0.7911 (t) REVERT: A 228 MET cc_start: 0.6206 (mmm) cc_final: 0.5832 (mtp) REVERT: A 351 LYS cc_start: 0.7519 (tmmt) cc_final: 0.7295 (tmmt) REVERT: B 171 MET cc_start: 0.6522 (ttm) cc_final: 0.6279 (ttm) REVERT: B 232 HIS cc_start: 0.4117 (OUTLIER) cc_final: 0.3812 (t-170) REVERT: C 8 MET cc_start: 0.6522 (mpp) cc_final: 0.6265 (mpp) REVERT: D 221 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7292 (mtp85) REVERT: F 220 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8193 (ttpt) REVERT: F 261 ILE cc_start: 0.7781 (mp) cc_final: 0.7468 (mp) REVERT: F 339 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8538 (mp) REVERT: G 402 MET cc_start: 0.6101 (ttp) cc_final: 0.5745 (tpt) REVERT: H 99 GLU cc_start: 0.7427 (mp0) cc_final: 0.6870 (tp30) REVERT: H 151 ASP cc_start: 0.6647 (t70) cc_final: 0.6348 (t70) REVERT: H 228 MET cc_start: 0.7320 (ttm) cc_final: 0.7105 (ttm) REVERT: H 336 VAL cc_start: 0.8408 (p) cc_final: 0.8127 (p) REVERT: H 402 MET cc_start: 0.7222 (mmt) cc_final: 0.6783 (mmt) REVERT: I 61 ASN cc_start: 0.7507 (m-40) cc_final: 0.7167 (m110) REVERT: I 199 TYR cc_start: 0.5780 (p90) cc_final: 0.5446 (p90) REVERT: I 210 THR cc_start: 0.8124 (p) cc_final: 0.7810 (m) REVERT: I 399 TYR cc_start: 0.6690 (m-80) cc_final: 0.6419 (t80) REVERT: J 299 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.7027 (pp) REVERT: J 361 LEU cc_start: 0.4944 (OUTLIER) cc_final: 0.4702 (pp) REVERT: K 97 MET cc_start: 0.5829 (tpt) cc_final: 0.5568 (tpt) REVERT: K 134 GLN cc_start: 0.6884 (tt0) cc_final: 0.6462 (mm-40) REVERT: K 215 MET cc_start: 0.7203 (mmt) cc_final: 0.6826 (mmt) REVERT: K 329 TRP cc_start: 0.7734 (OUTLIER) cc_final: 0.7201 (t-100) REVERT: L 50 ASP cc_start: 0.7696 (m-30) cc_final: 0.6663 (p0) REVERT: L 53 GLN cc_start: 0.7139 (tp40) cc_final: 0.6895 (tp-100) REVERT: O 157 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7961 (mptt) REVERT: O 183 LYS cc_start: 0.6971 (tppp) cc_final: 0.6764 (mtpt) REVERT: O 253 LYS cc_start: 0.8718 (tmmt) cc_final: 0.8262 (tptt) REVERT: Q 113 MET cc_start: 0.7621 (tpt) cc_final: 0.7148 (tpt) REVERT: Q 114 LYS cc_start: 0.6966 (pttm) cc_final: 0.6515 (ptpt) REVERT: Q 253 LYS cc_start: 0.7730 (tptp) cc_final: 0.7298 (tppt) outliers start: 124 outliers final: 68 residues processed: 613 average time/residue: 0.1799 time to fit residues: 185.5288 Evaluate side-chains 549 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 474 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 32 VAL Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 339 LEU Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 230 HIS Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 366 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 77 ASN Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 344 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 169 MET Chi-restraints excluded: chain J residue 298 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 298 THR Chi-restraints excluded: chain K residue 329 TRP Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 235 LEU Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain Q residue 170 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 45 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 126 optimal weight: 0.0020 chunk 267 optimal weight: 2.9990 chunk 340 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 332 ASN B 352 HIS F 3 HIS G 32 GLN G 187 GLN H 152 HIS H 394 HIS ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 348 HIS J 226 HIS J 255 HIS J 340 GLN J 348 HIS K 53 GLN K 226 HIS K 255 HIS K 285 HIS M 42 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.176456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.111885 restraints weight = 41560.606| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.18 r_work: 0.3220 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.8528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 34384 Z= 0.230 Angle : 0.841 11.506 46924 Z= 0.426 Chirality : 0.052 0.555 5296 Planarity : 0.006 0.068 5992 Dihedral : 6.460 59.911 5364 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.31 % Favored : 93.47 % Rotamer: Outliers : 4.61 % Allowed : 15.22 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -1.09 (0.12), residues: 4244 helix: 2.08 (0.23), residues: 536 sheet: -0.40 (0.15), residues: 1204 loop : -1.59 (0.11), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 244 TYR 0.032 0.002 TYR F 93 PHE 0.057 0.002 PHE K 50 TRP 0.022 0.002 TRP K 329 HIS 0.083 0.003 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00552 (34292) covalent geometry : angle 0.82649 (46704) SS BOND : bond 0.00505 ( 56) SS BOND : angle 1.73118 ( 112) hydrogen bonds : bond 0.04357 ( 1182) hydrogen bonds : angle 5.19654 ( 3216) link_BETA1-4 : bond 0.00919 ( 24) link_BETA1-4 : angle 2.74829 ( 72) link_NAG-ASN : bond 0.01181 ( 12) link_NAG-ASN : angle 3.51382 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 552 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 THR cc_start: 0.8870 (t) cc_final: 0.8625 (m) REVERT: A 220 LYS cc_start: 0.8864 (tttt) cc_final: 0.8560 (tttm) REVERT: B 75 ILE cc_start: 0.8463 (mt) cc_final: 0.8218 (mt) REVERT: B 165 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: B 174 ASP cc_start: 0.8017 (p0) cc_final: 0.7657 (p0) REVERT: B 260 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8900 (mp) REVERT: B 276 ILE cc_start: 0.8781 (mt) cc_final: 0.8500 (mp) REVERT: C 8 MET cc_start: 0.6823 (mpp) cc_final: 0.6451 (mpp) REVERT: D 221 ARG cc_start: 0.7843 (mtt-85) cc_final: 0.7477 (mtp180) REVERT: D 252 ASN cc_start: 0.7802 (m-40) cc_final: 0.7257 (m110) REVERT: F 18 HIS cc_start: 0.9107 (OUTLIER) cc_final: 0.8560 (t-170) REVERT: F 38 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8432 (tt) REVERT: F 93 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.5403 (p90) REVERT: G 246 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8237 (mm-30) REVERT: G 341 GLU cc_start: 0.8390 (pm20) cc_final: 0.8106 (pm20) REVERT: G 362 SER cc_start: 0.8983 (t) cc_final: 0.8645 (m) REVERT: G 402 MET cc_start: 0.6801 (ttp) cc_final: 0.6151 (tpt) REVERT: I 53 GLN cc_start: 0.7938 (pt0) cc_final: 0.7714 (pt0) REVERT: I 61 ASN cc_start: 0.7919 (m-40) cc_final: 0.7593 (m110) REVERT: I 84 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8263 (mttp) REVERT: I 196 LYS cc_start: 0.7641 (ptmt) cc_final: 0.7425 (ttpt) REVERT: I 199 TYR cc_start: 0.6068 (p90) cc_final: 0.5314 (p90) REVERT: I 325 MET cc_start: 0.9104 (tmm) cc_final: 0.8851 (tmm) REVERT: I 356 GLN cc_start: 0.8494 (tt0) cc_final: 0.8254 (tt0) REVERT: I 387 MET cc_start: 0.6924 (mmt) cc_final: 0.6019 (mtp) REVERT: J 53 GLN cc_start: 0.8467 (mt0) cc_final: 0.8152 (mt0) REVERT: J 71 ASP cc_start: 0.7817 (t0) cc_final: 0.7534 (p0) REVERT: J 196 LYS cc_start: 0.7110 (ptmm) cc_final: 0.6857 (ptmm) REVERT: K 53 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7191 (mp-120) REVERT: K 75 ILE cc_start: 0.8268 (pt) cc_final: 0.8035 (mt) REVERT: K 134 GLN cc_start: 0.7869 (tt0) cc_final: 0.7522 (mm-40) REVERT: K 215 MET cc_start: 0.7330 (mmt) cc_final: 0.7112 (mmt) REVERT: K 251 LYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6440 (pttp) REVERT: K 299 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7811 (pp) REVERT: K 302 ASP cc_start: 0.8855 (t0) cc_final: 0.8638 (t0) REVERT: N 8 MET cc_start: 0.6158 (pmm) cc_final: 0.5478 (pmm) REVERT: O 162 LYS cc_start: 0.7230 (tmtt) cc_final: 0.6960 (mtpt) REVERT: P 227 LYS cc_start: 0.7297 (mmtm) cc_final: 0.6607 (mtpp) REVERT: P 253 LYS cc_start: 0.6965 (tptp) cc_final: 0.6719 (pptt) REVERT: Q 111 MET cc_start: 0.6734 (ptp) cc_final: 0.6450 (ptm) REVERT: Q 157 LYS cc_start: 0.8037 (ptpp) cc_final: 0.7821 (ptpp) REVERT: Q 253 LYS cc_start: 0.7822 (tptp) cc_final: 0.7460 (tppt) REVERT: Q 255 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5441 (mmt) outliers start: 167 outliers final: 95 residues processed: 670 average time/residue: 0.1913 time to fit residues: 212.6228 Evaluate side-chains 543 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 438 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain F residue 18 HIS Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 93 TYR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 246 GLU Chi-restraints excluded: chain G residue 259 CYS Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 357 SER Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 229 VAL Chi-restraints excluded: chain H residue 276 ILE Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 353 THR Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 111 LEU Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 344 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain I residue 388 LEU Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 222 ILE Chi-restraints excluded: chain J residue 226 HIS Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 251 LYS Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 168 LEU Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain Q residue 170 CYS Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 255 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 285 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 261 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 379 optimal weight: 9.9990 chunk 212 optimal weight: 5.9990 chunk 365 optimal weight: 5.9990 chunk 288 optimal weight: 0.1980 chunk 361 optimal weight: 8.9990 chunk 152 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN B 49 GLN B 62 HIS B 232 HIS B 255 HIS F 116 HIS F 118 HIS F 394 HIS G 3 HIS H 175 ASN I 120 ASN ** I 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS K 331 ASN M 42 ASN O 176 HIS O 252 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.173119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.108214 restraints weight = 41318.023| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.16 r_work: 0.3168 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.8981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34384 Z= 0.147 Angle : 0.652 14.095 46924 Z= 0.327 Chirality : 0.046 0.346 5296 Planarity : 0.005 0.061 5992 Dihedral : 5.924 56.738 5364 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.04 % Favored : 94.82 % Rotamer: Outliers : 4.17 % Allowed : 17.18 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.88 (0.13), residues: 4244 helix: 2.59 (0.23), residues: 512 sheet: -0.43 (0.14), residues: 1244 loop : -1.40 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 68 TYR 0.022 0.002 TYR I 359 PHE 0.028 0.001 PHE K 50 TRP 0.014 0.001 TRP B 329 HIS 0.026 0.001 HIS J 226 Details of bonding type rmsd covalent geometry : bond 0.00355 (34292) covalent geometry : angle 0.63520 (46704) SS BOND : bond 0.00349 ( 56) SS BOND : angle 1.54882 ( 112) hydrogen bonds : bond 0.03643 ( 1182) hydrogen bonds : angle 4.86449 ( 3216) link_BETA1-4 : bond 0.00887 ( 24) link_BETA1-4 : angle 2.34623 ( 72) link_NAG-ASN : bond 0.00555 ( 12) link_NAG-ASN : angle 3.54377 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 480 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 THR cc_start: 0.8683 (t) cc_final: 0.8459 (m) REVERT: A 99 GLU cc_start: 0.8428 (pm20) cc_final: 0.8145 (pm20) REVERT: B 75 ILE cc_start: 0.8409 (mt) cc_final: 0.8197 (mt) REVERT: B 165 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6521 (mp0) REVERT: B 171 MET cc_start: 0.8500 (ttm) cc_final: 0.8293 (tpp) REVERT: B 174 ASP cc_start: 0.8203 (p0) cc_final: 0.7736 (p0) REVERT: B 215 MET cc_start: 0.7387 (mtm) cc_final: 0.6772 (mtp) REVERT: B 276 ILE cc_start: 0.8718 (mt) cc_final: 0.8499 (mp) REVERT: C 8 MET cc_start: 0.7011 (mpp) cc_final: 0.6646 (mpp) REVERT: D 113 MET cc_start: 0.8364 (mmm) cc_final: 0.7677 (mmm) REVERT: D 221 ARG cc_start: 0.7795 (mtt-85) cc_final: 0.6885 (mtp180) REVERT: D 252 ASN cc_start: 0.7774 (m-40) cc_final: 0.7276 (m110) REVERT: F 38 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8317 (tt) REVERT: F 117 ASP cc_start: 0.8352 (m-30) cc_final: 0.7851 (t0) REVERT: F 220 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8391 (ttmt) REVERT: F 402 MET cc_start: 0.7905 (tpt) cc_final: 0.6849 (mmm) REVERT: G 228 MET cc_start: 0.8779 (mtp) cc_final: 0.8450 (ttm) REVERT: G 341 GLU cc_start: 0.8273 (pm20) cc_final: 0.7945 (pm20) REVERT: G 362 SER cc_start: 0.8912 (t) cc_final: 0.8589 (m) REVERT: G 402 MET cc_start: 0.7136 (ttp) cc_final: 0.6509 (tpt) REVERT: H 79 LYS cc_start: 0.8327 (tttm) cc_final: 0.8013 (ttmm) REVERT: H 339 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9035 (mp) REVERT: I 53 GLN cc_start: 0.7880 (pt0) cc_final: 0.7676 (pt0) REVERT: I 61 ASN cc_start: 0.7758 (m-40) cc_final: 0.7480 (m-40) REVERT: I 84 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8189 (mttp) REVERT: I 199 TYR cc_start: 0.6063 (p90) cc_final: 0.5322 (p90) REVERT: I 325 MET cc_start: 0.9152 (tmm) cc_final: 0.8863 (tmm) REVERT: J 53 GLN cc_start: 0.8516 (mt0) cc_final: 0.8292 (mt0) REVERT: J 71 ASP cc_start: 0.7860 (t0) cc_final: 0.7432 (p0) REVERT: J 196 LYS cc_start: 0.6998 (ptmm) cc_final: 0.6757 (pttp) REVERT: J 289 ASP cc_start: 0.8330 (m-30) cc_final: 0.8110 (m-30) REVERT: K 90 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: K 134 GLN cc_start: 0.7870 (tt0) cc_final: 0.7531 (mm-40) REVERT: K 169 MET cc_start: 0.8025 (mtt) cc_final: 0.7537 (mtt) REVERT: K 215 MET cc_start: 0.7303 (mmt) cc_final: 0.7103 (mmt) REVERT: N 8 MET cc_start: 0.6055 (pmm) cc_final: 0.5356 (pmm) REVERT: O 157 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7857 (mptt) REVERT: O 253 LYS cc_start: 0.8759 (tmmt) cc_final: 0.8237 (tptt) REVERT: Q 157 LYS cc_start: 0.7943 (ptpp) cc_final: 0.7704 (pttm) REVERT: Q 253 LYS cc_start: 0.7728 (tptp) cc_final: 0.7377 (tppt) REVERT: Q 255 MET cc_start: 0.5891 (mmt) cc_final: 0.5551 (mmt) outliers start: 151 outliers final: 96 residues processed: 587 average time/residue: 0.1903 time to fit residues: 185.9477 Evaluate side-chains 532 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 430 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 281 ASN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 260 GLN Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 276 ILE Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 GLN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 344 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 222 ILE Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain Q residue 170 CYS Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 379 optimal weight: 10.0000 chunk 373 optimal weight: 40.0000 chunk 164 optimal weight: 8.9990 chunk 326 optimal weight: 0.9990 chunk 406 optimal weight: 0.0870 chunk 313 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 317 optimal weight: 2.9990 chunk 309 optimal weight: 10.0000 chunk 397 optimal weight: 50.0000 chunk 50 optimal weight: 2.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 212 ASN B 224 GLN B 232 HIS B 255 HIS ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN ** H 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 GLN I 331 ASN J 62 HIS ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS M 42 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 = 0.3985 r_free = 0.3985 target = 0.169539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117106 restraints weight = 40390.719| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.31 r_work: 0.3071 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.9636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 34384 Z= 0.187 Angle : 0.699 12.203 46924 Z= 0.350 Chirality : 0.047 0.266 5296 Planarity : 0.005 0.060 5992 Dihedral : 5.906 57.754 5364 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.08 % Favored : 93.80 % Rotamer: Outliers : 4.81 % Allowed : 16.57 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.97 (0.12), residues: 4244 helix: 2.55 (0.23), residues: 516 sheet: -0.49 (0.14), residues: 1228 loop : -1.47 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 119 TYR 0.031 0.002 TYR F 93 PHE 0.041 0.002 PHE K 50 TRP 0.015 0.001 TRP K 235 HIS 0.011 0.002 HIS J 226 Details of bonding type rmsd covalent geometry : bond 0.00470 (34292) covalent geometry : angle 0.68284 (46704) SS BOND : bond 0.00580 ( 56) SS BOND : angle 1.59139 ( 112) hydrogen bonds : bond 0.03917 ( 1182) hydrogen bonds : angle 4.88634 ( 3216) link_BETA1-4 : bond 0.00862 ( 24) link_BETA1-4 : angle 2.38735 ( 72) link_NAG-ASN : bond 0.00624 ( 12) link_NAG-ASN : angle 3.50742 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 436 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 THR cc_start: 0.8891 (m) cc_final: 0.8681 (m) REVERT: B 101 ILE cc_start: 0.8745 (tt) cc_final: 0.8418 (mt) REVERT: B 165 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: B 196 LYS cc_start: 0.7397 (ptmm) cc_final: 0.7145 (pttm) REVERT: B 215 MET cc_start: 0.7328 (mtm) cc_final: 0.6900 (mtp) REVERT: B 251 LYS cc_start: 0.7035 (mmtp) cc_final: 0.6704 (mtpp) REVERT: B 284 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8690 (mp) REVERT: D 113 MET cc_start: 0.8375 (mmm) cc_final: 0.7667 (mmm) REVERT: D 141 MET cc_start: 0.8294 (ptp) cc_final: 0.8052 (ptp) REVERT: D 169 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7159 (mt-10) REVERT: F 117 ASP cc_start: 0.8530 (m-30) cc_final: 0.8155 (t0) REVERT: F 347 LYS cc_start: 0.7196 (mtmm) cc_final: 0.6914 (mttm) REVERT: G 228 MET cc_start: 0.9085 (mtp) cc_final: 0.8813 (ttm) REVERT: G 287 PHE cc_start: 0.8526 (m-80) cc_final: 0.8239 (m-80) REVERT: G 362 SER cc_start: 0.9120 (t) cc_final: 0.8802 (m) REVERT: G 402 MET cc_start: 0.7470 (ttp) cc_final: 0.6848 (tpt) REVERT: H 79 LYS cc_start: 0.8497 (tttm) cc_final: 0.8239 (ttmm) REVERT: H 339 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9215 (mp) REVERT: H 340 GLN cc_start: 0.9105 (OUTLIER) cc_final: 0.8408 (tt0) REVERT: H 402 MET cc_start: 0.7900 (tpt) cc_final: 0.7485 (tpt) REVERT: I 61 ASN cc_start: 0.7950 (m-40) cc_final: 0.7706 (m-40) REVERT: I 75 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8559 (mp) REVERT: I 199 TYR cc_start: 0.6171 (p90) cc_final: 0.5606 (p90) REVERT: J 38 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8378 (mtt90) REVERT: J 71 ASP cc_start: 0.8058 (t0) cc_final: 0.7602 (p0) REVERT: J 196 LYS cc_start: 0.7197 (ptmm) cc_final: 0.6964 (ptmm) REVERT: K 75 ILE cc_start: 0.8577 (pt) cc_final: 0.8361 (mt) REVERT: K 169 MET cc_start: 0.8291 (mtt) cc_final: 0.7926 (mtt) REVERT: K 301 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8738 (tt0) REVERT: N 8 MET cc_start: 0.6261 (pmm) cc_final: 0.5539 (pmm) REVERT: O 253 LYS cc_start: 0.8763 (tmmt) cc_final: 0.8252 (tptt) REVERT: P 227 LYS cc_start: 0.7419 (mmtm) cc_final: 0.6884 (mtpp) REVERT: Q 114 LYS cc_start: 0.6825 (pttm) cc_final: 0.6432 (ptpt) REVERT: Q 157 LYS cc_start: 0.7901 (ptpp) cc_final: 0.7634 (pttm) REVERT: Q 253 LYS cc_start: 0.7773 (tptp) cc_final: 0.7461 (tppt) REVERT: Q 255 MET cc_start: 0.6142 (mmt) cc_final: 0.5587 (mmt) outliers start: 174 outliers final: 133 residues processed: 568 average time/residue: 0.1909 time to fit residues: 180.4685 Evaluate side-chains 546 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 408 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 305 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 62 CYS Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 259 CYS Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 387 ILE Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 155 THR Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 276 ILE Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 340 GLN Chi-restraints excluded: chain H residue 353 THR Chi-restraints excluded: chain H residue 375 THR Chi-restraints excluded: chain I residue 40 GLU Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 305 TYR Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 344 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 222 ILE Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain Q residue 170 CYS Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 199 optimal weight: 1.9990 chunk 345 optimal weight: 4.9990 chunk 318 optimal weight: 0.7980 chunk 311 optimal weight: 10.0000 chunk 407 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 343 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 53 GLN B 212 ASN B 226 HIS B 232 HIS G 9 ASN H 139 ASN H 175 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS M 42 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.175014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.110829 restraints weight = 40770.303| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.41 r_work: 0.3161 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.9805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34384 Z= 0.119 Angle : 0.614 10.448 46924 Z= 0.308 Chirality : 0.045 0.283 5296 Planarity : 0.004 0.056 5992 Dihedral : 5.673 56.709 5364 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.70 % Rotamer: Outliers : 4.03 % Allowed : 17.96 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.85 (0.13), residues: 4244 helix: 2.85 (0.23), residues: 512 sheet: -0.39 (0.14), residues: 1224 loop : -1.44 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 13 TYR 0.018 0.001 TYR F 93 PHE 0.026 0.001 PHE K 50 TRP 0.009 0.001 TRP B 329 HIS 0.008 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00282 (34292) covalent geometry : angle 0.59957 (46704) SS BOND : bond 0.00287 ( 56) SS BOND : angle 1.38708 ( 112) hydrogen bonds : bond 0.03365 ( 1182) hydrogen bonds : angle 4.70489 ( 3216) link_BETA1-4 : bond 0.00871 ( 24) link_BETA1-4 : angle 2.24901 ( 72) link_NAG-ASN : bond 0.00483 ( 12) link_NAG-ASN : angle 3.02793 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 428 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 THR cc_start: 0.8902 (m) cc_final: 0.8686 (m) REVERT: B 101 ILE cc_start: 0.8700 (tt) cc_final: 0.8312 (mt) REVERT: B 111 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8572 (tt) REVERT: B 165 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: B 196 LYS cc_start: 0.7534 (ptmm) cc_final: 0.7299 (pttm) REVERT: B 215 MET cc_start: 0.7378 (mtm) cc_final: 0.6917 (mtp) REVERT: B 224 GLN cc_start: 0.7759 (mt0) cc_final: 0.7530 (mt0) REVERT: B 251 LYS cc_start: 0.6924 (mmtp) cc_final: 0.6674 (mtpp) REVERT: D 113 MET cc_start: 0.8340 (mmm) cc_final: 0.7795 (mmm) REVERT: D 114 LYS cc_start: 0.8156 (ptmt) cc_final: 0.7915 (ptmm) REVERT: F 117 ASP cc_start: 0.8401 (m-30) cc_final: 0.8126 (t0) REVERT: F 347 LYS cc_start: 0.7329 (mtmm) cc_final: 0.7056 (mttm) REVERT: G 228 MET cc_start: 0.8978 (mtp) cc_final: 0.8698 (ttm) REVERT: G 362 SER cc_start: 0.9131 (t) cc_final: 0.8847 (m) REVERT: G 402 MET cc_start: 0.7488 (ttp) cc_final: 0.6935 (tpt) REVERT: H 31 MET cc_start: 0.8967 (mtm) cc_final: 0.8696 (mtm) REVERT: H 79 LYS cc_start: 0.8478 (tttm) cc_final: 0.8238 (ttmm) REVERT: H 84 VAL cc_start: 0.9299 (t) cc_final: 0.8937 (m) REVERT: H 339 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9189 (mp) REVERT: H 340 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: I 61 ASN cc_start: 0.7994 (m-40) cc_final: 0.7768 (m-40) REVERT: I 75 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8533 (mp) REVERT: I 175 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8201 (p) REVERT: I 199 TYR cc_start: 0.6212 (p90) cc_final: 0.5675 (p90) REVERT: I 224 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6366 (mt0) REVERT: J 71 ASP cc_start: 0.8004 (t0) cc_final: 0.7605 (p0) REVERT: J 196 LYS cc_start: 0.7190 (ptmm) cc_final: 0.6967 (ptmm) REVERT: J 221 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.6017 (mp) REVERT: K 169 MET cc_start: 0.8302 (mtt) cc_final: 0.7869 (mtt) REVERT: K 215 MET cc_start: 0.7159 (mmt) cc_final: 0.6930 (mmm) REVERT: K 301 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8713 (tt0) REVERT: L 50 ASP cc_start: 0.8249 (m-30) cc_final: 0.8038 (m-30) REVERT: N 8 MET cc_start: 0.6178 (pmm) cc_final: 0.5400 (pmm) REVERT: O 253 LYS cc_start: 0.8785 (tmmt) cc_final: 0.8251 (tptt) REVERT: P 227 LYS cc_start: 0.7420 (mmtm) cc_final: 0.6815 (mtpp) REVERT: P 253 LYS cc_start: 0.6772 (tptp) cc_final: 0.6551 (pptt) REVERT: Q 114 LYS cc_start: 0.7091 (pttm) cc_final: 0.6562 (ptpt) REVERT: Q 157 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7699 (pttm) REVERT: Q 253 LYS cc_start: 0.7754 (tptp) cc_final: 0.7460 (tppt) REVERT: Q 255 MET cc_start: 0.6133 (mmt) cc_final: 0.5545 (mmt) outliers start: 146 outliers final: 109 residues processed: 532 average time/residue: 0.1963 time to fit residues: 174.7966 Evaluate side-chains 530 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 413 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 100 ASN Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 296 ILE Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 379 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 276 ILE Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 340 GLN Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 GLN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 344 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 222 ILE Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 318 ILE Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 65 optimal weight: 8.9990 chunk 312 optimal weight: 10.0000 chunk 315 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 229 optimal weight: 0.0170 chunk 175 optimal weight: 5.9990 chunk 354 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 325 optimal weight: 7.9990 overall best weight: 1.7822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN B 212 ASN B 232 HIS D 196 HIS ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 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 = 0.4050 r_free = 0.4050 target = 0.173078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121175 restraints weight = 40452.164| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.32 r_work: 0.3151 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.9998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34384 Z= 0.135 Angle : 0.631 10.113 46924 Z= 0.315 Chirality : 0.045 0.291 5296 Planarity : 0.004 0.054 5992 Dihedral : 5.603 56.770 5364 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 4.01 % Allowed : 18.12 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.79 (0.13), residues: 4244 helix: 2.90 (0.23), residues: 512 sheet: -0.35 (0.14), residues: 1224 loop : -1.41 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 13 TYR 0.021 0.001 TYR F 93 PHE 0.028 0.001 PHE K 50 TRP 0.011 0.001 TRP K 235 HIS 0.007 0.001 HIS Q 125 Details of bonding type rmsd covalent geometry : bond 0.00330 (34292) covalent geometry : angle 0.61600 (46704) SS BOND : bond 0.00311 ( 56) SS BOND : angle 1.52173 ( 112) hydrogen bonds : bond 0.03379 ( 1182) hydrogen bonds : angle 4.66915 ( 3216) link_BETA1-4 : bond 0.00849 ( 24) link_BETA1-4 : angle 2.26017 ( 72) link_NAG-ASN : bond 0.00436 ( 12) link_NAG-ASN : angle 2.96312 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 418 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.7585 (t80) cc_final: 0.7322 (t80) REVERT: B 101 ILE cc_start: 0.8687 (tt) cc_final: 0.8271 (mt) REVERT: B 165 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: B 196 LYS cc_start: 0.7616 (ptmm) cc_final: 0.7382 (pttm) REVERT: B 215 MET cc_start: 0.7349 (mtm) cc_final: 0.6926 (mtp) REVERT: B 251 LYS cc_start: 0.7150 (mmtp) cc_final: 0.6839 (mtpp) REVERT: B 387 MET cc_start: 0.7182 (mtt) cc_final: 0.6901 (mtp) REVERT: D 114 LYS cc_start: 0.8146 (ptmt) cc_final: 0.7927 (ptmm) REVERT: F 31 MET cc_start: 0.9048 (mtm) cc_final: 0.8644 (mtm) REVERT: F 38 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8573 (tt) REVERT: F 117 ASP cc_start: 0.8454 (m-30) cc_final: 0.8191 (t0) REVERT: F 245 LYS cc_start: 0.8979 (ttmm) cc_final: 0.8547 (mtmt) REVERT: F 347 LYS cc_start: 0.7441 (mtmm) cc_final: 0.7143 (mttm) REVERT: G 228 MET cc_start: 0.9011 (mtp) cc_final: 0.8730 (ttm) REVERT: G 362 SER cc_start: 0.9143 (t) cc_final: 0.8878 (m) REVERT: G 402 MET cc_start: 0.7523 (ttp) cc_final: 0.6934 (tpt) REVERT: H 31 MET cc_start: 0.9040 (mtm) cc_final: 0.8745 (mtm) REVERT: H 79 LYS cc_start: 0.8480 (tttm) cc_final: 0.8258 (ttmm) REVERT: H 84 VAL cc_start: 0.9282 (t) cc_final: 0.8938 (m) REVERT: H 339 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9191 (mp) REVERT: H 340 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: I 53 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8062 (mt0) REVERT: I 61 ASN cc_start: 0.8072 (m-40) cc_final: 0.7824 (m-40) REVERT: I 75 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8494 (mp) REVERT: I 175 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8246 (p) REVERT: I 199 TYR cc_start: 0.6058 (p90) cc_final: 0.5567 (p90) REVERT: J 71 ASP cc_start: 0.8064 (t0) cc_final: 0.7569 (p0) REVERT: J 196 LYS cc_start: 0.7211 (ptmm) cc_final: 0.6982 (ptmm) REVERT: J 221 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.6033 (mp) REVERT: K 169 MET cc_start: 0.8328 (mtt) cc_final: 0.7973 (mtt) REVERT: K 215 MET cc_start: 0.7248 (mmt) cc_final: 0.7028 (mmm) REVERT: K 283 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8867 (m) REVERT: K 301 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8726 (tt0) REVERT: K 356 GLN cc_start: 0.8775 (tt0) cc_final: 0.8202 (mt0) REVERT: L 50 ASP cc_start: 0.8220 (m-30) cc_final: 0.8020 (m-30) REVERT: N 8 MET cc_start: 0.6143 (pmm) cc_final: 0.5600 (pmm) REVERT: P 227 LYS cc_start: 0.7531 (mmtm) cc_final: 0.6968 (mtpp) REVERT: P 253 LYS cc_start: 0.6827 (tptp) cc_final: 0.6558 (pptt) REVERT: Q 157 LYS cc_start: 0.7923 (ptpp) cc_final: 0.7671 (pttm) REVERT: Q 253 LYS cc_start: 0.7766 (tptp) cc_final: 0.7456 (tppt) REVERT: Q 255 MET cc_start: 0.6127 (mmt) cc_final: 0.5555 (mmt) outliers start: 145 outliers final: 116 residues processed: 525 average time/residue: 0.1775 time to fit residues: 155.5379 Evaluate side-chains 536 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 411 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 39 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 164 SER Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 280 MET Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 295 THR Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain G residue 425 ILE Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 276 ILE Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 302 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 340 GLN Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 290 HIS Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 326 GLU Chi-restraints excluded: chain I residue 344 GLU Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 175 THR Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 222 ILE Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 322 VAL Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 26 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 383 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 373 optimal weight: 30.0000 chunk 360 optimal weight: 0.0020 chunk 229 optimal weight: 0.0040 chunk 210 optimal weight: 0.9980 chunk 219 optimal weight: 9.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 139 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 255 HIS K 226 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 = 0.4047 r_free = 0.4047 target = 0.173517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.109297 restraints weight = 40817.374| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.39 r_work: 0.3187 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 1.0071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34384 Z= 0.099 Angle : 0.585 9.720 46924 Z= 0.293 Chirality : 0.044 0.283 5296 Planarity : 0.004 0.056 5992 Dihedral : 5.411 56.469 5364 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.23 % Favored : 94.67 % Rotamer: Outliers : 3.45 % Allowed : 18.78 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.58 (0.13), residues: 4244 helix: 3.00 (0.23), residues: 512 sheet: -0.27 (0.14), residues: 1356 loop : -1.25 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 13 TYR 0.017 0.001 TYR K 64 PHE 0.023 0.001 PHE K 50 TRP 0.011 0.001 TRP B 235 HIS 0.018 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00222 (34292) covalent geometry : angle 0.57172 (46704) SS BOND : bond 0.00214 ( 56) SS BOND : angle 1.36741 ( 112) hydrogen bonds : bond 0.03003 ( 1182) hydrogen bonds : angle 4.53425 ( 3216) link_BETA1-4 : bond 0.00853 ( 24) link_BETA1-4 : angle 2.16957 ( 72) link_NAG-ASN : bond 0.00425 ( 12) link_NAG-ASN : angle 2.67227 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 438 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LYS cc_start: 0.8257 (tppt) cc_final: 0.8039 (tppt) REVERT: B 165 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: B 196 LYS cc_start: 0.7616 (ptmm) cc_final: 0.7390 (pttm) REVERT: B 215 MET cc_start: 0.7388 (mtm) cc_final: 0.7143 (mtp) REVERT: B 232 HIS cc_start: 0.8482 (OUTLIER) cc_final: 0.8267 (t-170) REVERT: B 251 LYS cc_start: 0.7050 (mmtp) cc_final: 0.6765 (mtpp) REVERT: B 387 MET cc_start: 0.7200 (mtt) cc_final: 0.6911 (mtp) REVERT: C 33 GLU cc_start: 0.7334 (tp30) cc_final: 0.7108 (mp0) REVERT: D 113 MET cc_start: 0.8118 (mmm) cc_final: 0.7451 (mmm) REVERT: F 38 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8540 (tt) REVERT: F 117 ASP cc_start: 0.8369 (m-30) cc_final: 0.8131 (t0) REVERT: F 245 LYS cc_start: 0.9037 (ttmm) cc_final: 0.8560 (mtmt) REVERT: F 347 LYS cc_start: 0.7447 (mtmm) cc_final: 0.7151 (mttm) REVERT: G 162 ILE cc_start: 0.8106 (mm) cc_final: 0.7832 (mm) REVERT: G 228 MET cc_start: 0.8916 (mtp) cc_final: 0.8631 (ttm) REVERT: G 321 LYS cc_start: 0.7853 (ttmt) cc_final: 0.7565 (mttt) REVERT: G 362 SER cc_start: 0.9118 (t) cc_final: 0.8847 (m) REVERT: G 402 MET cc_start: 0.7453 (ttp) cc_final: 0.6909 (tpt) REVERT: H 31 MET cc_start: 0.9007 (mtm) cc_final: 0.8716 (mtm) REVERT: H 79 LYS cc_start: 0.8432 (tttm) cc_final: 0.8191 (ttmm) REVERT: H 84 VAL cc_start: 0.9276 (t) cc_final: 0.8981 (m) REVERT: H 339 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9132 (mp) REVERT: H 340 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: I 53 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7771 (mt0) REVERT: I 61 ASN cc_start: 0.8065 (m-40) cc_final: 0.7793 (m-40) REVERT: I 175 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8283 (p) REVERT: I 197 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7474 (t) REVERT: I 199 TYR cc_start: 0.6056 (p90) cc_final: 0.5594 (p90) REVERT: I 223 GLU cc_start: 0.8105 (pm20) cc_final: 0.7891 (pm20) REVERT: I 224 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6345 (mt0) REVERT: I 281 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8585 (tt0) REVERT: J 13 ARG cc_start: 0.8790 (ptt90) cc_final: 0.8386 (ptm-80) REVERT: J 71 ASP cc_start: 0.7985 (t0) cc_final: 0.7519 (p0) REVERT: J 196 LYS cc_start: 0.7214 (ptmm) cc_final: 0.6966 (ptmm) REVERT: J 251 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8329 (pmtt) REVERT: K 169 MET cc_start: 0.8259 (mtt) cc_final: 0.7944 (mtt) REVERT: K 283 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8837 (m) REVERT: K 301 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8688 (tt0) REVERT: K 356 GLN cc_start: 0.8771 (tt0) cc_final: 0.8217 (mt0) REVERT: L 50 ASP cc_start: 0.8213 (m-30) cc_final: 0.8012 (m-30) REVERT: N 8 MET cc_start: 0.6141 (pmm) cc_final: 0.5607 (pmm) REVERT: P 227 LYS cc_start: 0.7579 (mmtm) cc_final: 0.7018 (mtpp) REVERT: P 253 LYS cc_start: 0.6898 (tptp) cc_final: 0.6640 (pptt) REVERT: Q 157 LYS cc_start: 0.7958 (ptpp) cc_final: 0.7696 (pttm) REVERT: Q 253 LYS cc_start: 0.7752 (tptp) cc_final: 0.7457 (tppt) REVERT: Q 255 MET cc_start: 0.6155 (mmt) cc_final: 0.5582 (mmt) outliers start: 125 outliers final: 91 residues processed: 522 average time/residue: 0.1846 time to fit residues: 160.2082 Evaluate side-chains 520 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 417 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 296 ILE Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 271 CYS Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 276 ILE Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 340 GLN Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 224 GLN Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 222 ILE Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 251 LYS Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain K residue 362 TYR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain Q residue 175 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 76 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 403 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 125 optimal weight: 0.0020 chunk 258 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 overall best weight: 2.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 232 HIS F 411 GLN ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS J 120 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 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 = 0.4026 r_free = 0.4026 target = 0.171160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.106445 restraints weight = 40541.413| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.33 r_work: 0.3109 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 1.0324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34384 Z= 0.177 Angle : 0.685 10.367 46924 Z= 0.343 Chirality : 0.047 0.307 5296 Planarity : 0.005 0.055 5992 Dihedral : 5.641 57.024 5364 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.06 % Favored : 93.87 % Rotamer: Outliers : 3.34 % Allowed : 18.87 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: 4244 helix: 2.86 (0.23), residues: 512 sheet: -0.35 (0.15), residues: 1184 loop : -1.34 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 13 TYR 0.025 0.002 TYR F 93 PHE 0.038 0.002 PHE K 50 TRP 0.014 0.001 TRP K 235 HIS 0.007 0.001 HIS F 308 Details of bonding type rmsd covalent geometry : bond 0.00447 (34292) covalent geometry : angle 0.66917 (46704) SS BOND : bond 0.00359 ( 56) SS BOND : angle 1.84344 ( 112) hydrogen bonds : bond 0.03664 ( 1182) hydrogen bonds : angle 4.75129 ( 3216) link_BETA1-4 : bond 0.00873 ( 24) link_BETA1-4 : angle 2.28371 ( 72) link_NAG-ASN : bond 0.00463 ( 12) link_NAG-ASN : angle 3.13202 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8488 Ramachandran restraints generated. 4244 Oldfield, 0 Emsley, 4244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 418 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.8995 (mtp) cc_final: 0.8761 (ttm) REVERT: B 165 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: B 196 LYS cc_start: 0.7676 (ptmm) cc_final: 0.7455 (pttm) REVERT: B 251 LYS cc_start: 0.7481 (mmtp) cc_final: 0.7174 (mtpp) REVERT: B 387 MET cc_start: 0.7236 (mtt) cc_final: 0.6938 (mtp) REVERT: D 114 LYS cc_start: 0.8171 (ptmt) cc_final: 0.7967 (ptmm) REVERT: G 228 MET cc_start: 0.9148 (mtp) cc_final: 0.8897 (ttm) REVERT: G 362 SER cc_start: 0.9184 (t) cc_final: 0.8981 (m) REVERT: G 402 MET cc_start: 0.7612 (ttp) cc_final: 0.7028 (tpt) REVERT: H 31 MET cc_start: 0.9112 (mtm) cc_final: 0.8877 (mtm) REVERT: H 79 LYS cc_start: 0.8564 (tttm) cc_final: 0.8317 (ttmm) REVERT: H 84 VAL cc_start: 0.9318 (t) cc_final: 0.8975 (m) REVERT: H 339 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9206 (mp) REVERT: H 340 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: H 399 PHE cc_start: 0.9072 (t80) cc_final: 0.8867 (t80) REVERT: I 53 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8327 (mt0) REVERT: I 61 ASN cc_start: 0.8127 (m-40) cc_final: 0.7892 (m-40) REVERT: I 175 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8300 (p) REVERT: I 199 TYR cc_start: 0.6217 (p90) cc_final: 0.5703 (p90) REVERT: I 246 ASP cc_start: 0.8188 (p0) cc_final: 0.7827 (p0) REVERT: J 71 ASP cc_start: 0.8067 (t0) cc_final: 0.7484 (p0) REVERT: J 196 LYS cc_start: 0.7313 (ptmm) cc_final: 0.7072 (ptmm) REVERT: J 354 ILE cc_start: 0.8156 (mm) cc_final: 0.7948 (mt) REVERT: K 169 MET cc_start: 0.8475 (mtt) cc_final: 0.8261 (mtt) REVERT: K 196 LYS cc_start: 0.7145 (ptmm) cc_final: 0.6939 (ptpt) REVERT: K 283 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8917 (m) REVERT: K 301 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8660 (tt0) REVERT: K 356 GLN cc_start: 0.8839 (tt0) cc_final: 0.8315 (mt0) REVERT: L 50 ASP cc_start: 0.8207 (m-30) cc_final: 0.7996 (m-30) REVERT: N 8 MET cc_start: 0.6333 (pmm) cc_final: 0.5797 (pmm) REVERT: O 253 LYS cc_start: 0.8868 (tmmt) cc_final: 0.8259 (tptt) REVERT: P 227 LYS cc_start: 0.7682 (mmtm) cc_final: 0.7072 (mtpp) REVERT: P 253 LYS cc_start: 0.6968 (tptp) cc_final: 0.6668 (pptt) REVERT: Q 157 LYS cc_start: 0.7956 (ptpp) cc_final: 0.7691 (pttm) REVERT: Q 253 LYS cc_start: 0.7746 (tptp) cc_final: 0.7459 (tppt) REVERT: Q 255 MET cc_start: 0.6034 (mmt) cc_final: 0.5237 (mmt) outliers start: 121 outliers final: 101 residues processed: 503 average time/residue: 0.2179 time to fit residues: 180.4975 Evaluate side-chains 510 residues out of total 3620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 403 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 62 CYS Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 165 GLU Chi-restraints excluded: chain B residue 201 CYS Chi-restraints excluded: chain B residue 232 HIS Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 GLU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain C residue 9 CYS Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 247 SER Chi-restraints excluded: chain D residue 255 MET Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 68 CYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 271 CYS Chi-restraints excluded: chain F residue 296 ILE Chi-restraints excluded: chain F residue 366 VAL Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 88 MET Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 297 ILE Chi-restraints excluded: chain G residue 305 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain H residue 68 CYS Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 276 ILE Chi-restraints excluded: chain H residue 295 THR Chi-restraints excluded: chain H residue 339 LEU Chi-restraints excluded: chain H residue 340 GLN Chi-restraints excluded: chain H residue 370 CYS Chi-restraints excluded: chain I residue 50 PHE Chi-restraints excluded: chain I residue 53 GLN Chi-restraints excluded: chain I residue 54 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain I residue 112 GLN Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 222 ILE Chi-restraints excluded: chain I residue 281 GLU Chi-restraints excluded: chain I residue 295 SER Chi-restraints excluded: chain I residue 318 ILE Chi-restraints excluded: chain I residue 361 LEU Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 222 ILE Chi-restraints excluded: chain J residue 227 VAL Chi-restraints excluded: chain J residue 274 THR Chi-restraints excluded: chain J residue 290 HIS Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 305 TYR Chi-restraints excluded: chain J residue 343 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 105 CYS Chi-restraints excluded: chain K residue 167 ILE Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 220 CYS Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 272 GLU Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 290 HIS Chi-restraints excluded: chain K residue 362 TYR Chi-restraints excluded: chain M residue 38 MET Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 140 VAL Chi-restraints excluded: chain O residue 157 LYS Chi-restraints excluded: chain O residue 200 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 247 SER Chi-restraints excluded: chain O residue 248 VAL Chi-restraints excluded: chain O residue 255 MET Chi-restraints excluded: chain P residue 136 VAL Chi-restraints excluded: chain P residue 175 VAL Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain P residue 230 VAL Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 249 VAL Chi-restraints excluded: chain Q residue 249 VAL Chi-restraints excluded: chain Q residue 259 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 225 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 411 optimal weight: 0.0870 chunk 319 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 375 optimal weight: 0.6980 chunk 176 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 245 optimal weight: 0.3980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN B 53 GLN B 232 HIS ** G 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN ** I 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 HIS J 120 ASN ** J 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 HIS K 226 HIS M 42 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.171551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119434 restraints weight = 40388.855| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 3.24 r_work: 0.3116 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 1.0345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 34384 Z= 0.165 Angle : 0.783 59.200 46924 Z= 0.414 Chirality : 0.048 1.023 5296 Planarity : 0.005 0.165 5992 Dihedral : 5.653 56.993 5364 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.87 % Rotamer: Outliers : 3.31 % Allowed : 19.25 % Favored : 77.43 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.17 % 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: -0.76 (0.13), residues: 4244 helix: 2.87 (0.23), residues: 512 sheet: -0.36 (0.15), residues: 1184 loop : -1.35 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 134 TYR 0.023 0.001 TYR F 93 PHE 0.035 0.001 PHE K 50 TRP 0.013 0.001 TRP K 235 HIS 0.226 0.002 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00390 (34292) covalent geometry : angle 0.76947 (46704) SS BOND : bond 0.00336 ( 56) SS BOND : angle 1.84551 ( 112) hydrogen bonds : bond 0.03598 ( 1182) hydrogen bonds : angle 4.74982 ( 3216) link_BETA1-4 : bond 0.00944 ( 24) link_BETA1-4 : angle 2.32129 ( 72) link_NAG-ASN : bond 0.00471 ( 12) link_NAG-ASN : angle 3.13408 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13484.88 seconds wall clock time: 229 minutes 56.63 seconds (13796.63 seconds total)