Starting phenix.real_space_refine on Sat Mar 7 04:58:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sfw_25104/03_2026/7sfw_25104.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sfw_25104/03_2026/7sfw_25104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sfw_25104/03_2026/7sfw_25104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sfw_25104/03_2026/7sfw_25104.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sfw_25104/03_2026/7sfw_25104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sfw_25104/03_2026/7sfw_25104.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 244 5.16 5 C 24444 2.51 5 N 6552 2.21 5 O 7380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38620 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 411} Chain: "B" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3264 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 30, 'TRANS': 387} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1248 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain: "D" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 411} Chain: "E" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3264 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 30, 'TRANS': 387} Chain: "F" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1248 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain: "G" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 411} Chain: "H" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3264 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 30, 'TRANS': 387} Chain: "I" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1248 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain: "J" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3351 Classifications: {'peptide': 440} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 411} Chain: "K" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3264 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 30, 'TRANS': 387} Chain: "L" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1248 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain: "M" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "N" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "P" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "R" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 941 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "T" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 809 Classifications: {'peptide': 107} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 8, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.18, per 1000 atoms: 0.21 Number of scatterers: 38620 At special positions: 0 Unit cell: (224.05, 170.607, 249.743, 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 244 16.00 O 7380 8.00 N 6552 7.00 C 24444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=60, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 376 " distance=2.03 Simple disulfide: pdb=" SG CYS A 306 " - pdb=" SG CYS A 380 " distance=2.03 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 370 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 200 " - pdb=" SG CYS B 226 " distance=2.04 Simple disulfide: pdb=" SG CYS B 202 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 259 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 301 " - pdb=" SG CYS D 376 " distance=2.03 Simple disulfide: pdb=" SG CYS D 306 " - pdb=" SG CYS D 380 " distance=2.03 Simple disulfide: pdb=" SG CYS D 328 " - pdb=" SG CYS D 370 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 90 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 266 " distance=2.03 Simple disulfide: pdb=" SG CYS E 200 " - pdb=" SG CYS E 226 " distance=2.04 Simple disulfide: pdb=" SG CYS E 202 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 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 19 " - pdb=" SG CYS H 123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 27 " distance=2.01 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 151 " - pdb=" SG CYS H 266 " distance=2.03 Simple disulfide: pdb=" SG CYS H 200 " - pdb=" SG CYS H 226 " distance=2.04 Simple disulfide: pdb=" SG CYS H 202 " - pdb=" SG CYS H 220 " distance=2.03 Simple disulfide: pdb=" SG CYS J 49 " - pdb=" SG CYS J 114 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 94 " distance=2.03 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 259 " - pdb=" SG CYS J 271 " distance=2.03 Simple disulfide: pdb=" SG CYS J 301 " - pdb=" SG CYS J 376 " distance=2.03 Simple disulfide: pdb=" SG CYS J 306 " - pdb=" SG CYS J 380 " distance=2.03 Simple disulfide: pdb=" SG CYS J 328 " - pdb=" SG CYS J 370 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 123 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 27 " distance=2.02 Simple disulfide: pdb=" SG CYS K 90 " - pdb=" SG CYS K 104 " distance=2.03 Simple disulfide: pdb=" SG CYS K 151 " - pdb=" SG CYS K 266 " distance=2.03 Simple disulfide: pdb=" SG CYS K 200 " - pdb=" SG CYS K 226 " distance=2.03 Simple disulfide: pdb=" SG CYS K 202 " - pdb=" SG CYS K 220 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 88 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 88 " 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 NAG-ASN " NAG A 501 " - " ASN A 134 " " NAG B 502 " - " ASN B 318 " " NAG D 501 " - " ASN D 134 " " NAG G 501 " - " ASN G 134 " " NAG H 502 " - " ASN H 318 " " NAG J 501 " - " ASN J 134 " " NAG K 502 " - " ASN K 318 " Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.5 seconds 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9200 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 116 sheets defined 12.3% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 238 through 246 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 256 through 259 Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'A' and resid 403 through 439 removed outlier: 4.573A pdb=" N LEU A 413 " --> pdb=" O TRP A 409 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 365 through 402 removed outlier: 3.806A pdb=" N LEU B 369 " --> pdb=" O MET B 365 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) Proline residue: B 399 - end of helix removed outlier: 3.521A pdb=" N LEU B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 415 Processing helix chain 'C' and resid 118 through 122 removed outlier: 3.992A pdb=" N LEU C 122 " --> pdb=" O MET C 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 118 through 122' Processing helix chain 'C' and resid 159 through 164 Processing helix chain 'C' and resid 181 through 187 removed outlier: 3.798A pdb=" N ALA C 186 " --> pdb=" O ASN C 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 246 Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 256 through 259 Processing helix chain 'D' and resid 403 through 438 removed outlier: 4.463A pdb=" N GLY D 415 " --> pdb=" O THR D 411 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ALA D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 12 removed outlier: 3.556A pdb=" N LEU E 11 " --> pdb=" O GLU E 8 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR E 12 " --> pdb=" O TYR E 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 8 through 12' Processing helix chain 'E' and resid 80 through 82 No H-bonds generated for 'chain 'E' and resid 80 through 82' Processing helix chain 'E' and resid 222 through 226 removed outlier: 3.527A pdb=" N CYS E 226 " --> pdb=" O LYS E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 362 Processing helix chain 'E' and resid 365 through 402 removed outlier: 3.828A pdb=" N LEU E 369 " --> pdb=" O MET E 365 " (cutoff:3.500A) Proline residue: E 399 - end of helix Processing helix chain 'E' and resid 408 through 415 removed outlier: 4.113A pdb=" N LEU E 412 " --> pdb=" O ILE E 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 123 removed outlier: 3.756A pdb=" N GLU F 123 " --> pdb=" O MET F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 165 Processing helix chain 'F' and resid 182 through 187 removed outlier: 3.630A pdb=" N ALA F 186 " --> pdb=" O ASN F 183 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP F 187 " --> pdb=" O MET F 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 255 Processing helix chain 'G' and resid 256 through 259 Processing helix chain 'G' and resid 403 through 440 removed outlier: 3.876A pdb=" N SER G 417 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA G 418 " --> pdb=" O LEU G 414 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL G 419 " --> pdb=" O GLY G 415 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS G 440 " --> pdb=" O LEU G 436 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 removed outlier: 3.559A pdb=" N THR H 12 " --> pdb=" O TYR H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 82 No H-bonds generated for 'chain 'H' and resid 80 through 82' Processing helix chain 'H' and resid 222 through 224 No H-bonds generated for 'chain 'H' and resid 222 through 224' Processing helix chain 'H' and resid 351 through 362 Processing helix chain 'H' and resid 366 through 402 removed outlier: 3.506A pdb=" N GLY H 370 " --> pdb=" O SER H 366 " (cutoff:3.500A) Proline residue: H 399 - end of helix Processing helix chain 'H' and resid 408 through 415 removed outlier: 4.035A pdb=" N LEU H 412 " --> pdb=" O ILE H 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 122 removed outlier: 3.643A pdb=" N LYS I 121 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU I 122 " --> pdb=" O VAL I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 164 Processing helix chain 'I' and resid 181 through 185 Processing helix chain 'J' and resid 238 through 246 Processing helix chain 'J' and resid 250 through 255 removed outlier: 3.520A pdb=" N THR J 254 " --> pdb=" O SER J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 256 through 259 Processing helix chain 'J' and resid 289 through 293 Processing helix chain 'J' and resid 403 through 414 Processing helix chain 'J' and resid 415 through 437 removed outlier: 3.552A pdb=" N VAL J 419 " --> pdb=" O GLY J 415 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 12 removed outlier: 3.714A pdb=" N THR K 12 " --> pdb=" O TYR K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 224 No H-bonds generated for 'chain 'K' and resid 222 through 224' Processing helix chain 'K' and resid 351 through 362 Processing helix chain 'K' and resid 369 through 402 Proline residue: K 399 - end of helix Processing helix chain 'K' and resid 408 through 415 removed outlier: 4.020A pdb=" N LEU K 412 " --> pdb=" O ILE K 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 125 removed outlier: 3.802A pdb=" N LYS L 121 " --> pdb=" O MET L 118 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU L 123 " --> pdb=" O MET L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 164 Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 26 through 30 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'O' and resid 87 through 91 Processing helix chain 'P' and resid 26 through 30 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.658A pdb=" N ASP P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 30 Processing helix chain 'R' and resid 79 through 83 Processing helix chain 'T' and resid 26 through 30 Processing helix chain 'T' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 8 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 19 removed outlier: 7.086A pdb=" N ILE A 29 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 137 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 133 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA A 131 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS A 37 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL A 129 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA A 127 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 147 removed outlier: 6.421A pdb=" N ALA A 119 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A 47 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA A 121 " --> pdb=" O GLU A 45 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA A 127 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE A 39 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N VAL A 129 " --> pdb=" O LYS A 37 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS A 37 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA A 131 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS A 35 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU A 133 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 135 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 31 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 137 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ILE A 29 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=AA5, first strand: chain 'A' and resid 59 through 61 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 removed outlier: 3.560A pdb=" N VAL A 220 " --> pdb=" O THR A 234 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 296 through 305 removed outlier: 5.038A pdb=" N ALA A 298 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER A 321 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE A 315 " --> pdb=" O ASN 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 365 through 368 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 Processing sheet with id=AB4, first strand: chain 'B' and resid 33 through 37 removed outlier: 8.280A pdb=" N ILE B 33 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER B 50 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 37 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 9.859A pdb=" N SER B 50 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP B 69 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY B 54 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N THR B 65 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 33 through 37 removed outlier: 8.280A pdb=" N ILE B 33 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER B 50 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 37 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 49 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N TYR B 98 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N SER B 51 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N HIS B 96 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N TYR B 53 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 10.354A pdb=" N ASP B 94 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 15.255A pdb=" N LEU B 55 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 17.297A pdb=" N ILE B 92 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AB7, first strand: chain 'B' and resid 148 through 154 Processing sheet with id=AB8, first strand: chain 'B' and resid 237 through 238 Processing sheet with id=AB9, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.810A pdb=" N SER B 195 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 179 through 182 Processing sheet with id=AC2, first strand: chain 'B' and resid 275 through 279 Processing sheet with id=AC3, first strand: chain 'C' and resid 156 through 157 removed outlier: 4.651A pdb=" N GLY C 138 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU C 132 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ILE C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 198 through 200 removed outlier: 5.090A pdb=" N PHE C 214 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL C 256 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N VAL C 241 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE C 230 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 198 through 200 removed outlier: 5.090A pdb=" N PHE C 214 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AC7, first strand: chain 'D' and resid 15 through 19 removed outlier: 5.471A pdb=" N ILE D 31 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN D 134 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS D 35 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR D 126 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASN D 43 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU D 45 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N TYR D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 47 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLU D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 140 through 147 removed outlier: 6.722A pdb=" N GLU D 120 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 47 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N TYR D 122 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU D 45 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA D 124 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASN D 43 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR D 126 " --> pdb=" O THR D 41 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR D 41 " --> pdb=" O THR D 126 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS D 35 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN D 134 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR D 136 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE D 31 " --> pdb=" O THR D 136 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 51 through 55 Processing sheet with id=AD1, first strand: chain 'D' and resid 51 through 55 Processing sheet with id=AD2, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.602A pdb=" N GLY D 91 " --> pdb=" O MET D 88 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 203 through 204 Processing sheet with id=AD4, first strand: chain 'D' and resid 220 through 221 Processing sheet with id=AD5, first strand: chain 'D' and resid 296 through 305 removed outlier: 6.666A pdb=" N ALA D 299 " --> pdb=" O SER D 321 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N SER D 321 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N CYS D 301 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LYS D 319 " --> pdb=" O CYS D 301 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N LEU D 303 " --> pdb=" O THR D 317 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR D 317 " --> pdb=" O LEU D 303 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 343 through 346 Processing sheet with id=AD7, first strand: chain 'D' and resid 387 through 388 Processing sheet with id=AD8, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AD9, first strand: chain 'E' and resid 33 through 37 removed outlier: 6.561A pdb=" N GLN E 48 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL E 36 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG E 46 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N SER E 50 " --> pdb=" O ASP E 69 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ASP E 69 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N THR E 65 " --> pdb=" O GLY E 54 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 33 through 37 removed outlier: 6.561A pdb=" N GLN E 48 " --> pdb=" O GLU E 34 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL E 36 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ARG E 46 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N TYR E 98 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N SER E 51 " --> pdb=" O HIS E 96 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N HIS E 96 " --> pdb=" O SER E 51 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N TYR E 53 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 10.599A pdb=" N ASP E 94 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 14.616A pdb=" N LEU E 55 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 17.058A pdb=" N ILE E 92 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 83 through 85 Processing sheet with id=AE3, first strand: chain 'E' and resid 147 through 154 Processing sheet with id=AE4, first strand: chain 'E' and resid 237 through 238 removed outlier: 3.524A pdb=" N GLY E 253 " --> pdb=" O MET E 167 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 173 through 174 removed outlier: 3.584A pdb=" N GLU E 173 " --> pdb=" O ARG E 230 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 231 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER E 195 " --> pdb=" O LEU E 231 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 179 through 182 removed outlier: 3.728A pdb=" N VAL E 186 " --> pdb=" O PHE E 217 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 275 through 279 Processing sheet with id=AE8, first strand: chain 'F' and resid 156 through 157 removed outlier: 3.500A pdb=" N LYS F 156 " --> pdb=" O MET F 131 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 266 through 267 removed outlier: 3.818A pdb=" N LEU F 253 " --> pdb=" O PHE F 214 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N PHE F 214 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 8.941A pdb=" N ALA F 206 " --> pdb=" O PRO F 217 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA F 239 " --> pdb=" O ILE F 230 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY F 244 " --> pdb=" O GLU F 273 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU F 273 " --> pdb=" O GLY F 244 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 266 through 267 removed outlier: 6.377A pdb=" N VAL F 256 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N VAL F 241 " --> pdb=" O VAL F 256 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY F 244 " --> pdb=" O GLU F 273 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU F 273 " --> pdb=" O GLY F 244 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AF3, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.526A pdb=" N ILE G 31 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 134 " --> pdb=" O PRO G 33 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS G 35 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL G 47 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLU G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 140 through 147 removed outlier: 6.891A pdb=" N GLU G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL G 47 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS G 35 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 134 " --> pdb=" O PRO G 33 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N THR G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE G 31 " --> pdb=" O THR G 136 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 51 through 55 Processing sheet with id=AF6, first strand: chain 'G' and resid 51 through 55 Processing sheet with id=AF7, first strand: chain 'G' and resid 203 through 204 Processing sheet with id=AF8, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AF9, first strand: chain 'G' and resid 300 through 306 removed outlier: 3.622A pdb=" N ASN G 304 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE G 315 " --> pdb=" O ASN G 304 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 326 through 328 Processing sheet with id=AG2, first strand: chain 'G' and resid 364 through 368 Processing sheet with id=AG3, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AG4, first strand: chain 'H' and resid 17 through 19 Processing sheet with id=AG5, first strand: chain 'H' and resid 33 through 37 removed outlier: 6.584A pdb=" N GLN H 48 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL H 36 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG H 46 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N SER H 50 " --> pdb=" O ASP H 69 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ASP H 69 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N THR H 65 " --> pdb=" O GLY H 54 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 33 through 37 removed outlier: 6.584A pdb=" N GLN H 48 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL H 36 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG H 46 " --> pdb=" O VAL H 36 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N TYR H 98 " --> pdb=" O THR H 49 " (cutoff:3.500A) removed outlier: 9.435A pdb=" N SER H 51 " --> pdb=" O HIS H 96 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N HIS H 96 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N TYR H 53 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N ASP H 94 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 14.766A pdb=" N LEU H 55 " --> pdb=" O ILE H 92 " (cutoff:3.500A) removed outlier: 17.260A pdb=" N ILE H 92 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LEU H 84 " --> pdb=" O CYS H 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 147 through 154 Processing sheet with id=AG8, first strand: chain 'H' and resid 237 through 238 Processing sheet with id=AG9, first strand: chain 'H' and resid 173 through 174 removed outlier: 3.664A pdb=" N GLU H 173 " --> pdb=" O ARG H 230 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 179 through 182 removed outlier: 3.895A pdb=" N VAL H 186 " --> pdb=" O PHE H 217 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 275 through 279 Processing sheet with id=AH3, first strand: chain 'I' and resid 156 through 157 removed outlier: 4.460A pdb=" N GLY I 138 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU I 132 " --> pdb=" O ILE I 136 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE I 136 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N TYR I 139 " --> pdb=" O PRO I 150 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 266 through 267 removed outlier: 6.602A pdb=" N VAL I 256 " --> pdb=" O VAL I 241 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL I 241 " --> pdb=" O VAL I 256 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA I 239 " --> pdb=" O ILE I 230 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N ALA I 206 " --> pdb=" O PRO I 217 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE I 214 " --> pdb=" O LEU I 253 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 2 through 8 Processing sheet with id=AH6, first strand: chain 'J' and resid 15 through 19 removed outlier: 5.577A pdb=" N ILE J 31 " --> pdb=" O THR J 136 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN J 134 " --> pdb=" O PRO J 33 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS J 35 " --> pdb=" O PHE J 132 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR J 126 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN J 43 " --> pdb=" O ALA J 124 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLU J 45 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL J 47 " --> pdb=" O GLU J 120 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 140 through 147 removed outlier: 6.772A pdb=" N GLU J 120 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL J 47 " --> pdb=" O GLU J 120 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N TYR J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N GLU J 45 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN J 43 " --> pdb=" O ALA J 124 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR J 126 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS J 35 " --> pdb=" O PHE J 132 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN J 134 " --> pdb=" O PRO J 33 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N THR J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE J 31 " --> pdb=" O THR J 136 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 51 through 55 Processing sheet with id=AH9, first strand: chain 'J' and resid 51 through 55 Processing sheet with id=AI1, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AI2, first strand: chain 'J' and resid 203 through 204 Processing sheet with id=AI3, first strand: chain 'J' and resid 220 through 221 Processing sheet with id=AI4, first strand: chain 'J' and resid 296 through 297 removed outlier: 3.541A pdb=" N SER J 321 " --> pdb=" O SER J 297 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR J 317 " --> pdb=" O LEU J 303 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU J 303 " --> pdb=" O THR J 317 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N LYS J 319 " --> pdb=" O CYS J 301 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS J 301 " --> pdb=" O LYS J 319 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 296 through 297 removed outlier: 3.541A pdb=" N SER J 321 " --> pdb=" O SER J 297 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 343 through 346 Processing sheet with id=AI7, first strand: chain 'J' and resid 387 through 388 Processing sheet with id=AI8, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AI9, first strand: chain 'K' and resid 33 through 37 removed outlier: 8.347A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA K 35 " --> pdb=" O GLN K 48 " (cutoff:3.500A) removed outlier: 9.640A pdb=" N SER K 50 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP K 69 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR K 65 " --> pdb=" O GLY K 54 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 33 through 37 removed outlier: 8.347A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA K 35 " --> pdb=" O GLN K 48 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TYR K 98 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 9.481A pdb=" N SER K 51 " --> pdb=" O HIS K 96 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N HIS K 96 " --> pdb=" O SER K 51 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N TYR K 53 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 10.279A pdb=" N ASP K 94 " --> pdb=" O TYR K 53 " (cutoff:3.500A) removed outlier: 14.954A pdb=" N LEU K 55 " --> pdb=" O ILE K 92 " (cutoff:3.500A) removed outlier: 17.327A pdb=" N ILE K 92 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 82 through 85 Processing sheet with id=AJ3, first strand: chain 'K' and resid 147 through 154 Processing sheet with id=AJ4, first strand: chain 'K' and resid 237 through 238 Processing sheet with id=AJ5, first strand: chain 'K' and resid 173 through 174 removed outlier: 3.556A pdb=" N GLU K 173 " --> pdb=" O ARG K 230 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'K' and resid 179 through 181 Processing sheet with id=AJ7, first strand: chain 'K' and resid 275 through 279 Processing sheet with id=AJ8, first strand: chain 'L' and resid 156 through 157 removed outlier: 6.106A pdb=" N PHE L 128 " --> pdb=" O TYR L 139 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR L 139 " --> pdb=" O PHE L 128 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE L 130 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N TYR L 139 " --> pdb=" O PRO L 150 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'L' and resid 198 through 200 removed outlier: 5.130A pdb=" N PHE L 214 " --> pdb=" O LEU L 253 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL L 256 " --> pdb=" O VAL L 241 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL L 241 " --> pdb=" O VAL L 256 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'L' and resid 229 through 231 removed outlier: 4.249A pdb=" N ALA L 239 " --> pdb=" O ILE L 230 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N VAL L 241 " --> pdb=" O VAL L 256 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL L 256 " --> pdb=" O VAL L 241 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=AK3, first strand: chain 'M' and resid 46 through 52 removed outlier: 5.670A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY M 49 " --> pdb=" O TRP M 36 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.725A pdb=" N VAL N 12 " --> pdb=" O THR N 107 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP N 34 " --> pdb=" O VAL N 46 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'N' and resid 9 through 12 removed outlier: 3.725A pdb=" N VAL N 12 " --> pdb=" O THR N 107 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AK7, first strand: chain 'O' and resid 3 through 6 Processing sheet with id=AK8, first strand: chain 'O' and resid 3 through 6 removed outlier: 3.666A pdb=" N ALA O 78 " --> pdb=" O ASP O 73 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'O' and resid 10 through 11 removed outlier: 4.180A pdb=" N THR O 119 " --> pdb=" O GLU O 10 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE O 34 " --> pdb=" O TRP O 50 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP O 50 " --> pdb=" O ILE O 34 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TRP O 36 " --> pdb=" O MET O 48 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'O' and resid 10 through 11 removed outlier: 4.180A pdb=" N THR O 119 " --> pdb=" O GLU O 10 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR O 98 " --> pdb=" O TYR O 111 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'P' and resid 9 through 11 removed outlier: 7.100A pdb=" N VAL P 10 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR P 86 " --> pdb=" O THR P 104 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP P 34 " --> pdb=" O VAL P 46 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'P' and resid 9 through 11 removed outlier: 7.100A pdb=" N VAL P 10 " --> pdb=" O THR P 107 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR P 86 " --> pdb=" O THR P 104 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'P' and resid 18 through 23 Processing sheet with id=AL5, first strand: chain 'Q' and resid 3 through 6 Processing sheet with id=AL6, first strand: chain 'Q' and resid 3 through 6 removed outlier: 3.626A pdb=" N ALA Q 78 " --> pdb=" O ASP Q 73 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP Q 73 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'Q' and resid 58 through 60 removed outlier: 3.735A pdb=" N LYS Q 59 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP Q 50 " --> pdb=" O LYS Q 59 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TRP Q 47 " --> pdb=" O ARG Q 38 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ARG Q 38 " --> pdb=" O TRP Q 47 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.991A pdb=" N ALA R 84 " --> pdb=" O VAL R 106 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP R 34 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'R' and resid 11 through 12 removed outlier: 3.991A pdb=" N ALA R 84 " --> pdb=" O VAL R 106 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'R' and resid 17 through 23 Processing sheet with id=AM2, first strand: chain 'S' and resid 10 through 11 removed outlier: 3.882A pdb=" N THR S 119 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'S' and resid 10 through 11 removed outlier: 3.882A pdb=" N THR S 119 " --> pdb=" O GLU S 10 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.912A pdb=" N GLU S 82 " --> pdb=" O SER S 69 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER S 69 " --> pdb=" O GLU S 82 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'S' and resid 18 through 23 removed outlier: 3.692A pdb=" N ALA S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP S 73 " --> pdb=" O ALA S 78 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'T' and resid 9 through 12 removed outlier: 6.549A pdb=" N TRP T 34 " --> pdb=" O VAL T 46 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'T' and resid 9 through 12 Processing sheet with id=AM8, first strand: chain 'T' and resid 18 through 23 1493 hydrogen bonds defined for protein. 3723 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: 10.75 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12433 1.34 - 1.47: 9784 1.47 - 1.59: 17066 1.59 - 1.71: 1 1.71 - 1.83: 328 Bond restraints: 39612 Sorted by residual: bond pdb=" CB CYS K 27 " pdb=" SG CYS K 27 " ideal model delta sigma weight residual 1.808 1.734 0.074 3.30e-02 9.18e+02 5.02e+00 bond pdb=" CB PRO M 41 " pdb=" CG PRO M 41 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.56e+00 bond pdb=" C THR G 152 " pdb=" N PRO G 153 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.22e-02 6.72e+03 3.04e+00 bond pdb=" CB CYS H 27 " pdb=" SG CYS H 27 " ideal model delta sigma weight residual 1.808 1.755 0.053 3.30e-02 9.18e+02 2.62e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 ... (remaining 39607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 52815 1.91 - 3.83: 978 3.83 - 5.74: 111 5.74 - 7.66: 16 7.66 - 9.57: 4 Bond angle restraints: 53924 Sorted by residual: angle pdb=" CA PRO M 41 " pdb=" N PRO M 41 " pdb=" CD PRO M 41 " ideal model delta sigma weight residual 112.00 105.80 6.20 1.40e+00 5.10e-01 1.96e+01 angle pdb=" N VAL C 238 " pdb=" CA VAL C 238 " pdb=" C VAL C 238 " ideal model delta sigma weight residual 112.96 108.96 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" N VAL G 148 " pdb=" CA VAL G 148 " pdb=" C VAL G 148 " ideal model delta sigma weight residual 111.91 108.37 3.54 8.90e-01 1.26e+00 1.58e+01 angle pdb=" CA MET C 151 " pdb=" CB MET C 151 " pdb=" CG MET C 151 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 angle pdb=" N VAL B 198 " pdb=" CA VAL B 198 " pdb=" C VAL B 198 " ideal model delta sigma weight residual 106.72 112.51 -5.79 1.59e+00 3.96e-01 1.33e+01 ... (remaining 53919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 22039 21.48 - 42.97: 1509 42.97 - 64.45: 187 64.45 - 85.93: 70 85.93 - 107.42: 39 Dihedral angle restraints: 23844 sinusoidal: 9416 harmonic: 14428 Sorted by residual: dihedral pdb=" CB CYS A 62 " pdb=" SG CYS A 62 " pdb=" SG CYS A 94 " pdb=" CB CYS A 94 " ideal model delta sinusoidal sigma weight residual -86.00 -173.21 87.21 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 266 " pdb=" CB CYS E 266 " ideal model delta sinusoidal sigma weight residual -86.00 -172.21 86.21 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS H 151 " pdb=" SG CYS H 151 " pdb=" SG CYS H 266 " pdb=" CB CYS H 266 " ideal model delta sinusoidal sigma weight residual -86.00 -171.07 85.07 1 1.00e+01 1.00e-02 8.78e+01 ... (remaining 23841 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4689 0.050 - 0.100: 1051 0.100 - 0.151: 257 0.151 - 0.201: 8 0.201 - 0.251: 2 Chirality restraints: 6007 Sorted by residual: chirality pdb=" C1 NAG H 502 " pdb=" ND2 ASN H 318 " pdb=" C2 NAG H 502 " pdb=" O5 NAG H 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C1 NAG K 502 " pdb=" ND2 ASN K 318 " pdb=" C2 NAG K 502 " pdb=" O5 NAG K 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TRP A 409 " pdb=" N TRP A 409 " pdb=" C TRP A 409 " pdb=" CB TRP A 409 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 6004 not shown) Planarity restraints: 6919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 152 " -0.091 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO G 153 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO G 153 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO G 153 " -0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA M 40 " 0.079 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO M 41 " -0.200 5.00e-02 4.00e+02 pdb=" CA PRO M 41 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO M 41 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 128 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO L 129 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO L 129 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO L 129 " 0.055 5.00e-02 4.00e+02 ... (remaining 6916 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 921 2.69 - 3.24: 36387 3.24 - 3.79: 59288 3.79 - 4.35: 80003 4.35 - 4.90: 134436 Nonbonded interactions: 311035 Sorted by model distance: nonbonded pdb=" O SER E 184 " pdb=" ND2 ASN O 31 " model vdw 2.133 3.120 nonbonded pdb=" OG1 THR D 358 " pdb=" OD1 ASN D 360 " model vdw 2.173 3.040 nonbonded pdb=" OD1 ASN Q 106 " pdb=" N GLY Q 107 " model vdw 2.178 3.120 nonbonded pdb=" NH2 ARG S 44 " pdb=" OE2 GLU T 3 " model vdw 2.184 3.120 nonbonded pdb=" OG SER J 291 " pdb=" OE1 GLU J 292 " model vdw 2.194 3.040 ... (remaining 311030 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 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 36.080 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.150 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.004 0.107 39679 Z= 0.154 Angle : 0.625 9.572 54065 Z= 0.328 Chirality : 0.045 0.251 6007 Planarity : 0.005 0.140 6912 Dihedral : 14.960 107.418 14464 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.05 % Allowed : 0.43 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.12), residues: 4944 helix: 1.22 (0.26), residues: 461 sheet: -0.01 (0.12), residues: 1708 loop : -0.58 (0.12), residues: 2775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 185 TYR 0.046 0.001 TYR E 53 PHE 0.025 0.001 PHE S 29 TRP 0.015 0.001 TRP M 36 HIS 0.006 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00355 (39612) covalent geometry : angle 0.61791 (53924) SS BOND : bond 0.00358 ( 60) SS BOND : angle 1.66845 ( 120) hydrogen bonds : bond 0.14073 ( 1384) hydrogen bonds : angle 7.27117 ( 3723) link_NAG-ASN : bond 0.00373 ( 7) link_NAG-ASN : angle 3.07831 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 648 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 390 HIS cc_start: 0.6618 (m-70) cc_final: 0.6347 (m-70) REVERT: D 434 TYR cc_start: 0.8598 (t80) cc_final: 0.8355 (t80) REVERT: E 199 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7414 (mm-30) REVERT: E 201 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7775 (tm-30) REVERT: E 365 MET cc_start: 0.6571 (tpp) cc_final: 0.6320 (tmm) REVERT: I 174 ASP cc_start: 0.8324 (t70) cc_final: 0.8067 (t0) REVERT: I 191 TYR cc_start: 0.7927 (p90) cc_final: 0.7219 (p90) REVERT: I 208 GLN cc_start: 0.8137 (pt0) cc_final: 0.7774 (pt0) REVERT: J 24 TYR cc_start: 0.8310 (m-80) cc_final: 0.8061 (m-10) REVERT: L 184 MET cc_start: 0.8378 (ptm) cc_final: 0.8081 (ptt) REVERT: N 104 THR cc_start: 0.8611 (m) cc_final: 0.8325 (t) REVERT: O 32 TYR cc_start: 0.4662 (m-80) cc_final: 0.3232 (m-80) REVERT: P 44 VAL cc_start: 0.9039 (t) cc_final: 0.8679 (p) REVERT: R 34 TRP cc_start: 0.8344 (m100) cc_final: 0.8092 (m100) REVERT: T 4 LEU cc_start: 0.8591 (mt) cc_final: 0.8005 (mt) REVERT: T 97 GLU cc_start: 0.7536 (pm20) cc_final: 0.7322 (pm20) outliers start: 2 outliers final: 1 residues processed: 649 average time/residue: 0.2197 time to fit residues: 237.7727 Evaluate side-chains 541 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 540 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 GLN D 77 GLN D 235 GLN D 368 GLN E 361 HIS F 234 GLN G 264 ASN H 159 GLN H 212 ASN H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN K 361 HIS M 35 HIS ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 GLN O 114 GLN P 37 GLN Q 55 ASN S 6 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.175570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124848 restraints weight = 48513.757| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 1.98 r_work: 0.2857 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 39679 Z= 0.213 Angle : 0.656 9.720 54065 Z= 0.336 Chirality : 0.047 0.275 6007 Planarity : 0.005 0.081 6912 Dihedral : 7.637 76.364 5663 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 1.33 % Allowed : 8.17 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.12), residues: 4944 helix: 1.12 (0.25), residues: 473 sheet: -0.05 (0.12), residues: 1724 loop : -0.57 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 185 TYR 0.021 0.002 TYR G 308 PHE 0.020 0.002 PHE A 365 TRP 0.016 0.001 TRP P 34 HIS 0.009 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00520 (39612) covalent geometry : angle 0.64847 (53924) SS BOND : bond 0.00544 ( 60) SS BOND : angle 1.75806 ( 120) hydrogen bonds : bond 0.03682 ( 1384) hydrogen bonds : angle 5.83236 ( 3723) link_NAG-ASN : bond 0.00507 ( 7) link_NAG-ASN : angle 3.23129 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 578 time to evaluate : 1.554 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: B 21 ARG cc_start: 0.8000 (tpt90) cc_final: 0.7664 (mmm160) REVERT: B 70 MET cc_start: 0.8364 (mmm) cc_final: 0.8082 (tpt) REVERT: B 311 ILE cc_start: 0.8526 (pt) cc_final: 0.8261 (pt) REVERT: B 347 ASN cc_start: 0.8650 (t0) cc_final: 0.8372 (t0) REVERT: D 87 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8746 (m-80) REVERT: D 390 HIS cc_start: 0.7500 (m-70) cc_final: 0.7267 (m-70) REVERT: E 173 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7627 (pt0) REVERT: E 201 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7816 (tm-30) REVERT: E 365 MET cc_start: 0.7397 (tpp) cc_final: 0.6528 (tmm) REVERT: F 118 MET cc_start: 0.5772 (ptt) cc_final: 0.5409 (ptt) REVERT: F 123 GLU cc_start: 0.8340 (pp20) cc_final: 0.8077 (pm20) REVERT: F 151 MET cc_start: 0.8790 (tpp) cc_final: 0.8139 (tpp) REVERT: I 169 LYS cc_start: 0.9026 (mptt) cc_final: 0.8728 (mmtt) REVERT: I 174 ASP cc_start: 0.8478 (t70) cc_final: 0.8235 (t0) REVERT: I 191 TYR cc_start: 0.8475 (p90) cc_final: 0.7682 (p90) REVERT: J 24 TYR cc_start: 0.8656 (m-80) cc_final: 0.8379 (m-80) REVERT: J 142 ILE cc_start: 0.8017 (tt) cc_final: 0.7737 (tp) REVERT: J 212 ASP cc_start: 0.8554 (p0) cc_final: 0.8345 (p0) REVERT: L 184 MET cc_start: 0.8745 (ptm) cc_final: 0.8510 (ptt) REVERT: N 104 THR cc_start: 0.8708 (m) cc_final: 0.8406 (t) REVERT: P 44 VAL cc_start: 0.9075 (t) cc_final: 0.8819 (p) REVERT: P 53 ARG cc_start: 0.8200 (ptt-90) cc_final: 0.7756 (ptt90) REVERT: P 69 THR cc_start: 0.8014 (t) cc_final: 0.7798 (m) REVERT: R 34 TRP cc_start: 0.8198 (m100) cc_final: 0.7910 (m100) REVERT: T 4 LEU cc_start: 0.8615 (mt) cc_final: 0.8407 (mp) REVERT: T 30 GLN cc_start: 0.8351 (mt0) cc_final: 0.8058 (mt0) REVERT: T 87 TYR cc_start: 0.8540 (m-80) cc_final: 0.8283 (m-80) outliers start: 56 outliers final: 35 residues processed: 606 average time/residue: 0.2219 time to fit residues: 222.9021 Evaluate side-chains 566 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 530 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 438 ASN Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain G residue 396 GLN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain R residue 69 THR Chi-restraints excluded: chain S residue 24 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 457 optimal weight: 30.0000 chunk 443 optimal weight: 20.0000 chunk 80 optimal weight: 0.4980 chunk 209 optimal weight: 0.8980 chunk 389 optimal weight: 8.9990 chunk 232 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 183 optimal weight: 0.0770 chunk 472 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN B 361 HIS C 197 GLN D 77 GLN D 349 GLN D 368 GLN E 361 HIS G 230 HIS G 264 ASN H 341 GLN H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 208 GLN K 225 GLN N 30 GLN O 114 GLN P 30 GLN Q 52 ASN Q 100 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.177697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127206 restraints weight = 48334.430| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.89 r_work: 0.2867 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39679 Z= 0.134 Angle : 0.587 8.191 54065 Z= 0.300 Chirality : 0.045 0.259 6007 Planarity : 0.004 0.058 6912 Dihedral : 6.108 76.193 5663 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.64 % Allowed : 11.60 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.12), residues: 4944 helix: 1.24 (0.25), residues: 473 sheet: -0.04 (0.12), residues: 1719 loop : -0.51 (0.12), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 366 TYR 0.016 0.001 TYR G 308 PHE 0.017 0.001 PHE A 365 TRP 0.019 0.001 TRP O 36 HIS 0.005 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00317 (39612) covalent geometry : angle 0.58193 (53924) SS BOND : bond 0.00316 ( 60) SS BOND : angle 1.28902 ( 120) hydrogen bonds : bond 0.03374 ( 1384) hydrogen bonds : angle 5.57210 ( 3723) link_NAG-ASN : bond 0.00307 ( 7) link_NAG-ASN : angle 2.94578 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 557 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8243 (ttp80) REVERT: A 385 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.7911 (p0) REVERT: B 21 ARG cc_start: 0.7930 (tpt90) cc_final: 0.7644 (mmm160) REVERT: B 70 MET cc_start: 0.8359 (mmm) cc_final: 0.8065 (tpt) REVERT: B 311 ILE cc_start: 0.8447 (pt) cc_final: 0.8197 (pt) REVERT: B 347 ASN cc_start: 0.8693 (t0) cc_final: 0.8334 (t0) REVERT: D 87 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8779 (m-80) REVERT: D 99 GLU cc_start: 0.9015 (pm20) cc_final: 0.8756 (pm20) REVERT: D 145 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8502 (p) REVERT: D 368 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: D 385 ASP cc_start: 0.8342 (p0) cc_final: 0.8088 (p0) REVERT: D 390 HIS cc_start: 0.7415 (m-70) cc_final: 0.7203 (m90) REVERT: E 173 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7462 (pt0) REVERT: E 199 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7787 (mm-30) REVERT: E 201 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7731 (tm-30) REVERT: E 365 MET cc_start: 0.7212 (tpp) cc_final: 0.6460 (tmm) REVERT: F 123 GLU cc_start: 0.8269 (pp20) cc_final: 0.7986 (pm20) REVERT: F 151 MET cc_start: 0.8693 (tpp) cc_final: 0.8120 (tpp) REVERT: F 218 LYS cc_start: 0.8622 (tttt) cc_final: 0.8370 (tppt) REVERT: H 64 ARG cc_start: 0.7886 (mtt-85) cc_final: 0.7566 (mtt180) REVERT: I 169 LYS cc_start: 0.8995 (mptt) cc_final: 0.8637 (mmtt) REVERT: I 174 ASP cc_start: 0.8490 (t70) cc_final: 0.8012 (t0) REVERT: I 191 TYR cc_start: 0.8472 (p90) cc_final: 0.7695 (p90) REVERT: J 24 TYR cc_start: 0.8735 (m-80) cc_final: 0.8405 (m-80) REVERT: J 142 ILE cc_start: 0.7926 (tt) cc_final: 0.7666 (tp) REVERT: J 212 ASP cc_start: 0.8558 (p0) cc_final: 0.8329 (p0) REVERT: K 113 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8495 (mt-10) REVERT: K 224 GLU cc_start: 0.8046 (mp0) cc_final: 0.7775 (mp0) REVERT: N 69 THR cc_start: 0.8191 (t) cc_final: 0.7978 (m) REVERT: N 104 THR cc_start: 0.8702 (m) cc_final: 0.8381 (t) REVERT: P 44 VAL cc_start: 0.9157 (t) cc_final: 0.8750 (p) REVERT: R 34 TRP cc_start: 0.8095 (m100) cc_final: 0.7876 (m100) REVERT: T 4 LEU cc_start: 0.8597 (mt) cc_final: 0.8380 (mp) REVERT: T 30 GLN cc_start: 0.8289 (mt0) cc_final: 0.7984 (mt0) REVERT: T 87 TYR cc_start: 0.8505 (m-80) cc_final: 0.8194 (m-80) REVERT: T 97 GLU cc_start: 0.8081 (pm20) cc_final: 0.7868 (pm20) outliers start: 69 outliers final: 44 residues processed: 595 average time/residue: 0.2192 time to fit residues: 216.4494 Evaluate side-chains 561 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 513 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 120 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 412 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 315 optimal weight: 0.8980 chunk 460 optimal weight: 3.9990 chunk 341 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN B 361 HIS C 197 GLN D 77 GLN D 438 ASN E 361 HIS G 264 ASN H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 155 ASN O 114 GLN S 3 GLN T 16 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.176524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.125790 restraints weight = 48261.181| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.97 r_work: 0.2838 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 39679 Z= 0.163 Angle : 0.594 8.166 54065 Z= 0.303 Chirality : 0.045 0.262 6007 Planarity : 0.004 0.058 6912 Dihedral : 5.584 76.276 5663 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.33 % Allowed : 13.14 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.12), residues: 4944 helix: 1.30 (0.25), residues: 473 sheet: 0.02 (0.13), residues: 1676 loop : -0.55 (0.12), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 289 TYR 0.018 0.001 TYR G 308 PHE 0.017 0.001 PHE A 365 TRP 0.023 0.001 TRP O 36 HIS 0.007 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00396 (39612) covalent geometry : angle 0.58716 (53924) SS BOND : bond 0.00369 ( 60) SS BOND : angle 1.48476 ( 120) hydrogen bonds : bond 0.03268 ( 1384) hydrogen bonds : angle 5.47461 ( 3723) link_NAG-ASN : bond 0.00414 ( 7) link_NAG-ASN : angle 3.04549 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 537 time to evaluate : 1.414 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: A 385 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.7919 (p0) REVERT: B 9 TYR cc_start: 0.8892 (m-80) cc_final: 0.8566 (m-80) REVERT: B 21 ARG cc_start: 0.7913 (tpt90) cc_final: 0.7627 (mmm160) REVERT: B 70 MET cc_start: 0.8383 (mmm) cc_final: 0.8046 (tpt) REVERT: B 311 ILE cc_start: 0.8495 (pt) cc_final: 0.8233 (pt) REVERT: B 347 ASN cc_start: 0.8701 (t0) cc_final: 0.8300 (t0) REVERT: C 118 MET cc_start: 0.6283 (mmm) cc_final: 0.5777 (mmm) REVERT: C 211 ASN cc_start: 0.8560 (t0) cc_final: 0.8172 (t0) REVERT: D 87 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8832 (m-80) REVERT: D 145 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8507 (p) REVERT: D 368 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7732 (tm-30) REVERT: D 385 ASP cc_start: 0.8399 (p0) cc_final: 0.7842 (p0) REVERT: D 390 HIS cc_start: 0.7412 (m-70) cc_final: 0.7209 (m90) REVERT: E 173 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7517 (pt0) REVERT: E 199 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7709 (mm-30) REVERT: F 123 GLU cc_start: 0.8277 (pp20) cc_final: 0.7963 (pm20) REVERT: F 151 MET cc_start: 0.8816 (tpp) cc_final: 0.8206 (tpp) REVERT: F 218 LYS cc_start: 0.8657 (tttt) cc_final: 0.8377 (tppt) REVERT: H 64 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7645 (mtt180) REVERT: I 169 LYS cc_start: 0.9007 (mptt) cc_final: 0.8471 (mmtt) REVERT: I 174 ASP cc_start: 0.8552 (t70) cc_final: 0.7967 (t0) REVERT: I 191 TYR cc_start: 0.8501 (p90) cc_final: 0.7644 (p90) REVERT: J 24 TYR cc_start: 0.8748 (m-80) cc_final: 0.8461 (m-80) REVERT: J 142 ILE cc_start: 0.7977 (tt) cc_final: 0.7752 (tp) REVERT: J 166 LEU cc_start: 0.8738 (tp) cc_final: 0.8260 (mp) REVERT: J 212 ASP cc_start: 0.8546 (p0) cc_final: 0.8311 (p0) REVERT: J 346 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7750 (mp) REVERT: K 108 ASP cc_start: 0.8844 (p0) cc_final: 0.8574 (p0) REVERT: N 104 THR cc_start: 0.8712 (m) cc_final: 0.8392 (t) REVERT: P 44 VAL cc_start: 0.9128 (t) cc_final: 0.8891 (m) REVERT: R 34 TRP cc_start: 0.8044 (m100) cc_final: 0.7842 (m100) REVERT: T 4 LEU cc_start: 0.8618 (mt) cc_final: 0.8403 (mp) REVERT: T 30 GLN cc_start: 0.8330 (mt0) cc_final: 0.8022 (mt0) REVERT: T 87 TYR cc_start: 0.8491 (m-80) cc_final: 0.8181 (m-80) REVERT: T 97 GLU cc_start: 0.8088 (pm20) cc_final: 0.7844 (pm20) outliers start: 98 outliers final: 75 residues processed: 599 average time/residue: 0.2182 time to fit residues: 216.5937 Evaluate side-chains 587 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 508 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 438 ASN Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 396 GLN Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 155 ASN Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 26 optimal weight: 2.9990 chunk 423 optimal weight: 0.0970 chunk 116 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 402 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN G 264 ASN H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 30 GLN O 114 GLN T 16 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.176483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.125606 restraints weight = 48197.092| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.89 r_work: 0.2845 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 39679 Z= 0.160 Angle : 0.588 8.500 54065 Z= 0.301 Chirality : 0.045 0.261 6007 Planarity : 0.004 0.057 6912 Dihedral : 5.444 76.368 5663 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.93 % Allowed : 13.74 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.12), residues: 4944 helix: 1.33 (0.25), residues: 473 sheet: 0.03 (0.13), residues: 1653 loop : -0.53 (0.12), residues: 2818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 289 TYR 0.018 0.001 TYR G 308 PHE 0.016 0.001 PHE A 365 TRP 0.024 0.001 TRP O 36 HIS 0.007 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00386 (39612) covalent geometry : angle 0.58161 (53924) SS BOND : bond 0.00385 ( 60) SS BOND : angle 1.48402 ( 120) hydrogen bonds : bond 0.03224 ( 1384) hydrogen bonds : angle 5.39742 ( 3723) link_NAG-ASN : bond 0.00426 ( 7) link_NAG-ASN : angle 3.20399 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 513 time to evaluate : 1.401 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: A 260 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: A 366 ARG cc_start: 0.8668 (mmm-85) cc_final: 0.8237 (ttp80) REVERT: A 385 ASP cc_start: 0.8737 (OUTLIER) cc_final: 0.7894 (p0) REVERT: B 9 TYR cc_start: 0.8899 (m-80) cc_final: 0.8571 (m-80) REVERT: B 21 ARG cc_start: 0.7775 (tpt90) cc_final: 0.7547 (mmm160) REVERT: B 70 MET cc_start: 0.8325 (mmm) cc_final: 0.8057 (tpt) REVERT: B 114 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7952 (t80) REVERT: B 311 ILE cc_start: 0.8519 (pt) cc_final: 0.8241 (pt) REVERT: D 87 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8827 (m-80) REVERT: D 385 ASP cc_start: 0.8407 (p0) cc_final: 0.7969 (p0) REVERT: E 173 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7459 (pt0) REVERT: E 199 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7693 (mm-30) REVERT: F 151 MET cc_start: 0.8815 (tpp) cc_final: 0.8249 (tpp) REVERT: F 218 LYS cc_start: 0.8673 (tttt) cc_final: 0.8392 (tppt) REVERT: H 287 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.8989 (mt) REVERT: I 174 ASP cc_start: 0.8565 (t70) cc_final: 0.7950 (t0) REVERT: I 191 TYR cc_start: 0.8495 (p90) cc_final: 0.7732 (p90) REVERT: J 120 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8775 (pt0) REVERT: J 212 ASP cc_start: 0.8534 (p0) cc_final: 0.8307 (p0) REVERT: J 346 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7711 (mp) REVERT: K 108 ASP cc_start: 0.8837 (p0) cc_final: 0.8566 (p0) REVERT: L 125 ASP cc_start: 0.6444 (OUTLIER) cc_final: 0.6242 (t0) REVERT: P 44 VAL cc_start: 0.9129 (t) cc_final: 0.8899 (m) REVERT: Q 101 MET cc_start: 0.4614 (ppp) cc_final: 0.4376 (ppp) REVERT: T 4 LEU cc_start: 0.8641 (mt) cc_final: 0.8421 (mp) REVERT: T 30 GLN cc_start: 0.8319 (mt0) cc_final: 0.8008 (mt0) REVERT: T 87 TYR cc_start: 0.8476 (m-80) cc_final: 0.8095 (m-80) REVERT: T 97 GLU cc_start: 0.8084 (pm20) cc_final: 0.7828 (pm20) outliers start: 123 outliers final: 89 residues processed: 590 average time/residue: 0.2081 time to fit residues: 204.5127 Evaluate side-chains 594 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 497 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 CYS Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 125 ASP Chi-restraints excluded: chain L residue 230 ILE Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 470 optimal weight: 30.0000 chunk 382 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 468 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 242 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN E 81 GLN E 232 GLN ** E 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN H 256 HIS H 361 HIS K 239 ASN N 30 GLN O 114 GLN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 16 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.171352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119575 restraints weight = 48377.160| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.91 r_work: 0.2751 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.141 39679 Z= 0.360 Angle : 0.742 12.197 54065 Z= 0.377 Chirality : 0.051 0.299 6007 Planarity : 0.005 0.057 6912 Dihedral : 6.016 77.425 5663 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.48 % Allowed : 14.79 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: -0.56 (0.12), residues: 4944 helix: 1.02 (0.25), residues: 473 sheet: -0.19 (0.12), residues: 1739 loop : -0.69 (0.12), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 362 TYR 0.027 0.002 TYR G 308 PHE 0.021 0.002 PHE A 365 TRP 0.018 0.002 TRP B 330 HIS 0.015 0.002 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00886 (39612) covalent geometry : angle 0.73084 (53924) SS BOND : bond 0.00700 ( 60) SS BOND : angle 2.29430 ( 120) hydrogen bonds : bond 0.03805 ( 1384) hydrogen bonds : angle 5.69705 ( 3723) link_NAG-ASN : bond 0.00937 ( 7) link_NAG-ASN : angle 3.78038 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 506 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7292 (mp0) REVERT: A 385 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8013 (p0) REVERT: B 114 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8024 (t80) REVERT: C 118 MET cc_start: 0.5809 (mmm) cc_final: 0.5510 (mmm) REVERT: C 211 ASN cc_start: 0.8590 (t0) cc_final: 0.8081 (t0) REVERT: D 24 TYR cc_start: 0.8812 (m-80) cc_final: 0.8407 (m-80) REVERT: D 45 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8076 (pm20) REVERT: D 87 PHE cc_start: 0.9250 (OUTLIER) cc_final: 0.8985 (m-80) REVERT: D 145 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8621 (p) REVERT: E 81 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8699 (mt0) REVERT: F 151 MET cc_start: 0.8839 (tpp) cc_final: 0.8216 (tpp) REVERT: F 218 LYS cc_start: 0.8721 (tttt) cc_final: 0.8343 (tppt) REVERT: H 64 ARG cc_start: 0.8047 (mtt-85) cc_final: 0.7834 (mtt-85) REVERT: H 201 GLU cc_start: 0.8212 (tt0) cc_final: 0.7940 (tt0) REVERT: H 287 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9006 (mt) REVERT: I 185 ARG cc_start: 0.8498 (ttm110) cc_final: 0.8289 (ttm110) REVERT: I 191 TYR cc_start: 0.8547 (p90) cc_final: 0.7738 (p90) REVERT: J 120 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8840 (pt0) REVERT: J 346 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7799 (mp) REVERT: K 108 ASP cc_start: 0.8949 (p0) cc_final: 0.8739 (p0) REVERT: L 247 GLU cc_start: 0.4046 (OUTLIER) cc_final: 0.2619 (tt0) REVERT: O 32 TYR cc_start: 0.5636 (m-80) cc_final: 0.4756 (m-80) REVERT: Q 101 MET cc_start: 0.4509 (ppp) cc_final: 0.4151 (ppp) REVERT: S 111 TYR cc_start: 0.5730 (t80) cc_final: 0.5155 (t80) REVERT: T 4 LEU cc_start: 0.8729 (mt) cc_final: 0.8495 (mp) REVERT: T 30 GLN cc_start: 0.8498 (mt0) cc_final: 0.8204 (mt0) REVERT: T 53 ARG cc_start: 0.8117 (ptp90) cc_final: 0.7626 (ptp90) REVERT: T 87 TYR cc_start: 0.8559 (m-80) cc_final: 0.8169 (m-80) outliers start: 146 outliers final: 103 residues processed: 603 average time/residue: 0.2100 time to fit residues: 208.5645 Evaluate side-chains 602 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 488 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 195 SER Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 390 HIS Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 324 LYS Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 140 THR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 398 THR Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 247 GLU Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain M residue 32 TYR Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 288 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 446 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 218 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 343 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 417 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN B 361 HIS C 197 GLN E 232 GLN G 43 ASN G 264 ASN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 HIS H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 233 ASN ** K 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS ** M 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.173603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.121946 restraints weight = 48349.372| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.86 r_work: 0.2836 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 39679 Z= 0.144 Angle : 0.601 9.305 54065 Z= 0.308 Chirality : 0.045 0.277 6007 Planarity : 0.004 0.058 6912 Dihedral : 5.586 76.855 5663 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.67 % Allowed : 16.02 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.12), residues: 4944 helix: 1.27 (0.25), residues: 473 sheet: -0.18 (0.12), residues: 1778 loop : -0.60 (0.12), residues: 2693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 366 TYR 0.019 0.001 TYR F 209 PHE 0.015 0.001 PHE A 365 TRP 0.018 0.001 TRP P 34 HIS 0.007 0.001 HIS E 80 Details of bonding type rmsd covalent geometry : bond 0.00345 (39612) covalent geometry : angle 0.59418 (53924) SS BOND : bond 0.00428 ( 60) SS BOND : angle 1.45394 ( 120) hydrogen bonds : bond 0.03186 ( 1384) hydrogen bonds : angle 5.44264 ( 3723) link_NAG-ASN : bond 0.00297 ( 7) link_NAG-ASN : angle 3.29741 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 507 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8132 (pt0) REVERT: A 260 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: A 366 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8492 (ttp80) REVERT: A 385 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.7958 (p0) REVERT: B 9 TYR cc_start: 0.8867 (m-80) cc_final: 0.8557 (m-80) REVERT: B 114 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.8026 (t80) REVERT: B 201 GLU cc_start: 0.8005 (pp20) cc_final: 0.7650 (pp20) REVERT: C 211 ASN cc_start: 0.8554 (t0) cc_final: 0.8138 (t0) REVERT: D 24 TYR cc_start: 0.8832 (m-80) cc_final: 0.8264 (m-80) REVERT: D 45 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: D 87 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8901 (m-80) REVERT: D 145 THR cc_start: 0.8778 (OUTLIER) cc_final: 0.8559 (m) REVERT: E 199 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7677 (mm-30) REVERT: G 346 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7536 (mp) REVERT: H 201 GLU cc_start: 0.8165 (tt0) cc_final: 0.7924 (tt0) REVERT: H 287 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.8991 (mt) REVERT: I 191 TYR cc_start: 0.8531 (p90) cc_final: 0.7737 (p90) REVERT: J 24 TYR cc_start: 0.8958 (m-80) cc_final: 0.8580 (m-80) REVERT: J 120 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8789 (pt0) REVERT: J 212 ASP cc_start: 0.8540 (p0) cc_final: 0.8309 (p0) REVERT: J 346 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7767 (mp) REVERT: K 108 ASP cc_start: 0.8840 (p0) cc_final: 0.8574 (p0) REVERT: L 190 LYS cc_start: 0.8498 (pttp) cc_final: 0.8140 (pptt) REVERT: O 32 TYR cc_start: 0.5203 (m-80) cc_final: 0.4524 (m-80) REVERT: Q 101 MET cc_start: 0.4956 (ppp) cc_final: 0.4563 (ppp) REVERT: S 111 TYR cc_start: 0.5639 (t80) cc_final: 0.5058 (t80) REVERT: T 4 LEU cc_start: 0.8692 (mt) cc_final: 0.8474 (mp) REVERT: T 30 GLN cc_start: 0.8363 (mt0) cc_final: 0.8047 (mt0) REVERT: T 87 TYR cc_start: 0.8516 (m-80) cc_final: 0.8150 (m-80) outliers start: 112 outliers final: 82 residues processed: 582 average time/residue: 0.2097 time to fit residues: 202.3828 Evaluate side-chains 583 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 490 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 390 HIS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain J residue 436 LEU Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 222 optimal weight: 4.9990 chunk 329 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 383 optimal weight: 3.9990 chunk 453 optimal weight: 20.0000 chunk 449 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 319 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN E 361 HIS G 264 ASN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 233 ASN K 361 HIS O 114 GLN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.172244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121054 restraints weight = 48244.877| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.01 r_work: 0.2788 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 39679 Z= 0.209 Angle : 0.635 9.791 54065 Z= 0.323 Chirality : 0.046 0.282 6007 Planarity : 0.005 0.058 6912 Dihedral : 5.591 77.837 5663 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.07 % Allowed : 16.19 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.12), residues: 4944 helix: 1.38 (0.25), residues: 461 sheet: -0.19 (0.12), residues: 1692 loop : -0.64 (0.12), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 289 TYR 0.021 0.002 TYR D 15 PHE 0.017 0.002 PHE A 365 TRP 0.035 0.001 TRP O 36 HIS 0.008 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00512 (39612) covalent geometry : angle 0.62701 (53924) SS BOND : bond 0.00511 ( 60) SS BOND : angle 1.67040 ( 120) hydrogen bonds : bond 0.03317 ( 1384) hydrogen bonds : angle 5.43446 ( 3723) link_NAG-ASN : bond 0.00513 ( 7) link_NAG-ASN : angle 3.38114 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 495 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8209 (pt0) REVERT: A 260 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: A 385 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.7985 (p0) REVERT: B 114 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.8035 (t80) REVERT: B 201 GLU cc_start: 0.8079 (pp20) cc_final: 0.7680 (pp20) REVERT: C 211 ASN cc_start: 0.8561 (t0) cc_final: 0.8075 (t0) REVERT: D 45 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: D 87 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8954 (m-80) REVERT: D 145 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8568 (p) REVERT: E 70 MET cc_start: 0.8899 (tpt) cc_final: 0.8678 (tpt) REVERT: E 199 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7777 (mm-30) REVERT: F 208 GLN cc_start: 0.6989 (pm20) cc_final: 0.6581 (pm20) REVERT: F 220 VAL cc_start: 0.8524 (t) cc_final: 0.8116 (p) REVERT: G 346 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7565 (mp) REVERT: H 161 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7933 (mpt90) REVERT: H 287 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9014 (mt) REVERT: I 185 ARG cc_start: 0.8435 (ttm110) cc_final: 0.8215 (ttm110) REVERT: J 24 TYR cc_start: 0.8872 (m-80) cc_final: 0.8594 (m-80) REVERT: J 120 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8824 (pt0) REVERT: J 346 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7718 (mp) REVERT: K 108 ASP cc_start: 0.8860 (p0) cc_final: 0.8590 (p0) REVERT: O 32 TYR cc_start: 0.5263 (m-80) cc_final: 0.4413 (m-80) REVERT: O 47 TRP cc_start: 0.8312 (t60) cc_final: 0.7423 (t60) REVERT: Q 101 MET cc_start: 0.4928 (ppp) cc_final: 0.4481 (ppp) REVERT: S 111 TYR cc_start: 0.5728 (t80) cc_final: 0.5133 (t80) REVERT: T 4 LEU cc_start: 0.8711 (mt) cc_final: 0.8492 (mp) REVERT: T 30 GLN cc_start: 0.8390 (mt0) cc_final: 0.8079 (mt0) REVERT: T 53 ARG cc_start: 0.8056 (ptp90) cc_final: 0.7575 (ptp90) REVERT: T 87 TYR cc_start: 0.8494 (m-80) cc_final: 0.8081 (m-80) outliers start: 129 outliers final: 92 residues processed: 583 average time/residue: 0.2142 time to fit residues: 206.6802 Evaluate side-chains 594 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 491 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 319 LYS Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 390 HIS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 346 LEU Chi-restraints excluded: chain J residue 361 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 19 optimal weight: 5.9990 chunk 462 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 314 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 416 optimal weight: 5.9990 chunk 461 optimal weight: 0.0670 chunk 189 optimal weight: 0.2980 chunk 202 optimal weight: 3.9990 chunk 386 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.4122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN E 361 HIS ** G 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 233 ASN K 361 HIS O 114 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.175863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.125542 restraints weight = 48308.674| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.85 r_work: 0.2840 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39679 Z= 0.138 Angle : 0.593 10.120 54065 Z= 0.303 Chirality : 0.045 0.265 6007 Planarity : 0.004 0.057 6912 Dihedral : 5.345 77.549 5663 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.64 % Allowed : 17.02 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.12), residues: 4944 helix: 1.52 (0.26), residues: 463 sheet: -0.16 (0.12), residues: 1696 loop : -0.58 (0.12), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 289 TYR 0.020 0.001 TYR D 15 PHE 0.015 0.001 PHE A 287 TRP 0.041 0.001 TRP O 36 HIS 0.005 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00332 (39612) covalent geometry : angle 0.58712 (53924) SS BOND : bond 0.00388 ( 60) SS BOND : angle 1.34969 ( 120) hydrogen bonds : bond 0.03070 ( 1384) hydrogen bonds : angle 5.31146 ( 3723) link_NAG-ASN : bond 0.00318 ( 7) link_NAG-ASN : angle 3.07256 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 512 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: A 260 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: A 366 ARG cc_start: 0.8723 (mmm-85) cc_final: 0.8393 (ttp80) REVERT: A 385 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.7892 (p0) REVERT: B 47 LEU cc_start: 0.8794 (tt) cc_final: 0.8493 (mp) REVERT: B 114 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.8003 (t80) REVERT: B 127 TYR cc_start: 0.8812 (m-80) cc_final: 0.8374 (m-80) REVERT: B 201 GLU cc_start: 0.8079 (pp20) cc_final: 0.7692 (pp20) REVERT: B 311 ILE cc_start: 0.8453 (pt) cc_final: 0.8250 (pt) REVERT: C 211 ASN cc_start: 0.8526 (t0) cc_final: 0.8083 (t0) REVERT: D 45 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7678 (pm20) REVERT: D 87 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8886 (m-80) REVERT: D 145 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8530 (m) REVERT: E 199 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7726 (mm-30) REVERT: F 220 VAL cc_start: 0.8507 (t) cc_final: 0.8102 (p) REVERT: G 346 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7619 (mp) REVERT: H 287 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9004 (mt) REVERT: H 401 ARG cc_start: 0.8922 (tpp80) cc_final: 0.8700 (tpp80) REVERT: J 120 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8788 (pt0) REVERT: J 166 LEU cc_start: 0.8765 (tp) cc_final: 0.8321 (mp) REVERT: J 212 ASP cc_start: 0.8525 (p0) cc_final: 0.8304 (p0) REVERT: K 108 ASP cc_start: 0.8840 (p0) cc_final: 0.8577 (p0) REVERT: L 247 GLU cc_start: 0.3936 (OUTLIER) cc_final: 0.2545 (tt0) REVERT: O 47 TRP cc_start: 0.8257 (t60) cc_final: 0.7413 (t60) REVERT: P 53 ARG cc_start: 0.8241 (ptt-90) cc_final: 0.7906 (ptt90) REVERT: Q 81 MET cc_start: 0.7433 (tmm) cc_final: 0.6932 (tmm) REVERT: Q 101 MET cc_start: 0.5002 (ppp) cc_final: 0.4559 (ppp) REVERT: S 4 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6233 (pp) REVERT: S 111 TYR cc_start: 0.5638 (t80) cc_final: 0.5070 (t80) REVERT: T 4 LEU cc_start: 0.8678 (mt) cc_final: 0.8467 (mp) REVERT: T 30 GLN cc_start: 0.8305 (mt0) cc_final: 0.7998 (mt0) REVERT: T 53 ARG cc_start: 0.8050 (ptp90) cc_final: 0.7563 (ptp90) REVERT: T 87 TYR cc_start: 0.8452 (m-80) cc_final: 0.8085 (m-80) outliers start: 111 outliers final: 92 residues processed: 589 average time/residue: 0.2098 time to fit residues: 204.3703 Evaluate side-chains 599 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 495 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 77 GLN Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 390 HIS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain I residue 120 MET Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 370 CYS Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain K residue 66 MET Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain L residue 247 GLU Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 325 optimal weight: 0.9990 chunk 408 optimal weight: 20.0000 chunk 290 optimal weight: 7.9990 chunk 319 optimal weight: 2.9990 chunk 90 optimal weight: 0.0070 chunk 30 optimal weight: 8.9990 chunk 328 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 336 optimal weight: 4.9990 chunk 209 optimal weight: 0.0170 chunk 52 optimal weight: 3.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN B 232 GLN B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN E 361 HIS G 264 ASN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS O 114 GLN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.175411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124484 restraints weight = 48118.410| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.84 r_work: 0.2848 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 39679 Z= 0.150 Angle : 0.599 10.361 54065 Z= 0.306 Chirality : 0.045 0.265 6007 Planarity : 0.004 0.056 6912 Dihedral : 5.289 77.578 5663 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.64 % Allowed : 16.95 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.12), residues: 4944 helix: 1.55 (0.25), residues: 463 sheet: -0.15 (0.12), residues: 1702 loop : -0.58 (0.12), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 366 TYR 0.021 0.001 TYR F 209 PHE 0.020 0.001 PHE J 365 TRP 0.048 0.001 TRP O 36 HIS 0.005 0.001 HIS J 230 Details of bonding type rmsd covalent geometry : bond 0.00364 (39612) covalent geometry : angle 0.59313 (53924) SS BOND : bond 0.00437 ( 60) SS BOND : angle 1.42409 ( 120) hydrogen bonds : bond 0.03098 ( 1384) hydrogen bonds : angle 5.26558 ( 3723) link_NAG-ASN : bond 0.00354 ( 7) link_NAG-ASN : angle 3.00772 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9888 Ramachandran restraints generated. 4944 Oldfield, 0 Emsley, 4944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 499 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: A 260 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: A 385 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.7873 (p0) REVERT: B 114 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7995 (t80) REVERT: B 127 TYR cc_start: 0.8828 (m-80) cc_final: 0.8397 (m-80) REVERT: B 201 GLU cc_start: 0.8102 (pp20) cc_final: 0.7709 (pp20) REVERT: C 211 ASN cc_start: 0.8550 (t0) cc_final: 0.8108 (t0) REVERT: D 24 TYR cc_start: 0.8821 (m-80) cc_final: 0.8161 (m-80) REVERT: D 45 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: D 87 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8882 (m-80) REVERT: D 145 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8536 (m) REVERT: E 199 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7683 (mm-30) REVERT: F 220 VAL cc_start: 0.8540 (t) cc_final: 0.8157 (p) REVERT: F 257 MET cc_start: 0.8186 (ptp) cc_final: 0.7948 (ptp) REVERT: G 346 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7614 (mp) REVERT: H 287 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.8979 (mt) REVERT: H 401 ARG cc_start: 0.8907 (tpp80) cc_final: 0.8692 (tpp80) REVERT: J 120 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8782 (pt0) REVERT: J 166 LEU cc_start: 0.8773 (tp) cc_final: 0.8334 (mp) REVERT: J 212 ASP cc_start: 0.8542 (p0) cc_final: 0.8305 (p0) REVERT: J 366 ARG cc_start: 0.9005 (ttp80) cc_final: 0.8452 (ttp80) REVERT: L 173 TYR cc_start: 0.8686 (m-80) cc_final: 0.8449 (m-10) REVERT: L 211 ASN cc_start: 0.8985 (t0) cc_final: 0.8630 (t0) REVERT: L 247 GLU cc_start: 0.3871 (OUTLIER) cc_final: 0.2473 (tt0) REVERT: O 47 TRP cc_start: 0.8275 (t60) cc_final: 0.7424 (t60) REVERT: P 53 ARG cc_start: 0.8270 (ptt-90) cc_final: 0.7930 (ptt90) REVERT: Q 81 MET cc_start: 0.7436 (tmm) cc_final: 0.6927 (tmm) REVERT: Q 101 MET cc_start: 0.4705 (ppp) cc_final: 0.4235 (ppp) REVERT: S 4 LEU cc_start: 0.6579 (OUTLIER) cc_final: 0.6189 (pp) REVERT: S 111 TYR cc_start: 0.5631 (t80) cc_final: 0.5068 (t80) REVERT: T 4 LEU cc_start: 0.8690 (mt) cc_final: 0.8475 (mp) REVERT: T 30 GLN cc_start: 0.8286 (mt0) cc_final: 0.7978 (mt0) REVERT: T 50 ASP cc_start: 0.8431 (t0) cc_final: 0.8228 (t0) REVERT: T 53 ARG cc_start: 0.8056 (ptp90) cc_final: 0.7562 (ptp90) REVERT: T 87 TYR cc_start: 0.8464 (m-80) cc_final: 0.8047 (m-80) outliers start: 111 outliers final: 91 residues processed: 578 average time/residue: 0.2124 time to fit residues: 202.5477 Evaluate side-chains 597 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 494 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 200 CYS Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 218 LYS Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 45 GLU Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 390 HIS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 192 ASP Chi-restraints excluded: chain E residue 200 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 237 VAL Chi-restraints excluded: chain E residue 263 ASP Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 374 CYS Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 61 LEU Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 287 LEU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 367 THR Chi-restraints excluded: chain I residue 245 VAL Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain J residue 55 MET Chi-restraints excluded: chain J residue 63 CYS Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 120 GLU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 302 THR Chi-restraints excluded: chain J residue 315 ILE Chi-restraints excluded: chain J residue 374 VAL Chi-restraints excluded: chain J residue 397 THR Chi-restraints excluded: chain K residue 82 VAL Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 192 THR Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 247 GLU Chi-restraints excluded: chain L residue 265 VAL Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 55 SER Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain P residue 45 LEU Chi-restraints excluded: chain P residue 63 SER Chi-restraints excluded: chain Q residue 24 SER Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain T residue 29 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 14 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 474 optimal weight: 0.9990 chunk 422 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 278 optimal weight: 0.9990 chunk 351 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 296 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 439 optimal weight: 5.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN D 386 HIS E 361 HIS G 264 ASN H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS O 114 GLN ** Q 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.177444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.125408 restraints weight = 48291.515| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 1.93 r_work: 0.2869 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 39679 Z= 0.111 Angle : 0.572 10.785 54065 Z= 0.293 Chirality : 0.044 0.245 6007 Planarity : 0.004 0.057 6912 Dihedral : 5.008 76.836 5660 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.17 % Allowed : 17.55 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.12), residues: 4944 helix: 1.65 (0.26), residues: 463 sheet: -0.03 (0.13), residues: 1619 loop : -0.57 (0.12), residues: 2862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 366 TYR 0.023 0.001 TYR D 15 PHE 0.021 0.001 PHE A 365 TRP 0.041 0.001 TRP O 36 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00262 (39612) covalent geometry : angle 0.56720 (53924) SS BOND : bond 0.00330 ( 60) SS BOND : angle 1.22945 ( 120) hydrogen bonds : bond 0.02892 ( 1384) hydrogen bonds : angle 5.15303 ( 3723) link_NAG-ASN : bond 0.00301 ( 7) link_NAG-ASN : angle 2.72995 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14286.91 seconds wall clock time: 243 minutes 46.46 seconds (14626.46 seconds total)