Starting phenix.real_space_refine on Mon Jul 6 18:57:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sfw_25104/07_2026/7sfw_25104.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sfw_25104/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7sfw_25104/07_2026/7sfw_25104.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sfw_25104/07_2026/7sfw_25104.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sfw_25104/07_2026/7sfw_25104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sfw_25104/07_2026/7sfw_25104.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sfw_25104/07_2026/7sfw_25104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sfw_25104/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 chiralities: 2 Time building chain proxies: 8.93, per 1000 atoms: 0.23 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: 3.11 Conformation dependent library (CDL) restraints added in 1.9 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: 1.85 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: 10.70 Time building geometry restraints manager: 4.31 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 - 17.97: 21274 17.97 - 35.93: 1863 35.93 - 53.90: 340 53.90 - 71.86: 65 71.86 - 89.83: 50 Dihedral angle restraints: 23592 sinusoidal: 9164 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 23589 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: 2.550 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: 0.040 Extract box with map and model: 0.860 Check model and map are aligned: 0.170 Set scattering table: 0.140 Process input model: 38.700 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 14.023 89.830 14212 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/Z covalent geometry : bond 0.00355 / 0.15 (39612) covalent geometry : angle 0.61791 / 0.33 (53924) SS BOND : bond 0.00358 / 0.24 ( 60) SS BOND : angle 1.66845 / 1.15 ( 120) hydrogen bonds : bond 0.14073 / 9.79 ( 1384) hydrogen bonds : angle 7.27117 / 5.07 ( 3723) link_NAG-ASN : bond 0.00373 / 0.18 ( 7) link_NAG-ASN : angle 3.07831 / 1.70 ( 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 : 1.397 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: 0.2269 time to fit residues: 244.5513 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 : 1.986 ------------------------------------------------------------------------------- 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... C 197 GLN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.174692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123081 restraints weight = 48582.774| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.94 r_work: 0.3018 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 39679 Z= 0.214 Angle : 0.647 9.145 54065 Z= 0.334 Chirality : 0.047 0.269 6007 Planarity : 0.005 0.083 6912 Dihedral : 5.221 76.331 5411 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.61 % Favored : 95.37 % Rotamer: Outliers : 1.29 % Allowed : 7.95 % Favored : 90.76 % 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: -0.37 (0.12), residues: 4944 helix: 1.13 (0.25), residues: 473 sheet: -0.05 (0.12), residues: 1724 loop : -0.56 (0.12), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 185 TYR 0.020 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/Z covalent geometry : bond 0.00522 / 0.21 (39612) covalent geometry : angle 0.63961 / 0.33 (53924) SS BOND : bond 0.00491 / 0.32 ( 60) SS BOND : angle 1.76787 / 1.23 ( 120) hydrogen bonds : bond 0.03787 / 2.52 ( 1384) hydrogen bonds : angle 5.85591 / 4.05 ( 3723) link_NAG-ASN : bond 0.00508 / 0.25 ( 7) link_NAG-ASN : angle 3.20506 / 1.85 ( 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 631 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 577 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 21 ARG cc_start: 0.8119 (tpt90) cc_final: 0.7786 (mmm160) REVERT: B 70 MET cc_start: 0.8414 (mmm) cc_final: 0.8154 (tpt) REVERT: B 311 ILE cc_start: 0.8484 (pt) cc_final: 0.8209 (pt) REVERT: B 347 ASN cc_start: 0.8721 (t0) cc_final: 0.8481 (t0) REVERT: C 121 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7773 (mmtm) REVERT: D 87 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: D 390 HIS cc_start: 0.7540 (m-70) cc_final: 0.7329 (m-70) REVERT: E 173 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7700 (pt0) REVERT: E 201 GLU cc_start: 0.8370 (tm-30) cc_final: 0.7800 (tm-30) REVERT: E 365 MET cc_start: 0.7384 (tpp) cc_final: 0.6596 (tmm) REVERT: F 118 MET cc_start: 0.5693 (ptt) cc_final: 0.5334 (ptt) REVERT: F 151 MET cc_start: 0.8719 (tpp) cc_final: 0.8238 (tpp) REVERT: I 174 ASP cc_start: 0.8483 (t70) cc_final: 0.8269 (t0) REVERT: I 191 TYR cc_start: 0.8490 (p90) cc_final: 0.7784 (p90) REVERT: J 24 TYR cc_start: 0.8640 (m-80) cc_final: 0.8372 (m-80) REVERT: J 142 ILE cc_start: 0.8089 (tt) cc_final: 0.7814 (tp) REVERT: L 184 MET cc_start: 0.8696 (ptm) cc_final: 0.8450 (ptt) REVERT: N 104 THR cc_start: 0.8712 (m) cc_final: 0.8399 (t) REVERT: P 44 VAL cc_start: 0.9136 (t) cc_final: 0.8869 (p) REVERT: P 53 ARG cc_start: 0.8328 (ptt-90) cc_final: 0.7896 (ptt90) REVERT: P 69 THR cc_start: 0.8126 (t) cc_final: 0.7844 (m) REVERT: R 34 TRP cc_start: 0.8223 (m100) cc_final: 0.7941 (m100) REVERT: T 4 LEU cc_start: 0.8644 (mt) cc_final: 0.8426 (mp) REVERT: T 30 GLN cc_start: 0.8442 (mt0) cc_final: 0.8162 (mt0) REVERT: T 87 TYR cc_start: 0.8525 (m-80) cc_final: 0.8258 (m-80) outliers start: 54 outliers final: 35 residues processed: 605 average time/residue: 0.2163 time to fit residues: 217.5404 Evaluate side-chains 567 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 531 time to evaluate : 1.476 ------------------------------------------------------------------------------- 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: 8.9990 chunk 80 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 389 optimal weight: 20.0000 chunk 232 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 472 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 332 ASN B 361 HIS C 197 GLN D 77 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 N 30 GLN O 114 GLN Q 52 ASN Q 100 GLN ** S 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.175204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.123727 restraints weight = 48408.201| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 1.92 r_work: 0.2823 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 39679 Z= 0.208 Angle : 0.628 8.551 54065 Z= 0.322 Chirality : 0.046 0.269 6007 Planarity : 0.005 0.058 6912 Dihedral : 5.210 76.378 5411 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.02 % Allowed : 11.50 % Favored : 86.48 % 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: -0.37 (0.12), residues: 4944 helix: 1.15 (0.25), residues: 473 sheet: -0.01 (0.13), residues: 1669 loop : -0.59 (0.12), residues: 2802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 366 TYR 0.021 0.001 TYR G 308 PHE 0.019 0.002 PHE A 365 TRP 0.020 0.001 TRP O 36 HIS 0.009 0.001 HIS J 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.21 (39612) covalent geometry : angle 0.62138 / 0.32 (53924) SS BOND : bond 0.00414 / 0.29 ( 60) SS BOND : angle 1.57965 / 1.13 ( 120) hydrogen bonds : bond 0.03576 / 2.38 ( 1384) hydrogen bonds : angle 5.65880 / 3.93 ( 3723) link_NAG-ASN : bond 0.00508 / 0.25 ( 7) link_NAG-ASN : angle 3.22686 / 1.87 ( 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 633 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 548 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.7898 (p0) REVERT: B 21 ARG cc_start: 0.7856 (tpt90) cc_final: 0.7561 (mmm160) REVERT: B 70 MET cc_start: 0.8413 (mmm) cc_final: 0.8136 (tpt) REVERT: B 311 ILE cc_start: 0.8601 (pt) cc_final: 0.8296 (pt) REVERT: B 347 ASN cc_start: 0.8702 (t0) cc_final: 0.8315 (t0) REVERT: C 211 ASN cc_start: 0.8444 (t0) cc_final: 0.7956 (t0) REVERT: D 87 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8857 (m-80) REVERT: D 145 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8541 (p) REVERT: D 368 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: D 385 ASP cc_start: 0.8389 (p0) cc_final: 0.8111 (p0) REVERT: E 167 MET cc_start: 0.9344 (ptp) cc_final: 0.9139 (ptp) REVERT: E 199 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7841 (mm-30) REVERT: E 201 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8147 (tm-30) REVERT: F 151 MET cc_start: 0.8740 (tpp) cc_final: 0.8150 (tpp) REVERT: F 218 LYS cc_start: 0.8669 (tttt) cc_final: 0.8425 (tppt) REVERT: I 174 ASP cc_start: 0.8506 (t70) cc_final: 0.7986 (t0) REVERT: I 191 TYR cc_start: 0.8463 (p90) cc_final: 0.7696 (p90) REVERT: J 142 ILE cc_start: 0.7996 (tt) cc_final: 0.7749 (tp) REVERT: N 104 THR cc_start: 0.8707 (m) cc_final: 0.8391 (t) REVERT: P 44 VAL cc_start: 0.9164 (t) cc_final: 0.8740 (p) REVERT: P 53 ARG cc_start: 0.8171 (ptt-90) cc_final: 0.7845 (ptt90) REVERT: P 69 THR cc_start: 0.7993 (t) cc_final: 0.7783 (m) REVERT: R 34 TRP cc_start: 0.8121 (m100) cc_final: 0.7902 (m100) REVERT: T 4 LEU cc_start: 0.8610 (mt) cc_final: 0.8396 (mp) REVERT: T 30 GLN cc_start: 0.8352 (mt0) cc_final: 0.8054 (mt0) REVERT: T 87 TYR cc_start: 0.8535 (m-80) cc_final: 0.8204 (m-80) REVERT: T 97 GLU cc_start: 0.8097 (pm20) cc_final: 0.7892 (pm20) outliers start: 85 outliers final: 59 residues processed: 598 average time/residue: 0.2249 time to fit residues: 223.2765 Evaluate side-chains 583 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 520 time to evaluate : 1.442 ------------------------------------------------------------------------------- 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 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 A residue 411 THR Chi-restraints excluded: chain A residue 429 THR 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 257 VAL 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 197 GLN Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 87 PHE Chi-restraints excluded: chain D residue 145 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 368 GLN Chi-restraints excluded: chain D residue 433 MET 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 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 186 VAL Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 297 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 137 VAL 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 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 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 48 MET Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain S residue 24 SER 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: 3.9990 chunk 219 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 412 optimal weight: 0.1980 chunk 91 optimal weight: 20.0000 chunk 315 optimal weight: 0.8980 chunk 460 optimal weight: 10.0000 chunk 341 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 363 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 361 HIS C 197 GLN D 77 GLN D 349 GLN D 368 GLN D 438 ASN G 264 ASN H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 225 GLN N 30 GLN O 114 GLN Q 52 ASN T 16 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.176675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.125506 restraints weight = 48220.973| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.97 r_work: 0.2853 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 39679 Z= 0.138 Angle : 0.581 8.192 54065 Z= 0.298 Chirality : 0.045 0.258 6007 Planarity : 0.004 0.058 6912 Dihedral : 5.055 76.238 5411 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.31 % Allowed : 13.29 % Favored : 84.40 % 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: -0.31 (0.12), residues: 4944 helix: 1.26 (0.25), residues: 473 sheet: 0.02 (0.13), residues: 1673 loop : -0.56 (0.12), residues: 2798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 289 TYR 0.017 0.001 TYR G 308 PHE 0.016 0.001 PHE A 365 TRP 0.022 0.001 TRP O 36 HIS 0.005 0.001 HIS J 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (39612) covalent geometry : angle 0.57499 / 0.30 (53924) SS BOND : bond 0.00324 / 0.23 ( 60) SS BOND : angle 1.39316 / 0.96 ( 120) hydrogen bonds : bond 0.03214 / 2.13 ( 1384) hydrogen bonds : angle 5.48245 / 3.80 ( 3723) link_NAG-ASN : bond 0.00327 / 0.16 ( 7) link_NAG-ASN : angle 3.02281 / 1.75 ( 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 642 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 545 time to evaluate : 1.122 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: 0.8313 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: A 385 ASP cc_start: 0.8745 (OUTLIER) cc_final: 0.7899 (p0) REVERT: B 21 ARG cc_start: 0.7906 (tpt90) cc_final: 0.7586 (mmm160) REVERT: B 70 MET cc_start: 0.8343 (mmm) cc_final: 0.8000 (tpt) REVERT: B 114 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7982 (t80) REVERT: B 231 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8494 (pp) REVERT: B 311 ILE cc_start: 0.8525 (pt) cc_final: 0.8225 (pt) REVERT: C 211 ASN cc_start: 0.8568 (t0) cc_final: 0.8174 (t0) REVERT: D 18 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8427 (tt) REVERT: D 87 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8793 (m-80) REVERT: D 261 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9182 (mp) REVERT: D 368 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7954 (tm-30) REVERT: D 385 ASP cc_start: 0.8389 (p0) cc_final: 0.7944 (p0) REVERT: E 199 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7653 (mm-30) REVERT: F 151 MET cc_start: 0.8812 (tpp) cc_final: 0.8232 (tpp) REVERT: F 218 LYS cc_start: 0.8701 (tttt) cc_final: 0.8421 (tppt) REVERT: I 174 ASP cc_start: 0.8565 (t70) cc_final: 0.7997 (t0) REVERT: I 191 TYR cc_start: 0.8495 (p90) cc_final: 0.7737 (p90) REVERT: J 346 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7760 (mp) REVERT: J 364 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7922 (mm-30) REVERT: N 104 THR cc_start: 0.8651 (m) cc_final: 0.8313 (t) REVERT: P 44 VAL cc_start: 0.9111 (t) cc_final: 0.8880 (m) REVERT: P 69 THR cc_start: 0.8071 (t) cc_final: 0.7804 (m) REVERT: Q 22 CYS cc_start: 0.7558 (t) cc_final: 0.7332 (t) REVERT: Q 52 ASN cc_start: 0.8118 (t0) cc_final: 0.7499 (t0) REVERT: T 4 LEU cc_start: 0.8621 (mt) cc_final: 0.8407 (mp) REVERT: T 30 GLN cc_start: 0.8319 (mt0) cc_final: 0.8010 (mt0) REVERT: T 87 TYR cc_start: 0.8459 (m-80) cc_final: 0.8143 (m-80) REVERT: T 97 GLU cc_start: 0.8094 (pm20) cc_final: 0.7861 (pm20) outliers start: 97 outliers final: 64 residues processed: 608 average time/residue: 0.2183 time to fit residues: 219.9496 Evaluate side-chains 587 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 514 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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 115 LEU 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 376 CYS Chi-restraints excluded: chain A residue 385 ASP Chi-restraints excluded: chain A residue 409 TRP 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 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 231 LEU Chi-restraints excluded: chain B residue 232 GLN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain D residue 18 ILE 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 154 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 THR Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 438 ASN Chi-restraints excluded: chain E residue 49 THR 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 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 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 293 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 277 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain L residue 230 ILE 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: 9.9990 chunk 116 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 179 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 402 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 240 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 ASN B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 S 3 GLN T 16 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.174379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122645 restraints weight = 48175.613| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.85 r_work: 0.2812 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 39679 Z= 0.231 Angle : 0.636 9.673 54065 Z= 0.325 Chirality : 0.047 0.271 6007 Planarity : 0.005 0.057 6912 Dihedral : 5.201 76.622 5411 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.17 % Allowed : 14.36 % Favored : 82.48 % 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: 1.20 (0.25), residues: 473 sheet: -0.03 (0.13), residues: 1643 loop : -0.59 (0.12), residues: 2828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 362 TYR 0.021 0.002 TYR G 308 PHE 0.020 0.002 PHE A 365 TRP 0.024 0.001 TRP O 36 HIS 0.010 0.001 HIS J 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.23 (39612) covalent geometry : angle 0.62788 / 0.32 (53924) SS BOND : bond 0.00498 / 0.35 ( 60) SS BOND : angle 1.82859 / 1.32 ( 120) hydrogen bonds : bond 0.03422 / 2.28 ( 1384) hydrogen bonds : angle 5.53221 / 3.84 ( 3723) link_NAG-ASN : bond 0.00547 / 0.27 ( 7) link_NAG-ASN : angle 3.37945 / 1.93 ( 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 653 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 520 time to evaluate : 1.345 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: 0.8358 (OUTLIER) cc_final: 0.7187 (mp0) REVERT: A 366 ARG cc_start: 0.8578 (mtp85) cc_final: 0.8086 (ttp80) REVERT: A 385 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.7938 (p0) REVERT: B 9 TYR cc_start: 0.8915 (m-80) cc_final: 0.8589 (m-80) REVERT: B 21 ARG cc_start: 0.7953 (tpt90) cc_final: 0.7591 (mmm160) REVERT: B 70 MET cc_start: 0.8381 (mmm) cc_final: 0.8113 (tpt) REVERT: B 114 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.8032 (t80) REVERT: B 231 LEU cc_start: 0.8753 (tt) cc_final: 0.8518 (pp) REVERT: B 311 ILE cc_start: 0.8680 (pt) cc_final: 0.8316 (pt) REVERT: C 211 ASN cc_start: 0.8530 (t0) cc_final: 0.8024 (t0) REVERT: D 87 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8912 (m-80) REVERT: D 145 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8538 (p) REVERT: D 261 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9194 (mp) REVERT: E 199 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7698 (mm-30) REVERT: E 232 GLN cc_start: 0.7916 (tt0) cc_final: 0.7493 (tt0) REVERT: F 151 MET cc_start: 0.8847 (tpp) cc_final: 0.8258 (tpp) REVERT: F 218 LYS cc_start: 0.8717 (tttt) cc_final: 0.8419 (tppt) REVERT: H 287 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.8995 (mt) REVERT: H 401 ARG cc_start: 0.8929 (tpp80) cc_final: 0.8682 (tpp80) REVERT: I 174 ASP cc_start: 0.8588 (t70) cc_final: 0.7954 (t0) REVERT: I 191 TYR cc_start: 0.8506 (p90) cc_final: 0.7739 (p90) REVERT: J 120 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8786 (pt0) REVERT: J 247 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5373 (mmmt) REVERT: J 346 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7773 (mp) REVERT: K 108 ASP cc_start: 0.8860 (p0) cc_final: 0.8623 (p0) REVERT: K 232 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: P 44 VAL cc_start: 0.9154 (t) cc_final: 0.8927 (m) REVERT: P 69 THR cc_start: 0.8188 (t) cc_final: 0.7813 (m) REVERT: Q 101 MET cc_start: 0.4639 (ppp) cc_final: 0.4399 (ppp) REVERT: T 4 LEU cc_start: 0.8668 (mt) cc_final: 0.8450 (mp) REVERT: T 30 GLN cc_start: 0.8390 (mt0) cc_final: 0.8070 (mt0) REVERT: T 53 ARG cc_start: 0.8059 (ptp90) cc_final: 0.7554 (ptp90) REVERT: T 87 TYR cc_start: 0.8493 (m-80) cc_final: 0.8119 (m-80) REVERT: T 97 GLU cc_start: 0.8116 (pm20) cc_final: 0.7869 (pm20) outliers start: 133 outliers final: 97 residues processed: 606 average time/residue: 0.2135 time to fit residues: 216.1326 Evaluate side-chains 609 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 501 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 68 CYS 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 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 260 GLU 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 195 SER Chi-restraints excluded: chain B residue 200 CYS 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 257 VAL 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 142 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 241 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 18 ILE 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 145 THR Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 261 ILE 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 390 HIS Chi-restraints excluded: chain D residue 433 MET Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 180 SER 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 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 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 247 LYS 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 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 232 GLN 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 L residue 265 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 470 optimal weight: 4.9990 chunk 382 optimal weight: 9.9990 chunk 78 optimal weight: 0.9980 chunk 468 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 242 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 60 ASN B 361 HIS C 197 GLN D 77 GLN E 81 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** K 361 HIS N 30 GLN O 114 GLN T 16 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.174118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123488 restraints weight = 48268.371| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.86 r_work: 0.2814 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 39679 Z= 0.206 Angle : 0.621 9.559 54065 Z= 0.317 Chirality : 0.046 0.271 6007 Planarity : 0.005 0.057 6912 Dihedral : 5.196 76.716 5411 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.45 % Allowed : 15.07 % Favored : 81.48 % 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: -0.42 (0.12), residues: 4944 helix: 1.22 (0.25), residues: 473 sheet: -0.09 (0.13), residues: 1645 loop : -0.61 (0.12), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 366 TYR 0.020 0.001 TYR G 308 PHE 0.018 0.002 PHE A 365 TRP 0.018 0.001 TRP O 36 HIS 0.008 0.001 HIS J 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 (39612) covalent geometry : angle 0.61338 / 0.31 (53924) SS BOND : bond 0.00515 / 0.38 ( 60) SS BOND : angle 1.59780 / 1.13 ( 120) hydrogen bonds : bond 0.03313 / 2.20 ( 1384) hydrogen bonds : angle 5.47440 / 3.81 ( 3723) link_NAG-ASN : bond 0.00467 / 0.23 ( 7) link_NAG-ASN : angle 3.30276 / 1.90 ( 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 658 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 513 time to evaluate : 1.500 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 151 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8180 (pt0) REVERT: A 260 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: A 366 ARG cc_start: 0.8608 (mtp85) cc_final: 0.8223 (ttp80) REVERT: A 385 ASP cc_start: 0.8750 (OUTLIER) cc_final: 0.7946 (p0) REVERT: B 9 TYR cc_start: 0.8901 (m-80) cc_final: 0.8578 (m-80) REVERT: B 21 ARG cc_start: 0.7724 (tpt90) cc_final: 0.7472 (mmm160) REVERT: B 114 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8047 (t80) REVERT: C 211 ASN cc_start: 0.8555 (t0) cc_final: 0.8058 (t0) REVERT: D 87 PHE cc_start: 0.9180 (OUTLIER) cc_final: 0.8940 (m-80) REVERT: D 145 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8537 (p) REVERT: E 81 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: F 151 MET cc_start: 0.8866 (tpp) cc_final: 0.8279 (tpp) REVERT: F 218 LYS cc_start: 0.8710 (tttt) cc_final: 0.8436 (tppt) REVERT: H 287 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9013 (mt) REVERT: H 401 ARG cc_start: 0.8927 (tpp80) cc_final: 0.8661 (tpp80) REVERT: I 191 TYR cc_start: 0.8523 (p90) cc_final: 0.7752 (p90) REVERT: J 120 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8792 (pt0) REVERT: J 142 ILE cc_start: 0.8050 (tt) cc_final: 0.7748 (tp) REVERT: J 247 LYS cc_start: 0.6272 (OUTLIER) cc_final: 0.5390 (mmmt) REVERT: J 346 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7780 (mp) REVERT: K 108 ASP cc_start: 0.8852 (p0) cc_final: 0.8636 (p0) REVERT: K 232 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: L 247 GLU cc_start: 0.3857 (OUTLIER) cc_final: 0.2491 (tt0) REVERT: P 44 VAL cc_start: 0.9176 (t) cc_final: 0.8959 (m) REVERT: Q 101 MET cc_start: 0.4802 (ppp) cc_final: 0.4486 (ppp) REVERT: S 111 TYR cc_start: 0.5618 (t80) cc_final: 0.4988 (t80) REVERT: T 4 LEU cc_start: 0.8667 (mt) cc_final: 0.8442 (mp) REVERT: T 30 GLN cc_start: 0.8359 (mt0) cc_final: 0.8043 (mt0) REVERT: T 53 ARG cc_start: 0.8058 (ptp90) cc_final: 0.7550 (ptp90) REVERT: T 87 TYR cc_start: 0.8482 (m-80) cc_final: 0.8057 (m-80) REVERT: T 97 GLU cc_start: 0.8119 (pm20) cc_final: 0.7871 (pm20) outliers start: 145 outliers final: 103 residues processed: 607 average time/residue: 0.2206 time to fit residues: 223.5041 Evaluate side-chains 620 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 504 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL 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 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 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 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 257 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 197 GLN 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 18 ILE 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 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 348 GLU Chi-restraints excluded: chain D residue 390 HIS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 81 GLN Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 167 MET Chi-restraints excluded: chain E residue 180 SER 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 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 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 247 LYS 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 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 232 GLN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 288 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 chunk 446 optimal weight: 8.9990 chunk 188 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 225 optimal weight: 3.9990 chunk 23 optimal weight: 0.0670 chunk 343 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 417 optimal weight: 0.8980 overall best weight: 2.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 361 HIS C 197 GLN G 43 ASN G 264 ASN H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 ASN ** K 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.174340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.123229 restraints weight = 48277.007| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.92 r_work: 0.2791 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 39679 Z= 0.196 Angle : 0.618 9.655 54065 Z= 0.316 Chirality : 0.046 0.270 6007 Planarity : 0.005 0.057 6912 Dihedral : 5.191 77.201 5411 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.48 % Allowed : 15.79 % 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: -0.42 (0.12), residues: 4944 helix: 1.38 (0.25), residues: 461 sheet: -0.13 (0.12), residues: 1690 loop : -0.61 (0.12), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 366 TYR 0.020 0.001 TYR G 308 PHE 0.017 0.001 PHE A 365 TRP 0.029 0.001 TRP O 36 HIS 0.008 0.001 HIS J 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (39612) covalent geometry : angle 0.61029 / 0.31 (53924) SS BOND : bond 0.00556 / 0.40 ( 60) SS BOND : angle 1.66704 / 1.17 ( 120) hydrogen bonds : bond 0.03298 / 2.19 ( 1384) hydrogen bonds : angle 5.43431 / 3.78 ( 3723) link_NAG-ASN : bond 0.00451 / 0.22 ( 7) link_NAG-ASN : angle 3.26456 / 1.88 ( 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 650 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 504 time to evaluate : 1.457 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: 0.8366 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: A 366 ARG cc_start: 0.8647 (mtp85) cc_final: 0.8333 (ttp80) REVERT: A 385 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.7971 (p0) REVERT: B 9 TYR cc_start: 0.8900 (m-80) cc_final: 0.8580 (m-80) REVERT: B 21 ARG cc_start: 0.7877 (tpt90) cc_final: 0.7582 (mmm160) REVERT: B 114 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8060 (t80) REVERT: B 201 GLU cc_start: 0.7981 (pp20) cc_final: 0.7622 (pp20) REVERT: C 211 ASN cc_start: 0.8591 (t0) cc_final: 0.8168 (t0) REVERT: D 87 PHE cc_start: 0.9183 (OUTLIER) cc_final: 0.8951 (m-80) REVERT: D 145 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8550 (p) REVERT: E 199 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7741 (mm-30) REVERT: F 208 GLN cc_start: 0.7060 (pm20) cc_final: 0.6838 (pm20) REVERT: H 287 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9008 (mt) REVERT: H 401 ARG cc_start: 0.8954 (tpp80) cc_final: 0.8672 (tpp80) REVERT: I 191 TYR cc_start: 0.8541 (p90) cc_final: 0.7779 (p90) REVERT: J 120 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8784 (pt0) REVERT: J 142 ILE cc_start: 0.8075 (tt) cc_final: 0.7799 (tp) REVERT: J 247 LYS cc_start: 0.6285 (OUTLIER) cc_final: 0.4555 (mtpp) REVERT: J 346 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7793 (mp) REVERT: K 108 ASP cc_start: 0.8847 (p0) cc_final: 0.8628 (p0) REVERT: K 232 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: O 47 TRP cc_start: 0.8336 (t60) cc_final: 0.7450 (t60) REVERT: P 44 VAL cc_start: 0.9179 (t) cc_final: 0.8962 (m) REVERT: Q 101 MET cc_start: 0.4979 (ppp) cc_final: 0.4568 (ppp) REVERT: S 111 TYR cc_start: 0.5608 (t80) cc_final: 0.5003 (t80) REVERT: T 4 LEU cc_start: 0.8673 (mt) cc_final: 0.8447 (mp) REVERT: T 30 GLN cc_start: 0.8397 (mt0) cc_final: 0.8082 (mt0) REVERT: T 53 ARG cc_start: 0.8078 (ptp90) cc_final: 0.7569 (ptp90) REVERT: T 87 TYR cc_start: 0.8514 (m-80) cc_final: 0.8113 (m-80) outliers start: 146 outliers final: 115 residues processed: 603 average time/residue: 0.2339 time to fit residues: 234.3148 Evaluate side-chains 619 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 494 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 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 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 186 VAL 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 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 257 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 300 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 251 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 18 ILE 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 120 GLU 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 348 GLU Chi-restraints excluded: chain D residue 390 HIS Chi-restraints excluded: chain D residue 397 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 140 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 F residue 256 VAL 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 247 LYS 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 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 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 232 GLN 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 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 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 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: 2.9990 chunk 329 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 383 optimal weight: 1.9990 chunk 453 optimal weight: 9.9990 chunk 449 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS O 114 GLN S 35 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.175140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.124162 restraints weight = 48087.503| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.85 r_work: 0.2837 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1740 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= 0.167 Angle : 0.602 9.667 54065 Z= 0.307 Chirality : 0.045 0.265 6007 Planarity : 0.004 0.057 6912 Dihedral : 5.109 77.297 5411 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.31 % Allowed : 16.07 % Favored : 80.62 % 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: -0.39 (0.12), residues: 4944 helix: 1.45 (0.26), residues: 461 sheet: -0.11 (0.13), residues: 1688 loop : -0.60 (0.12), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 289 TYR 0.019 0.001 TYR G 308 PHE 0.015 0.001 PHE A 365 TRP 0.036 0.001 TRP O 36 HIS 0.006 0.001 HIS J 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (39612) covalent geometry : angle 0.59444 / 0.30 (53924) SS BOND : bond 0.00438 / 0.31 ( 60) SS BOND : angle 1.54939 / 1.08 ( 120) hydrogen bonds : bond 0.03156 / 2.10 ( 1384) hydrogen bonds : angle 5.36604 / 3.73 ( 3723) link_NAG-ASN : bond 0.00396 / 0.19 ( 7) link_NAG-ASN : angle 3.25971 / 1.86 ( 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 645 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 506 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: A 260 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: A 366 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8356 (ttp80) REVERT: A 385 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.7889 (p0) REVERT: B 9 TYR cc_start: 0.8874 (m-80) cc_final: 0.8545 (m-80) REVERT: B 21 ARG cc_start: 0.7826 (tpt90) cc_final: 0.7549 (mmm160) REVERT: B 114 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7993 (t80) REVERT: B 201 GLU cc_start: 0.8084 (pp20) cc_final: 0.7677 (pp20) REVERT: B 311 ILE cc_start: 0.8686 (pt) cc_final: 0.8285 (pt) REVERT: B 347 ASN cc_start: 0.8706 (t0) cc_final: 0.8174 (t0) REVERT: D 87 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8925 (m-80) REVERT: D 145 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8521 (p) REVERT: E 199 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7651 (mm-30) REVERT: F 208 GLN cc_start: 0.7122 (pm20) cc_final: 0.6850 (pm20) REVERT: F 220 VAL cc_start: 0.8547 (t) cc_final: 0.8147 (p) REVERT: G 346 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7569 (mp) REVERT: H 287 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9000 (mt) REVERT: I 191 TYR cc_start: 0.8508 (p90) cc_final: 0.7708 (p90) REVERT: J 120 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8790 (pt0) REVERT: J 142 ILE cc_start: 0.8018 (tt) cc_final: 0.7760 (tp) REVERT: J 166 LEU cc_start: 0.8772 (tp) cc_final: 0.8379 (mp) REVERT: J 247 LYS cc_start: 0.6368 (OUTLIER) cc_final: 0.5205 (mmmt) REVERT: J 346 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7726 (mp) REVERT: K 108 ASP cc_start: 0.8821 (p0) cc_final: 0.8612 (p0) REVERT: K 232 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7488 (mp10) REVERT: L 247 GLU cc_start: 0.3838 (OUTLIER) cc_final: 0.2488 (tt0) REVERT: O 47 TRP cc_start: 0.8272 (t60) cc_final: 0.7428 (t60) REVERT: P 44 VAL cc_start: 0.9152 (t) cc_final: 0.8944 (m) REVERT: Q 101 MET cc_start: 0.4910 (ppp) cc_final: 0.4485 (ppp) REVERT: S 111 TYR cc_start: 0.5635 (t80) cc_final: 0.5039 (t80) REVERT: T 4 LEU cc_start: 0.8685 (mt) cc_final: 0.8461 (mp) REVERT: T 30 GLN cc_start: 0.8356 (mt0) cc_final: 0.8051 (mt0) REVERT: T 53 ARG cc_start: 0.8029 (ptp90) cc_final: 0.7502 (ptp90) REVERT: T 87 TYR cc_start: 0.8465 (m-80) cc_final: 0.8093 (m-80) REVERT: T 97 GLU cc_start: 0.8059 (pm20) cc_final: 0.7854 (pm20) outliers start: 139 outliers final: 111 residues processed: 602 average time/residue: 0.2370 time to fit residues: 237.0289 Evaluate side-chains 619 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 495 time to evaluate : 1.546 ------------------------------------------------------------------------------- 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 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 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 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 257 VAL Chi-restraints excluded: chain B residue 300 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 251 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 18 ILE 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 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 348 GLU Chi-restraints excluded: chain D residue 390 HIS Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 140 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 F residue 256 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 115 LEU 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 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 137 VAL Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 246 ASP Chi-restraints excluded: chain J residue 247 LYS 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 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 232 GLN 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 R residue 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 20 VAL 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: 4.9990 chunk 462 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 chunk 416 optimal weight: 9.9990 chunk 461 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 386 optimal weight: 9.9990 chunk 8 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 ASN H 361 HIS I 152 HIS J 157 ASN ** K 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS O 114 GLN Q 55 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.175067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.124534 restraints weight = 48286.482| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.96 r_work: 0.2821 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 39679 Z= 0.167 Angle : 0.601 10.168 54065 Z= 0.307 Chirality : 0.045 0.263 6007 Planarity : 0.004 0.057 6912 Dihedral : 5.086 77.186 5411 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.38 % Allowed : 16.31 % Favored : 80.31 % 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: -0.39 (0.12), residues: 4944 helix: 1.48 (0.25), residues: 463 sheet: -0.10 (0.13), residues: 1688 loop : -0.61 (0.12), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 366 TYR 0.018 0.001 TYR D 320 PHE 0.016 0.001 PHE A 365 TRP 0.039 0.001 TRP O 36 HIS 0.006 0.001 HIS J 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (39612) covalent geometry : angle 0.59440 / 0.30 (53924) SS BOND : bond 0.00427 / 0.31 ( 60) SS BOND : angle 1.51972 / 1.07 ( 120) hydrogen bonds : bond 0.03142 / 2.09 ( 1384) hydrogen bonds : angle 5.32345 / 3.70 ( 3723) link_NAG-ASN : bond 0.00395 / 0.19 ( 7) link_NAG-ASN : angle 3.15006 / 1.80 ( 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 645 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 503 time to evaluate : 1.533 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 88 MET cc_start: 0.8631 (mmm) cc_final: 0.8413 (mtt) REVERT: A 151 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8212 (pt0) REVERT: A 260 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: A 385 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.7889 (p0) REVERT: B 9 TYR cc_start: 0.8870 (m-80) cc_final: 0.8536 (m-80) REVERT: B 21 ARG cc_start: 0.7906 (tpt90) cc_final: 0.7575 (mmm160) REVERT: B 114 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7981 (t80) REVERT: B 127 TYR cc_start: 0.8832 (m-80) cc_final: 0.8386 (m-80) REVERT: B 201 GLU cc_start: 0.8121 (pp20) cc_final: 0.7675 (pp20) REVERT: B 311 ILE cc_start: 0.8691 (pt) cc_final: 0.8291 (pt) REVERT: B 347 ASN cc_start: 0.8709 (t0) cc_final: 0.8501 (t0) REVERT: C 211 ASN cc_start: 0.8596 (t0) cc_final: 0.8112 (t0) REVERT: D 87 PHE cc_start: 0.9161 (OUTLIER) cc_final: 0.8917 (m-80) REVERT: D 145 THR cc_start: 0.8777 (OUTLIER) cc_final: 0.8561 (m) REVERT: E 199 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7674 (mm-30) REVERT: F 208 GLN cc_start: 0.7143 (pm20) cc_final: 0.6876 (pm20) REVERT: F 220 VAL cc_start: 0.8549 (t) cc_final: 0.8125 (p) REVERT: G 346 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7624 (mp) REVERT: H 287 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.8984 (mt) REVERT: J 120 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8817 (pt0) REVERT: J 142 ILE cc_start: 0.8005 (tt) cc_final: 0.7749 (tp) REVERT: J 247 LYS cc_start: 0.6357 (OUTLIER) cc_final: 0.4679 (mtpp) REVERT: J 346 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7704 (mp) REVERT: K 232 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: L 211 ASN cc_start: 0.8996 (t0) cc_final: 0.8643 (t0) REVERT: L 247 GLU cc_start: 0.3824 (OUTLIER) cc_final: 0.2451 (tt0) REVERT: O 47 TRP cc_start: 0.8237 (t60) cc_final: 0.7399 (t60) REVERT: P 44 VAL cc_start: 0.9132 (t) cc_final: 0.8925 (m) REVERT: Q 101 MET cc_start: 0.5041 (ppp) cc_final: 0.4574 (ppp) REVERT: S 111 TYR cc_start: 0.5694 (t80) cc_final: 0.5100 (t80) REVERT: T 4 LEU cc_start: 0.8685 (mt) cc_final: 0.8464 (mp) REVERT: T 30 GLN cc_start: 0.8312 (mt0) cc_final: 0.8000 (mt0) REVERT: T 53 ARG cc_start: 0.8007 (ptp90) cc_final: 0.7470 (ptp90) REVERT: T 87 TYR cc_start: 0.8480 (m-80) cc_final: 0.8042 (m-80) outliers start: 142 outliers final: 119 residues processed: 602 average time/residue: 0.2376 time to fit residues: 237.6075 Evaluate side-chains 627 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 495 time to evaluate : 1.334 ------------------------------------------------------------------------------- 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 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 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 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 257 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 300 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 251 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 18 ILE 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 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 293 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 D residue 397 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 140 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 211 ILE 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 F residue 256 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 376 CYS 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 63 CYS 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 247 LYS 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 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 232 GLN 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 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 20 VAL 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: 0.9980 chunk 408 optimal weight: 20.0000 chunk 290 optimal weight: 0.9980 chunk 319 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 328 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 209 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 361 HIS ** C 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN G 264 ASN H 361 HIS ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS O 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.175624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124799 restraints weight = 48086.184| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.91 r_work: 0.2840 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 39679 Z= 0.148 Angle : 0.595 10.527 54065 Z= 0.303 Chirality : 0.045 0.259 6007 Planarity : 0.004 0.056 6912 Dihedral : 5.036 77.228 5411 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.33 % Allowed : 16.45 % Favored : 80.21 % 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: -0.37 (0.12), residues: 4944 helix: 1.53 (0.26), residues: 463 sheet: -0.10 (0.13), residues: 1694 loop : -0.60 (0.12), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 366 TYR 0.020 0.001 TYR D 320 PHE 0.019 0.001 PHE D 365 TRP 0.041 0.001 TRP O 36 HIS 0.005 0.001 HIS J 230 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (39612) covalent geometry : angle 0.58754 / 0.30 (53924) SS BOND : bond 0.00391 / 0.28 ( 60) SS BOND : angle 1.42987 / 1.01 ( 120) hydrogen bonds : bond 0.03075 / 2.04 ( 1384) hydrogen bonds : angle 5.27766 / 3.67 ( 3723) link_NAG-ASN : bond 0.00345 / 0.17 ( 7) link_NAG-ASN : angle 3.64575 / 1.94 ( 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 646 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 506 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8183 (pt0) REVERT: A 260 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: A 366 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8047 (ttp80) REVERT: A 385 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.7871 (p0) REVERT: B 9 TYR cc_start: 0.8872 (m-80) cc_final: 0.8536 (m-80) REVERT: B 21 ARG cc_start: 0.7765 (tpt90) cc_final: 0.7483 (mmm160) REVERT: B 114 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7946 (t80) REVERT: B 127 TYR cc_start: 0.8818 (m-80) cc_final: 0.8371 (m-80) REVERT: B 201 GLU cc_start: 0.8156 (pp20) cc_final: 0.7707 (pp20) REVERT: B 311 ILE cc_start: 0.8651 (pt) cc_final: 0.8259 (pt) REVERT: B 347 ASN cc_start: 0.8699 (t0) cc_final: 0.8495 (t0) REVERT: D 87 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8892 (m-80) REVERT: D 145 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8565 (m) REVERT: E 199 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7642 (mm-30) REVERT: F 208 GLN cc_start: 0.7144 (pm20) cc_final: 0.6899 (pm20) REVERT: F 220 VAL cc_start: 0.8532 (t) cc_final: 0.8142 (p) REVERT: G 346 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7613 (mp) REVERT: H 287 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8975 (mt) REVERT: J 120 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8795 (pt0) REVERT: J 247 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5169 (mmmt) REVERT: J 346 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7678 (mp) REVERT: J 366 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8431 (ttp80) REVERT: K 232 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: L 173 TYR cc_start: 0.8674 (m-80) cc_final: 0.8426 (m-10) REVERT: L 211 ASN cc_start: 0.9004 (t0) cc_final: 0.8660 (t0) REVERT: L 247 GLU cc_start: 0.3798 (OUTLIER) cc_final: 0.2444 (tt0) REVERT: O 47 TRP cc_start: 0.8233 (t60) cc_final: 0.7388 (t60) REVERT: P 44 VAL cc_start: 0.9121 (t) cc_final: 0.8919 (m) REVERT: Q 81 MET cc_start: 0.7444 (tmm) cc_final: 0.6965 (tmm) REVERT: Q 101 MET cc_start: 0.4774 (ppp) cc_final: 0.4317 (ppp) REVERT: R 61 ARG cc_start: 0.8549 (ptt-90) cc_final: 0.8262 (ptp-170) REVERT: S 111 TYR cc_start: 0.5770 (t80) cc_final: 0.5109 (t80) REVERT: T 4 LEU cc_start: 0.8682 (mt) cc_final: 0.8455 (mp) REVERT: T 30 GLN cc_start: 0.8305 (mt0) cc_final: 0.8003 (mt0) REVERT: T 50 ASP cc_start: 0.8455 (t0) cc_final: 0.8206 (t0) REVERT: T 53 ARG cc_start: 0.7987 (ptp90) cc_final: 0.7449 (ptp90) REVERT: T 87 TYR cc_start: 0.8471 (m-80) cc_final: 0.8045 (m-80) outliers start: 140 outliers final: 117 residues processed: 605 average time/residue: 0.2383 time to fit residues: 239.1154 Evaluate side-chains 634 residues out of total 4200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 504 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 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 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 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 257 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 300 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 251 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 18 ILE 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 290 VAL Chi-restraints excluded: chain D residue 293 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 D residue 397 THR Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 140 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 211 ILE 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 F residue 256 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 346 LEU Chi-restraints excluded: chain G residue 369 ILE Chi-restraints excluded: chain G residue 376 CYS 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 63 CYS 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 247 LYS 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 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 232 GLN 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 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 75 ILE Chi-restraints excluded: chain R residue 108 VAL Chi-restraints excluded: chain S residue 20 VAL 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: 10.0000 chunk 474 optimal weight: 8.9990 chunk 422 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 278 optimal weight: 0.9990 chunk 351 optimal weight: 1.9990 chunk 194 optimal weight: 0.0000 chunk 296 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 439 optimal weight: 0.0670 overall best weight: 0.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN C 197 GLN D 386 HIS G 264 ASN H 361 HIS ** K 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 361 HIS O 114 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.178166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126673 restraints weight = 48383.549| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.87 r_work: 0.2893 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 39679 Z= 0.103 Angle : 0.563 10.618 54065 Z= 0.288 Chirality : 0.044 0.241 6007 Planarity : 0.004 0.056 6912 Dihedral : 4.836 76.757 5411 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.52 % Allowed : 17.26 % Favored : 80.21 % 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: 1.65 (0.26), residues: 463 sheet: -0.06 (0.13), residues: 1674 loop : -0.56 (0.12), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 289 TYR 0.017 0.001 TYR D 320 PHE 0.018 0.001 PHE D 365 TRP 0.043 0.001 TRP O 36 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (39612) covalent geometry : angle 0.55746 / 0.29 (53924) SS BOND : bond 0.00288 / 0.20 ( 60) SS BOND : angle 1.21929 / 0.84 ( 120) hydrogen bonds : bond 0.02876 / 1.91 ( 1384) hydrogen bonds : angle 5.13394 / 3.56 ( 3723) link_NAG-ASN : bond 0.00294 / 0.16 ( 7) link_NAG-ASN : angle 2.93716 / 1.62 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14226.60 seconds wall clock time: 243 minutes 6.98 seconds (14586.98 seconds total)