Starting phenix.real_space_refine on Mon Aug 25 20:43:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufa_42188/08_2025/8ufa_42188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufa_42188/08_2025/8ufa_42188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ufa_42188/08_2025/8ufa_42188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufa_42188/08_2025/8ufa_42188.map" model { file = "/net/cci-nas-00/data/ceres_data/8ufa_42188/08_2025/8ufa_42188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufa_42188/08_2025/8ufa_42188.cif" } resolution = 2.86 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= 0.001 sd= 0.078 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 192 5.16 5 C 19836 2.51 5 N 5428 2.21 5 O 5804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31260 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "B" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "C" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "D" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "E" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "F" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "G" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "H" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "I" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "J" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3370 Classifications: {'peptide': 441} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 412} Chain: "K" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3253 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 31, 'TRANS': 382} Chain: "L" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1164 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 9, 'TRANS': 141} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.76, per 1000 atoms: 0.25 Number of scatterers: 31260 At special positions: 0 Unit cell: (161.069, 166.474, 196.742, 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 192 16.00 O 5804 8.00 N 5428 7.00 C 19836 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=2.02 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 68 " - pdb=" SG CYS A 78 " distance=2.03 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 122 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 263 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 201 " - pdb=" SG CYS B 217 " distance=2.04 Simple disulfide: pdb=" SG CYS B 393 " - pdb=" SG CYS B 413 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.04 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 272 " distance=2.03 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 377 " distance=2.03 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 329 " - pdb=" SG CYS D 371 " distance=2.03 Simple disulfide: pdb=" SG CYS E 19 " - pdb=" SG CYS E 122 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 103 " distance=2.03 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 263 " distance=2.03 Simple disulfide: pdb=" SG CYS E 199 " - pdb=" SG CYS E 223 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 393 " - pdb=" SG CYS E 413 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.02 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 68 " - pdb=" SG CYS G 78 " distance=2.04 Simple disulfide: pdb=" SG CYS G 260 " - pdb=" SG CYS G 272 " distance=2.03 Simple disulfide: pdb=" SG CYS G 302 " - pdb=" SG CYS G 377 " distance=2.03 Simple disulfide: pdb=" SG CYS G 307 " - pdb=" SG CYS G 381 " distance=2.03 Simple disulfide: pdb=" SG CYS G 329 " - pdb=" SG CYS G 371 " distance=2.03 Simple disulfide: pdb=" SG CYS H 19 " - pdb=" SG CYS H 122 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 27 " distance=2.03 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 103 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 263 " distance=2.03 Simple disulfide: pdb=" SG CYS H 199 " - pdb=" SG CYS H 223 " distance=2.03 Simple disulfide: pdb=" SG CYS H 201 " - pdb=" SG CYS H 217 " distance=2.04 Simple disulfide: pdb=" SG CYS H 393 " - pdb=" SG CYS H 413 " 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 68 " - pdb=" SG CYS J 78 " distance=2.04 Simple disulfide: pdb=" SG CYS J 260 " - pdb=" SG CYS J 272 " distance=2.03 Simple disulfide: pdb=" SG CYS J 302 " - pdb=" SG CYS J 377 " distance=2.03 Simple disulfide: pdb=" SG CYS J 307 " - pdb=" SG CYS J 381 " distance=2.03 Simple disulfide: pdb=" SG CYS J 329 " - pdb=" SG CYS J 371 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 122 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 27 " distance=2.03 Simple disulfide: pdb=" SG CYS K 89 " - pdb=" SG CYS K 103 " distance=2.03 Simple disulfide: pdb=" SG CYS K 150 " - pdb=" SG CYS K 263 " distance=2.03 Simple disulfide: pdb=" SG CYS K 199 " - pdb=" SG CYS K 223 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 217 " distance=2.03 Simple disulfide: pdb=" SG CYS K 393 " - pdb=" SG CYS K 413 " distance=2.04 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 501 " - " ASN B 315 " " NAG D 501 " - " ASN D 134 " " NAG E 501 " - " ASN E 315 " " NAG G 501 " - " ASN G 134 " " NAG H 501 " - " ASN H 315 " " NAG J 501 " - " ASN J 134 " " NAG K 501 " - " ASN K 315 " Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.4 microseconds 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7432 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 93 sheets defined 15.9% alpha, 43.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 239 through 248 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 257 through 260 Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 404 through 441 Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 348 through 360 Processing helix chain 'B' and resid 360 through 399 Proline residue: B 396 - end of helix Processing helix chain 'B' and resid 406 through 413 Processing helix chain 'C' and resid 35 through 40 Processing helix chain 'C' and resid 57 through 61 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'D' and resid 239 through 248 Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 257 through 260 Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.565A pdb=" N PHE D 288 " --> pdb=" O ASP D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 404 through 441 Processing helix chain 'E' and resid 2 through 7 removed outlier: 4.055A pdb=" N THR E 7 " --> pdb=" O THR E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 12 Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 348 through 360 Processing helix chain 'E' and resid 360 through 399 Proline residue: E 396 - end of helix Processing helix chain 'E' and resid 406 through 413 removed outlier: 3.636A pdb=" N ALA E 410 " --> pdb=" O PRO E 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 40 removed outlier: 3.973A pdb=" N ALA F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 removed outlier: 4.428A pdb=" N SER F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'G' and resid 200 through 202 No H-bonds generated for 'chain 'G' and resid 200 through 202' Processing helix chain 'G' and resid 239 through 248 Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 257 through 260 Processing helix chain 'G' and resid 284 through 288 Processing helix chain 'G' and resid 290 through 294 Processing helix chain 'G' and resid 404 through 441 Processing helix chain 'H' and resid 2 through 6 removed outlier: 3.547A pdb=" N PHE H 6 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 Processing helix chain 'H' and resid 219 through 221 No H-bonds generated for 'chain 'H' and resid 219 through 221' Processing helix chain 'H' and resid 348 through 360 Processing helix chain 'H' and resid 360 through 399 Proline residue: H 396 - end of helix Processing helix chain 'H' and resid 406 through 413 Processing helix chain 'I' and resid 37 through 41 removed outlier: 3.584A pdb=" N ALA I 40 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE I 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 37 through 41' Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'J' and resid 112 through 116 Processing helix chain 'J' and resid 239 through 248 Processing helix chain 'J' and resid 251 through 256 Processing helix chain 'J' and resid 257 through 260 Processing helix chain 'J' and resid 284 through 288 Processing helix chain 'J' and resid 290 through 294 Processing helix chain 'J' and resid 404 through 441 Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 8 through 12 Processing helix chain 'K' and resid 219 through 221 No H-bonds generated for 'chain 'K' and resid 219 through 221' Processing helix chain 'K' and resid 348 through 360 Processing helix chain 'K' and resid 360 through 399 Proline residue: K 396 - end of helix Processing helix chain 'K' and resid 406 through 413 Processing helix chain 'L' and resid 35 through 40 Processing helix chain 'L' and resid 47 through 49 No H-bonds generated for 'chain 'L' and resid 47 through 49' Processing helix chain 'L' and resid 57 through 61 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: 6.445A pdb=" N MET A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR A 36 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE A 38 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 128 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A 46 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 148 removed outlier: 5.301A pdb=" N SER A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TYR A 137 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS A 120 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR A 46 " --> pdb=" O LYS A 120 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR A 122 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU A 44 " --> pdb=" O TYR A 122 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 124 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR A 42 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR A 126 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 128 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ILE A 38 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR A 36 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N MET A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA7, first strand: chain 'A' and resid 204 through 206 Processing sheet with id=AA8, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AA9, first strand: chain 'A' and resid 297 through 306 removed outlier: 6.468A pdb=" N LEU A 300 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N LYS A 322 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N CYS A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA A 320 " --> pdb=" O CYS A 302 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ILE A 304 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR A 318 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AB2, first strand: chain 'A' and resid 365 through 368 Processing sheet with id=AB3, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AB5, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.599A pdb=" N GLN B 48 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 36 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 10.282A pdb=" N SER B 50 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N MET B 68 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR B 64 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N LYS B 56 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 9.304A pdb=" N LEU B 62 " --> pdb=" O LYS B 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 33 through 37 removed outlier: 6.599A pdb=" N GLN B 48 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL B 36 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG B 46 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N TYR B 97 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ALA B 51 " --> pdb=" O HIS B 95 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N HIS B 95 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N PHE B 53 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N SER B 93 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 16.394A pdb=" N LEU B 55 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 18.800A pdb=" N LEU B 91 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 82 through 84 removed outlier: 5.544A pdb=" N HIS B 126 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N THR B 110 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL B 124 " --> pdb=" O THR B 110 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLY B 112 " --> pdb=" O CYS B 122 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N CYS B 122 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N HIS B 114 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS B 120 " --> pdb=" O HIS B 114 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 146 through 153 Processing sheet with id=AB9, first strand: chain 'B' and resid 234 through 235 Processing sheet with id=AC1, first strand: chain 'B' and resid 172 through 173 Processing sheet with id=AC2, first strand: chain 'B' and resid 178 through 179 Processing sheet with id=AC3, first strand: chain 'B' and resid 272 through 276 Processing sheet with id=AC4, first strand: chain 'C' and resid 32 through 33 removed outlier: 3.712A pdb=" N GLY C 14 " --> pdb=" O ILE C 6 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N TYR C 15 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 140 through 143 removed outlier: 4.941A pdb=" N PHE C 90 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N ALA C 82 " --> pdb=" O PRO C 93 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE C 106 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 120 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 140 through 143 removed outlier: 7.028A pdb=" N ARG C 126 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASN C 122 " --> pdb=" O ARG C 126 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 128 " --> pdb=" O GLY C 120 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY C 120 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER C 130 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TRP C 134 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N VAL C 114 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C 120 " --> pdb=" O GLU C 149 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AC8, first strand: chain 'D' and resid 15 through 19 removed outlier: 6.407A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE D 38 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR D 128 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR D 126 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR D 42 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL D 124 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU D 44 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR D 122 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR D 46 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS D 120 " --> pdb=" O TYR D 46 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 140 through 148 removed outlier: 5.318A pdb=" N SER D 141 " --> pdb=" O TYR D 137 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TYR D 137 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS D 120 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N TYR D 46 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR D 122 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU D 44 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL D 124 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR D 42 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR D 126 " --> pdb=" O PRO D 40 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR D 128 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ILE D 38 " --> pdb=" O THR D 128 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN D 130 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR D 36 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AD2, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AD3, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AD4, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AD5, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AD6, first strand: chain 'D' and resid 297 through 306 removed outlier: 6.184A pdb=" N LEU D 300 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N LYS D 322 " --> pdb=" O LEU D 300 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N CYS D 302 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ALA D 320 " --> pdb=" O CYS D 302 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ILE D 304 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR D 318 " --> pdb=" O ILE D 304 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 344 through 347 Processing sheet with id=AD8, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AD9, first strand: chain 'E' and resid 17 through 22 removed outlier: 5.400A pdb=" N ASP E 18 " --> pdb=" O SER E 29 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER E 29 " --> pdb=" O ASP E 18 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N CYS E 27 " --> pdb=" O PRO E 20 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER E 25 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 33 through 37 removed outlier: 6.866A pdb=" N TYR E 98 " --> pdb=" O HIS E 94 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS E 94 " --> pdb=" O TYR E 98 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU E 100 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 52 through 56 removed outlier: 5.748A pdb=" N TYR E 64 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N LYS E 56 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 9.326A pdb=" N LEU E 62 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 72 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 82 through 84 removed outlier: 5.360A pdb=" N HIS E 126 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N THR E 110 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL E 124 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N GLY E 112 " --> pdb=" O CYS E 122 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N CYS E 122 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N HIS E 114 " --> pdb=" O HIS E 120 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N HIS E 120 " --> pdb=" O HIS E 114 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 146 through 153 Processing sheet with id=AE5, first strand: chain 'E' and resid 234 through 235 Processing sheet with id=AE6, first strand: chain 'E' and resid 172 through 173 removed outlier: 3.512A pdb=" N VAL E 172 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 178 through 179 Processing sheet with id=AE8, first strand: chain 'E' and resid 272 through 276 Processing sheet with id=AE9, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.197A pdb=" N PHE F 4 " --> pdb=" O TYR F 15 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N TYR F 15 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE F 6 " --> pdb=" O ASN F 13 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N TYR F 15 " --> pdb=" O PRO F 26 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 140 through 143 removed outlier: 5.200A pdb=" N PHE F 90 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N ALA F 82 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ARG F 104 " --> pdb=" O ILE F 116 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE F 116 " --> pdb=" O ARG F 104 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE F 106 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 140 through 143 removed outlier: 6.961A pdb=" N VAL F 132 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N VAL F 117 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N TRP F 134 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA F 115 " --> pdb=" O TRP F 134 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AF4, first strand: chain 'G' and resid 15 through 19 removed outlier: 5.309A pdb=" N ILE G 31 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU G 33 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN G 134 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN G 35 " --> pdb=" O MET G 132 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE G 47 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 140 through 148 removed outlier: 5.459A pdb=" N SER G 141 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N TYR G 137 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LYS G 120 " --> pdb=" O ILE G 47 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE G 47 " --> pdb=" O LYS G 120 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ASN G 43 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N THR G 126 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER G 41 " --> pdb=" O THR G 126 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN G 35 " --> pdb=" O MET G 132 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN G 134 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU G 33 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N THR G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE G 31 " --> pdb=" O THR G 136 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AF7, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AF8, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AF9, first strand: chain 'G' and resid 204 through 206 Processing sheet with id=AG1, first strand: chain 'G' and resid 221 through 222 Processing sheet with id=AG2, first strand: chain 'G' and resid 297 through 306 removed outlier: 4.697A pdb=" N ASP G 299 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS G 322 " --> pdb=" O ASP G 299 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE G 316 " --> pdb=" O THR G 305 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 344 through 346 Processing sheet with id=AG4, first strand: chain 'G' and resid 388 through 389 Processing sheet with id=AG5, first strand: chain 'H' and resid 17 through 22 removed outlier: 5.426A pdb=" N ASP H 18 " --> pdb=" O SER H 29 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N SER H 29 " --> pdb=" O ASP H 18 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N CYS H 27 " --> pdb=" O PRO H 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER H 25 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 33 through 37 removed outlier: 8.467A pdb=" N ILE H 33 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER H 50 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 27.650A pdb=" N ARG H 46 " --> pdb=" O ASN H 69 " (cutoff:3.500A) removed outlier: 22.838A pdb=" N ASN H 69 " --> pdb=" O ARG H 46 " (cutoff:3.500A) removed outlier: 16.896A pdb=" N GLN H 48 " --> pdb=" O PHE H 67 " (cutoff:3.500A) removed outlier: 13.755A pdb=" N PHE H 67 " --> pdb=" O GLN H 48 " (cutoff:3.500A) removed outlier: 12.513A pdb=" N SER H 50 " --> pdb=" O MET H 65 " (cutoff:3.500A) removed outlier: 11.448A pdb=" N MET H 65 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 11.531A pdb=" N MET H 52 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N ALA H 63 " --> pdb=" O MET H 52 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY H 54 " --> pdb=" O ASP H 61 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 33 through 37 removed outlier: 8.467A pdb=" N ILE H 33 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N SER H 50 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N TYR H 97 " --> pdb=" O THR H 49 " (cutoff:3.500A) removed outlier: 8.800A pdb=" N ALA H 51 " --> pdb=" O HIS H 95 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS H 95 " --> pdb=" O ALA H 51 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N PHE H 53 " --> pdb=" O SER H 93 " (cutoff:3.500A) removed outlier: 10.601A pdb=" N SER H 93 " --> pdb=" O PHE H 53 " (cutoff:3.500A) removed outlier: 16.231A pdb=" N LEU H 55 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 18.652A pdb=" N LEU H 91 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 82 through 84 removed outlier: 3.533A pdb=" N THR H 108 " --> pdb=" O HIS H 126 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N HIS H 126 " --> pdb=" O THR H 108 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N THR H 110 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL H 124 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLY H 112 " --> pdb=" O CYS H 122 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N CYS H 122 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N HIS H 114 " --> pdb=" O HIS H 120 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS H 120 " --> pdb=" O HIS H 114 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 146 through 153 Processing sheet with id=AH1, first strand: chain 'H' and resid 234 through 235 Processing sheet with id=AH2, first strand: chain 'H' and resid 172 through 173 Processing sheet with id=AH3, first strand: chain 'H' and resid 178 through 179 Processing sheet with id=AH4, first strand: chain 'H' and resid 272 through 276 Processing sheet with id=AH5, first strand: chain 'I' and resid 32 through 33 removed outlier: 3.858A pdb=" N GLY I 14 " --> pdb=" O ILE I 6 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N TYR I 15 " --> pdb=" O PRO I 26 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 140 through 143 removed outlier: 4.997A pdb=" N PHE I 90 " --> pdb=" O LEU I 129 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N ALA I 82 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY I 74 " --> pdb=" O TYR I 85 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG I 104 " --> pdb=" O VAL I 117 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA I 115 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 140 through 143 removed outlier: 7.004A pdb=" N ARG I 126 " --> pdb=" O ASN I 122 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASN I 122 " --> pdb=" O ARG I 126 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA I 128 " --> pdb=" O GLY I 120 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY I 120 " --> pdb=" O ALA I 128 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER I 130 " --> pdb=" O LEU I 118 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP I 134 " --> pdb=" O VAL I 114 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N VAL I 114 " --> pdb=" O TRP I 134 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 2 through 8 Processing sheet with id=AH9, first strand: chain 'J' and resid 15 through 19 removed outlier: 5.158A pdb=" N ILE J 31 " --> pdb=" O THR J 136 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU J 33 " --> pdb=" O ASN J 134 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN J 134 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN J 35 " --> pdb=" O MET J 132 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU J 45 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE J 47 " --> pdb=" O LYS J 120 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS J 120 " --> pdb=" O ILE J 47 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 140 through 148 removed outlier: 5.265A pdb=" N SER J 141 " --> pdb=" O TYR J 137 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N TYR J 137 " --> pdb=" O SER J 141 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LYS J 120 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE J 47 " --> pdb=" O LYS J 120 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N TYR J 122 " --> pdb=" O GLU J 45 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU J 45 " --> pdb=" O TYR J 122 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N VAL J 124 " --> pdb=" O ASN J 43 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN J 43 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR J 126 " --> pdb=" O SER J 41 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N SER J 41 " --> pdb=" O THR J 126 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN J 35 " --> pdb=" O MET J 132 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN J 134 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU J 33 " --> pdb=" O ASN J 134 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR J 136 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ILE J 31 " --> pdb=" O THR J 136 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AI3, first strand: chain 'J' and resid 51 through 54 Processing sheet with id=AI4, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=AI5, first strand: chain 'J' and resid 204 through 206 Processing sheet with id=AI6, first strand: chain 'J' and resid 221 through 222 Processing sheet with id=AI7, first strand: chain 'J' and resid 296 through 306 removed outlier: 5.861A pdb=" N VAL J 297 " --> pdb=" O SER J 324 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER J 324 " --> pdb=" O VAL J 297 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP J 299 " --> pdb=" O LYS J 322 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS J 322 " --> pdb=" O ASP J 299 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE J 316 " --> pdb=" O THR J 305 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 344 through 346 Processing sheet with id=AI9, first strand: chain 'J' and resid 388 through 389 Processing sheet with id=AJ1, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AJ2, first strand: chain 'K' and resid 33 through 37 removed outlier: 8.421A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N SER K 50 " --> pdb=" O MET K 68 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N MET K 68 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N TYR K 64 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N LYS K 56 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N LEU K 62 " --> pdb=" O LYS K 56 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'K' and resid 33 through 37 removed outlier: 8.421A pdb=" N ILE K 33 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER K 50 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TYR K 97 " --> pdb=" O THR K 49 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N ALA K 51 " --> pdb=" O HIS K 95 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N HIS K 95 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 9.377A pdb=" N PHE K 53 " --> pdb=" O SER K 93 " (cutoff:3.500A) removed outlier: 10.608A pdb=" N SER K 93 " --> pdb=" O PHE K 53 " (cutoff:3.500A) removed outlier: 16.268A pdb=" N LEU K 55 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 18.827A pdb=" N LEU K 91 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'K' and resid 82 through 84 removed outlier: 5.446A pdb=" N HIS K 126 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N THR K 110 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL K 124 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY K 112 " --> pdb=" O CYS K 122 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N CYS K 122 " --> pdb=" O GLY K 112 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N HIS K 114 " --> pdb=" O HIS K 120 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS K 120 " --> pdb=" O HIS K 114 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'K' and resid 146 through 153 Processing sheet with id=AJ6, first strand: chain 'K' and resid 234 through 235 Processing sheet with id=AJ7, first strand: chain 'K' and resid 172 through 173 Processing sheet with id=AJ8, first strand: chain 'K' and resid 178 through 179 Processing sheet with id=AJ9, first strand: chain 'K' and resid 272 through 276 Processing sheet with id=AK1, first strand: chain 'L' and resid 32 through 33 removed outlier: 3.928A pdb=" N GLY L 14 " --> pdb=" O ILE L 6 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N TYR L 15 " --> pdb=" O PRO L 26 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'L' and resid 140 through 143 removed outlier: 5.079A pdb=" N PHE L 90 " --> pdb=" O LEU L 129 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ALA L 82 " --> pdb=" O PRO L 93 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY L 120 " --> pdb=" O GLU L 149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU L 149 " --> pdb=" O GLY L 120 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'L' and resid 140 through 143 removed outlier: 7.265A pdb=" N ARG L 126 " --> pdb=" O ASN L 122 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ASN L 122 " --> pdb=" O ARG L 126 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA L 128 " --> pdb=" O GLY L 120 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY L 120 " --> pdb=" O ALA L 128 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER L 130 " --> pdb=" O LEU L 118 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TRP L 134 " --> pdb=" O VAL L 114 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N VAL L 114 " --> pdb=" O TRP L 134 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY L 120 " --> pdb=" O GLU L 149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU L 149 " --> pdb=" O GLY L 120 " (cutoff:3.500A) 1330 hydrogen bonds defined for protein. 3378 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.01 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10145 1.35 - 1.47: 8095 1.47 - 1.60: 13636 1.60 - 1.72: 0 1.72 - 1.85: 236 Bond restraints: 32112 Sorted by residual: bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.80e+00 bond pdb=" C1 NAG H 501 " pdb=" O5 NAG H 501 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.15e+00 bond pdb=" C1 NAG G 501 " pdb=" O5 NAG G 501 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" CA PRO K 331 " pdb=" C PRO K 331 " ideal model delta sigma weight residual 1.514 1.524 -0.010 5.50e-03 3.31e+04 3.01e+00 bond pdb=" C1 NAG E 501 " pdb=" O5 NAG E 501 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.92e+00 ... (remaining 32107 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 41224 1.35 - 2.69: 2043 2.69 - 4.04: 463 4.04 - 5.38: 34 5.38 - 6.73: 4 Bond angle restraints: 43768 Sorted by residual: angle pdb=" N PRO B 286 " pdb=" CA PRO B 286 " pdb=" C PRO B 286 " ideal model delta sigma weight residual 112.47 119.20 -6.73 2.06e+00 2.36e-01 1.07e+01 angle pdb=" CA CYS K 27 " pdb=" CB CYS K 27 " pdb=" SG CYS K 27 " ideal model delta sigma weight residual 114.40 120.93 -6.53 2.30e+00 1.89e-01 8.06e+00 angle pdb=" CA TYR F 67 " pdb=" CB TYR F 67 " pdb=" CG TYR F 67 " ideal model delta sigma weight residual 113.90 118.90 -5.00 1.80e+00 3.09e-01 7.71e+00 angle pdb=" CA TYR J 309 " pdb=" CB TYR J 309 " pdb=" CG TYR J 309 " ideal model delta sigma weight residual 113.90 118.84 -4.94 1.80e+00 3.09e-01 7.53e+00 angle pdb=" N GLY B 23 " pdb=" CA GLY B 23 " pdb=" C GLY B 23 " ideal model delta sigma weight residual 113.18 106.82 6.36 2.37e+00 1.78e-01 7.20e+00 ... (remaining 43763 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 18663 17.19 - 34.39: 483 34.39 - 51.58: 110 51.58 - 68.78: 56 68.78 - 85.97: 12 Dihedral angle restraints: 19324 sinusoidal: 7700 harmonic: 11624 Sorted by residual: dihedral pdb=" CB CYS J 329 " pdb=" SG CYS J 329 " pdb=" SG CYS J 371 " pdb=" CB CYS J 371 " ideal model delta sinusoidal sigma weight residual 93.00 151.47 -58.47 1 1.00e+01 1.00e-02 4.58e+01 dihedral pdb=" CB CYS A 260 " pdb=" SG CYS A 260 " pdb=" SG CYS A 272 " pdb=" CB CYS A 272 " ideal model delta sinusoidal sigma weight residual 93.00 131.51 -38.51 1 1.00e+01 1.00e-02 2.09e+01 dihedral pdb=" CB CYS J 260 " pdb=" SG CYS J 260 " pdb=" SG CYS J 272 " pdb=" CB CYS J 272 " ideal model delta sinusoidal sigma weight residual 93.00 131.23 -38.23 1 1.00e+01 1.00e-02 2.06e+01 ... (remaining 19321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3700 0.050 - 0.099: 909 0.099 - 0.149: 281 0.149 - 0.199: 5 0.199 - 0.249: 1 Chirality restraints: 4896 Sorted by residual: chirality pdb=" C1 NAG K 501 " pdb=" ND2 ASN K 315 " pdb=" C2 NAG K 501 " pdb=" O5 NAG K 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA PRO B 286 " pdb=" N PRO B 286 " pdb=" C PRO B 286 " pdb=" CB PRO B 286 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA PRO K 255 " pdb=" N PRO K 255 " pdb=" C PRO K 255 " pdb=" CB PRO K 255 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 4893 not shown) Planarity restraints: 5632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 89 " -0.219 9.50e-02 1.11e+02 9.87e-02 7.33e+00 pdb=" NE ARG C 89 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG C 89 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG C 89 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 89 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 67 " -0.006 2.00e-02 2.50e+03 1.91e-02 7.29e+00 pdb=" CG TYR I 67 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR I 67 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR I 67 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR I 67 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR I 67 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR I 67 " 0.023 2.00e-02 2.50e+03 pdb=" OH TYR I 67 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 110 " 0.175 9.50e-02 1.11e+02 7.98e-02 6.06e+00 pdb=" NE ARG D 110 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 110 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG D 110 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG D 110 " -0.002 2.00e-02 2.50e+03 ... (remaining 5629 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 9301 2.83 - 3.35: 26901 3.35 - 3.87: 52741 3.87 - 4.38: 60831 4.38 - 4.90: 107881 Nonbonded interactions: 257655 Sorted by model distance: nonbonded pdb=" O CYS J 371 " pdb=" OG1 THR J 372 " model vdw 2.316 3.040 nonbonded pdb=" O CYS D 371 " pdb=" OG1 THR D 372 " model vdw 2.327 3.040 nonbonded pdb=" O ASN E 391 " pdb=" OG1 THR E 395 " model vdw 2.360 3.040 nonbonded pdb=" OG SER G 57 " pdb=" O SER H 237 " model vdw 2.375 3.040 nonbonded pdb=" O CYS K 22 " pdb=" O SER K 25 " model vdw 2.379 3.040 ... (remaining 257650 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 30.570 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 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 0.048 32180 Z= 0.150 Angle : 0.688 6.729 43912 Z= 0.378 Chirality : 0.047 0.249 4896 Planarity : 0.007 0.099 5624 Dihedral : 9.386 85.974 11712 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.89 (0.13), residues: 4000 helix: 0.98 (0.23), residues: 464 sheet: 0.74 (0.14), residues: 1332 loop : 0.55 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.003 ARG E 37 TYR 0.033 0.005 TYR F 67 PHE 0.014 0.002 PHE G 421 TRP 0.019 0.003 TRP F 134 HIS 0.010 0.002 HIS L 79 Details of bonding type rmsd covalent geometry : bond 0.00357 (32112) covalent geometry : angle 0.68384 (43768) SS BOND : bond 0.00327 ( 60) SS BOND : angle 1.22796 ( 120) hydrogen bonds : bond 0.20336 ( 1264) hydrogen bonds : angle 8.59425 ( 3378) link_NAG-ASN : bond 0.00296 ( 8) link_NAG-ASN : angle 2.33883 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7014 (mt-10) REVERT: A 343 ASN cc_start: 0.8720 (m-40) cc_final: 0.8503 (m-40) REVERT: D 82 SER cc_start: 0.8575 (p) cc_final: 0.8331 (m) REVERT: E 166 MET cc_start: 0.8357 (ptt) cc_final: 0.8003 (ptt) REVERT: G 164 ILE cc_start: 0.7163 (mm) cc_final: 0.6945 (mp) REVERT: G 412 LYS cc_start: 0.5994 (mttt) cc_final: 0.5657 (mtmt) REVERT: H 35 GLU cc_start: 0.8083 (tt0) cc_final: 0.7803 (tt0) REVERT: H 68 MET cc_start: 0.8613 (mmm) cc_final: 0.8244 (mmt) REVERT: H 346 HIS cc_start: 0.8241 (m-70) cc_final: 0.8034 (m90) REVERT: J 30 GLN cc_start: 0.7952 (tt0) cc_final: 0.7726 (tt0) REVERT: J 88 MET cc_start: 0.7746 (mmm) cc_final: 0.7432 (mmm) REVERT: J 385 LYS cc_start: 0.7459 (mmtt) cc_final: 0.7107 (UNCLASSIFIED) REVERT: K 35 GLU cc_start: 0.8171 (tt0) cc_final: 0.7928 (tt0) REVERT: K 136 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7974 (mt-10) outliers start: 0 outliers final: 1 residues processed: 648 average time/residue: 0.6805 time to fit residues: 518.6172 Evaluate side-chains 418 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 417 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 163 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 175 HIS B 344 ASN B 358 ASN D 369 GLN ** E 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN E 302 ASN E 346 HIS F 37 GLN G 30 GLN G 77 GLN G 130 GLN G 219 ASN G 223 GLN H 302 ASN H 358 ASN I 11 GLN I 79 HIS J 28 HIS K 21 ASN K 102 GLN K 114 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.209570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.175854 restraints weight = 31628.787| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.46 r_work: 0.3749 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 32180 Z= 0.218 Angle : 0.659 12.914 43912 Z= 0.352 Chirality : 0.050 0.212 4896 Planarity : 0.005 0.046 5624 Dihedral : 5.420 57.954 4522 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.82 % Rotamer: Outliers : 2.45 % Allowed : 8.08 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.67 (0.13), residues: 4000 helix: 1.50 (0.23), residues: 468 sheet: 0.56 (0.14), residues: 1376 loop : 0.24 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 157 TYR 0.025 0.002 TYR J 309 PHE 0.018 0.002 PHE G 421 TRP 0.016 0.002 TRP B 327 HIS 0.013 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00531 (32112) covalent geometry : angle 0.64717 (43768) SS BOND : bond 0.00513 ( 60) SS BOND : angle 2.21274 ( 120) hydrogen bonds : bond 0.04953 ( 1264) hydrogen bonds : angle 6.21116 ( 3378) link_NAG-ASN : bond 0.00423 ( 8) link_NAG-ASN : angle 2.37160 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 416 time to evaluate : 1.238 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 20 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: A 105 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8139 (mt-10) REVERT: A 246 LYS cc_start: 0.8079 (mttp) cc_final: 0.7242 (mmtt) REVERT: A 373 SER cc_start: 0.8121 (t) cc_final: 0.7919 (m) REVERT: A 399 PHE cc_start: 0.7054 (t80) cc_final: 0.6519 (t80) REVERT: B 80 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7458 (m-40) REVERT: D 54 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7353 (tmtm) REVERT: D 82 SER cc_start: 0.8868 (p) cc_final: 0.8608 (m) REVERT: D 189 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8383 (t70) REVERT: E 37 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8752 (mmp-170) REVERT: E 166 MET cc_start: 0.8922 (ptt) cc_final: 0.8526 (ptt) REVERT: F 60 MET cc_start: 0.6257 (mtp) cc_final: 0.5915 (mtm) REVERT: G 32 GLN cc_start: 0.8889 (tt0) cc_final: 0.8603 (tt0) REVERT: G 48 THR cc_start: 0.7845 (m) cc_final: 0.7425 (m) REVERT: G 164 ILE cc_start: 0.8045 (mm) cc_final: 0.7719 (mp) REVERT: G 221 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7992 (tmtt) REVERT: G 412 LYS cc_start: 0.6534 (mttt) cc_final: 0.5690 (mtmt) REVERT: H 35 GLU cc_start: 0.8437 (tt0) cc_final: 0.8120 (tt0) REVERT: H 276 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8498 (mtmt) REVERT: I 140 THR cc_start: 0.7862 (m) cc_final: 0.7412 (p) REVERT: J 88 MET cc_start: 0.8077 (mmm) cc_final: 0.7660 (mmm) REVERT: J 143 ARG cc_start: 0.7474 (ttm-80) cc_final: 0.6829 (mtp180) REVERT: J 289 THR cc_start: 0.7401 (m) cc_final: 0.7162 (t) REVERT: J 303 LYS cc_start: 0.7697 (mmtt) cc_final: 0.7380 (mtmt) REVERT: J 378 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7700 (mtpp) REVERT: K 119 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7123 (mmt90) REVERT: K 351 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7702 (mt-10) outliers start: 84 outliers final: 38 residues processed: 457 average time/residue: 0.5822 time to fit residues: 317.6610 Evaluate side-chains 414 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 368 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 37 ARG Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 378 LYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 22 CYS Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 119 ARG Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 324 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 295 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 311 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 114 HIS ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN D 369 GLN E 102 GLN E 346 HIS ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 GLN H 302 ASN K 21 ASN K 102 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.207423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.173764 restraints weight = 31587.631| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.44 r_work: 0.3467 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 32180 Z= 0.243 Angle : 0.641 6.748 43912 Z= 0.340 Chirality : 0.050 0.215 4896 Planarity : 0.005 0.051 5624 Dihedral : 5.576 59.614 4520 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.98 % Allowed : 9.25 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.30 (0.13), residues: 4000 helix: 1.36 (0.23), residues: 476 sheet: 0.29 (0.14), residues: 1300 loop : -0.02 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 388 TYR 0.026 0.002 TYR J 309 PHE 0.018 0.002 PHE G 421 TRP 0.014 0.002 TRP I 134 HIS 0.008 0.001 HIS E 41 Details of bonding type rmsd covalent geometry : bond 0.00593 (32112) covalent geometry : angle 0.63456 (43768) SS BOND : bond 0.00475 ( 60) SS BOND : angle 1.56747 ( 120) hydrogen bonds : bond 0.04536 ( 1264) hydrogen bonds : angle 5.92188 ( 3378) link_NAG-ASN : bond 0.00368 ( 8) link_NAG-ASN : angle 2.39519 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 373 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7727 (mt-10) REVERT: A 99 GLU cc_start: 0.6756 (tt0) cc_final: 0.6358 (tt0) REVERT: A 105 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8105 (mt-10) REVERT: A 246 LYS cc_start: 0.7997 (mttp) cc_final: 0.7106 (mmtt) REVERT: A 293 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: A 399 PHE cc_start: 0.7147 (t80) cc_final: 0.6522 (t80) REVERT: B 80 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7381 (m-40) REVERT: B 157 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7490 (mtp85) REVERT: D 82 SER cc_start: 0.8931 (p) cc_final: 0.8596 (m) REVERT: D 143 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7556 (mtp180) REVERT: D 189 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8313 (t70) REVERT: D 349 GLU cc_start: 0.7248 (mp0) cc_final: 0.5870 (tm-30) REVERT: E 143 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7966 (tt0) REVERT: E 166 MET cc_start: 0.8887 (ptt) cc_final: 0.8415 (ptt) REVERT: E 296 SER cc_start: 0.8586 (t) cc_final: 0.8273 (m) REVERT: F 60 MET cc_start: 0.6192 (mtp) cc_final: 0.5863 (mtm) REVERT: G 32 GLN cc_start: 0.8894 (tt0) cc_final: 0.8569 (tt0) REVERT: G 47 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8184 (mt) REVERT: G 164 ILE cc_start: 0.7913 (mm) cc_final: 0.7547 (mp) REVERT: G 412 LYS cc_start: 0.6455 (mttt) cc_final: 0.5537 (mtmt) REVERT: H 21 ASN cc_start: 0.7955 (OUTLIER) cc_final: 0.7739 (t0) REVERT: H 221 LYS cc_start: 0.8248 (mtmm) cc_final: 0.8001 (mtmm) REVERT: H 276 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8498 (mtmt) REVERT: I 140 THR cc_start: 0.7759 (m) cc_final: 0.7288 (p) REVERT: J 13 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8450 (mm) REVERT: J 143 ARG cc_start: 0.7195 (ttm-80) cc_final: 0.6531 (mtp180) REVERT: J 303 LYS cc_start: 0.7671 (mmtt) cc_final: 0.7268 (mtmt) REVERT: J 378 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7737 (mtpp) REVERT: K 119 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7077 (mmt90) REVERT: K 139 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8149 (mtt-85) REVERT: K 279 THR cc_start: 0.8916 (m) cc_final: 0.8580 (m) REVERT: K 310 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7900 (ptp90) REVERT: K 351 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7621 (mt-10) outliers start: 102 outliers final: 59 residues processed: 422 average time/residue: 0.5781 time to fit residues: 292.3415 Evaluate side-chains 421 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 348 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain H residue 4 THR Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 68 CYS Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 378 LYS Chi-restraints excluded: chain J residue 409 SER Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 119 ARG Chi-restraints excluded: chain K residue 129 GLU Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 310 ARG Chi-restraints excluded: chain K residue 324 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 262 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 391 optimal weight: 0.0040 chunk 140 optimal weight: 7.9990 chunk 53 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 358 ASN E 102 GLN E 346 HIS G 223 GLN ** G 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 HIS H 160 GLN H 302 ASN K 102 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.210783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.177254 restraints weight = 31559.936| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 1.43 r_work: 0.3781 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32180 Z= 0.115 Angle : 0.518 6.221 43912 Z= 0.275 Chirality : 0.046 0.204 4896 Planarity : 0.004 0.046 5624 Dihedral : 5.129 56.557 4520 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.04 % Allowed : 10.88 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.49 (0.13), residues: 4000 helix: 1.72 (0.24), residues: 480 sheet: 0.44 (0.14), residues: 1324 loop : 0.03 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 388 TYR 0.021 0.001 TYR J 309 PHE 0.016 0.001 PHE D 95 TRP 0.013 0.001 TRP I 134 HIS 0.005 0.001 HIS G 441 Details of bonding type rmsd covalent geometry : bond 0.00262 (32112) covalent geometry : angle 0.51291 (43768) SS BOND : bond 0.00245 ( 60) SS BOND : angle 1.05445 ( 120) hydrogen bonds : bond 0.03568 ( 1264) hydrogen bonds : angle 5.50827 ( 3378) link_NAG-ASN : bond 0.00291 ( 8) link_NAG-ASN : angle 2.38324 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 381 time to evaluate : 1.262 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 20 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: A 99 GLU cc_start: 0.6793 (tt0) cc_final: 0.6491 (tt0) REVERT: A 105 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8035 (mt-10) REVERT: A 156 LYS cc_start: 0.8583 (mptt) cc_final: 0.8174 (mmmm) REVERT: A 246 LYS cc_start: 0.8015 (mttp) cc_final: 0.7202 (mmtt) REVERT: A 399 PHE cc_start: 0.7129 (t80) cc_final: 0.6479 (t80) REVERT: B 68 MET cc_start: 0.7670 (mmm) cc_final: 0.6619 (mmt) REVERT: B 80 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7465 (m-40) REVERT: B 157 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7516 (mtp85) REVERT: B 198 TYR cc_start: 0.7446 (t80) cc_final: 0.7099 (t80) REVERT: D 2 GLU cc_start: 0.8197 (tt0) cc_final: 0.7542 (tt0) REVERT: D 82 SER cc_start: 0.8942 (p) cc_final: 0.8637 (m) REVERT: D 143 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7742 (mtp180) REVERT: D 212 ASN cc_start: 0.7436 (OUTLIER) cc_final: 0.7009 (p0) REVERT: D 290 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7644 (mmt90) REVERT: D 349 GLU cc_start: 0.7286 (mp0) cc_final: 0.5934 (tm-30) REVERT: E 143 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: E 166 MET cc_start: 0.8845 (ptt) cc_final: 0.8526 (ptt) REVERT: F 60 MET cc_start: 0.6237 (mtp) cc_final: 0.6009 (mtm) REVERT: G 32 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8571 (tt0) REVERT: G 48 THR cc_start: 0.7867 (m) cc_final: 0.7478 (m) REVERT: G 164 ILE cc_start: 0.7800 (mm) cc_final: 0.7446 (mp) REVERT: G 412 LYS cc_start: 0.6551 (mttt) cc_final: 0.5747 (mtmt) REVERT: H 68 MET cc_start: 0.8552 (mmt) cc_final: 0.8007 (mmt) REVERT: H 270 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7369 (mp0) REVERT: I 140 THR cc_start: 0.7798 (m) cc_final: 0.7372 (p) REVERT: J 143 ARG cc_start: 0.7374 (ttm-80) cc_final: 0.6763 (mtp180) REVERT: J 289 THR cc_start: 0.7829 (OUTLIER) cc_final: 0.7614 (p) REVERT: J 303 LYS cc_start: 0.7753 (mmtt) cc_final: 0.7475 (mtmt) REVERT: K 139 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8237 (mtt-85) REVERT: K 279 THR cc_start: 0.8893 (m) cc_final: 0.8628 (m) REVERT: K 296 SER cc_start: 0.8765 (p) cc_final: 0.8552 (m) REVERT: K 310 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8064 (ptp90) REVERT: K 387 CYS cc_start: 0.6337 (m) cc_final: 0.6008 (m) outliers start: 70 outliers final: 31 residues processed: 419 average time/residue: 0.5942 time to fit residues: 297.8582 Evaluate side-chains 395 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 354 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain K residue 310 ARG Chi-restraints excluded: chain K residue 354 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 154 optimal weight: 6.9990 chunk 299 optimal weight: 7.9990 chunk 119 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 273 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 358 ASN D 369 GLN E 236 ASN E 302 ASN E 346 HIS G 30 GLN G 223 GLN ** G 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 ASN K 102 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.208421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.174551 restraints weight = 31605.801| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 1.44 r_work: 0.3736 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 32180 Z= 0.187 Angle : 0.575 9.044 43912 Z= 0.303 Chirality : 0.047 0.198 4896 Planarity : 0.005 0.059 5624 Dihedral : 5.282 55.644 4520 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.22 % Rotamer: Outliers : 3.00 % Allowed : 10.94 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.31 (0.13), residues: 4000 helix: 1.68 (0.24), residues: 480 sheet: 0.24 (0.14), residues: 1300 loop : -0.05 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 26 TYR 0.025 0.002 TYR J 309 PHE 0.018 0.002 PHE D 95 TRP 0.012 0.002 TRP B 327 HIS 0.006 0.001 HIS D 28 Details of bonding type rmsd covalent geometry : bond 0.00451 (32112) covalent geometry : angle 0.56765 (43768) SS BOND : bond 0.00432 ( 60) SS BOND : angle 1.52770 ( 120) hydrogen bonds : bond 0.03765 ( 1264) hydrogen bonds : angle 5.55102 ( 3378) link_NAG-ASN : bond 0.00260 ( 8) link_NAG-ASN : angle 2.36953 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 370 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7823 (mt-10) REVERT: A 99 GLU cc_start: 0.6911 (tt0) cc_final: 0.6602 (tt0) REVERT: A 105 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8264 (mt-10) REVERT: A 246 LYS cc_start: 0.8067 (mttp) cc_final: 0.7247 (mmtt) REVERT: A 399 PHE cc_start: 0.7183 (t80) cc_final: 0.6531 (t80) REVERT: B 80 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7519 (m-40) REVERT: B 157 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7534 (mtp85) REVERT: B 198 TYR cc_start: 0.7478 (t80) cc_final: 0.7110 (t80) REVERT: B 274 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8326 (mt-10) REVERT: D 82 SER cc_start: 0.8971 (p) cc_final: 0.8652 (m) REVERT: D 143 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7765 (mtp180) REVERT: D 212 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7072 (p0) REVERT: D 290 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7701 (mmt90) REVERT: D 349 GLU cc_start: 0.7329 (mp0) cc_final: 0.6006 (tm-30) REVERT: E 143 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: E 166 MET cc_start: 0.8894 (ptt) cc_final: 0.8510 (ptt) REVERT: E 296 SER cc_start: 0.8606 (t) cc_final: 0.8313 (m) REVERT: F 60 MET cc_start: 0.6261 (mtp) cc_final: 0.5919 (mtm) REVERT: G 32 GLN cc_start: 0.8887 (tt0) cc_final: 0.8563 (tt0) REVERT: G 47 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8084 (mt) REVERT: G 164 ILE cc_start: 0.7846 (mm) cc_final: 0.7544 (mp) REVERT: G 412 LYS cc_start: 0.6614 (mttt) cc_final: 0.5784 (mtmt) REVERT: G 421 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.4670 (t80) REVERT: H 270 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7450 (mp0) REVERT: I 140 THR cc_start: 0.7840 (m) cc_final: 0.7492 (p) REVERT: J 13 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8502 (mm) REVERT: J 289 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7592 (p) REVERT: J 303 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7580 (mtmt) REVERT: J 378 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7836 (mtpp) REVERT: K 139 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8230 (mtt-85) REVERT: K 279 THR cc_start: 0.8943 (m) cc_final: 0.8661 (m) REVERT: K 310 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8079 (ptp90) outliers start: 103 outliers final: 55 residues processed: 431 average time/residue: 0.5437 time to fit residues: 283.5330 Evaluate side-chains 424 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 356 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 398 SER Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 378 LYS Chi-restraints excluded: chain J residue 409 SER Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 310 ARG Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain L residue 131 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 274 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 chunk 95 optimal weight: 10.0000 chunk 208 optimal weight: 0.0570 chunk 212 optimal weight: 0.8980 chunk 277 optimal weight: 5.9990 chunk 170 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 358 ASN D 369 GLN E 102 GLN ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 346 HIS G 30 GLN ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 ASN K 102 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.210613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.177291 restraints weight = 31636.031| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.42 r_work: 0.3773 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32180 Z= 0.118 Angle : 0.514 6.710 43912 Z= 0.271 Chirality : 0.045 0.199 4896 Planarity : 0.004 0.060 5624 Dihedral : 5.050 53.859 4520 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.82 % Rotamer: Outliers : 2.42 % Allowed : 11.90 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.46 (0.13), residues: 4000 helix: 1.92 (0.24), residues: 480 sheet: 0.45 (0.14), residues: 1260 loop : -0.06 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 388 TYR 0.020 0.001 TYR J 309 PHE 0.015 0.001 PHE A 95 TRP 0.012 0.001 TRP I 134 HIS 0.003 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00271 (32112) covalent geometry : angle 0.50730 (43768) SS BOND : bond 0.00279 ( 60) SS BOND : angle 1.29042 ( 120) hydrogen bonds : bond 0.03390 ( 1264) hydrogen bonds : angle 5.35130 ( 3378) link_NAG-ASN : bond 0.00210 ( 8) link_NAG-ASN : angle 2.44127 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 376 time to evaluate : 1.177 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 20 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7712 (mt-10) REVERT: A 99 GLU cc_start: 0.6847 (tt0) cc_final: 0.6446 (tt0) REVERT: A 105 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8140 (mt-10) REVERT: A 246 LYS cc_start: 0.8022 (mttp) cc_final: 0.7181 (mmtm) REVERT: A 399 PHE cc_start: 0.7160 (t80) cc_final: 0.6508 (t80) REVERT: B 80 ASN cc_start: 0.7960 (OUTLIER) cc_final: 0.7446 (m-40) REVERT: B 157 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.7533 (mtp85) REVERT: B 198 TYR cc_start: 0.7509 (t80) cc_final: 0.7095 (t80) REVERT: D 82 SER cc_start: 0.8933 (p) cc_final: 0.8612 (m) REVERT: D 143 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7737 (mtp180) REVERT: D 290 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7690 (mmt90) REVERT: D 349 GLU cc_start: 0.7211 (mp0) cc_final: 0.5970 (tm-30) REVERT: D 367 LYS cc_start: 0.8126 (tmtt) cc_final: 0.7917 (tptm) REVERT: E 143 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: E 166 MET cc_start: 0.8858 (ptt) cc_final: 0.8545 (ptt) REVERT: E 296 SER cc_start: 0.8580 (t) cc_final: 0.8288 (m) REVERT: F 60 MET cc_start: 0.6176 (mtp) cc_final: 0.5948 (mtm) REVERT: G 48 THR cc_start: 0.7905 (m) cc_final: 0.7546 (m) REVERT: G 164 ILE cc_start: 0.7779 (mm) cc_final: 0.7397 (mp) REVERT: G 421 PHE cc_start: 0.5747 (OUTLIER) cc_final: 0.4800 (t80) REVERT: H 221 LYS cc_start: 0.8216 (mtmm) cc_final: 0.7560 (pmtt) REVERT: H 270 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7379 (mp0) REVERT: H 304 THR cc_start: 0.7987 (m) cc_final: 0.7617 (m) REVERT: I 140 THR cc_start: 0.7808 (m) cc_final: 0.7487 (p) REVERT: J 36 THR cc_start: 0.8438 (t) cc_final: 0.8059 (m) REVERT: J 289 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7622 (p) REVERT: J 303 LYS cc_start: 0.7638 (mmtt) cc_final: 0.7377 (mtmt) REVERT: J 426 LEU cc_start: 0.7489 (mt) cc_final: 0.7242 (mm) REVERT: K 279 THR cc_start: 0.8888 (m) cc_final: 0.8663 (m) REVERT: K 296 SER cc_start: 0.8812 (p) cc_final: 0.8554 (m) REVERT: K 310 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8060 (ptp90) REVERT: K 387 CYS cc_start: 0.6370 (m) cc_final: 0.6069 (m) outliers start: 83 outliers final: 46 residues processed: 427 average time/residue: 0.5733 time to fit residues: 295.3411 Evaluate side-chains 415 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 361 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 409 SER Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 310 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 393 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 220 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 chunk 308 optimal weight: 0.1980 chunk 110 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 287 optimal weight: 0.0470 chunk 251 optimal weight: 3.9990 chunk 198 optimal weight: 7.9990 overall best weight: 2.4484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 358 ASN C 88 ASN D 369 GLN E 102 GLN E 236 ASN E 302 ASN E 346 HIS G 30 GLN ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS H 302 ASN K 102 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.207893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.174096 restraints weight = 31606.372| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.42 r_work: 0.3725 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 32180 Z= 0.197 Angle : 0.574 6.343 43912 Z= 0.302 Chirality : 0.048 0.195 4896 Planarity : 0.005 0.062 5624 Dihedral : 5.222 53.033 4520 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.86 % Allowed : 12.14 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.26 (0.13), residues: 4000 helix: 1.80 (0.24), residues: 480 sheet: 0.28 (0.14), residues: 1260 loop : -0.18 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 388 TYR 0.025 0.002 TYR J 309 PHE 0.018 0.002 PHE D 95 TRP 0.013 0.002 TRP A 142 HIS 0.006 0.001 HIS D 28 Details of bonding type rmsd covalent geometry : bond 0.00479 (32112) covalent geometry : angle 0.56755 (43768) SS BOND : bond 0.00426 ( 60) SS BOND : angle 1.43882 ( 120) hydrogen bonds : bond 0.03678 ( 1264) hydrogen bonds : angle 5.47877 ( 3378) link_NAG-ASN : bond 0.00300 ( 8) link_NAG-ASN : angle 2.39257 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 362 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7800 (mt-10) REVERT: A 99 GLU cc_start: 0.6894 (tt0) cc_final: 0.6471 (tt0) REVERT: A 105 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8202 (mt-10) REVERT: A 246 LYS cc_start: 0.8075 (mttp) cc_final: 0.7238 (mmtm) REVERT: A 293 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: A 399 PHE cc_start: 0.7205 (t80) cc_final: 0.6562 (t80) REVERT: B 62 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7393 (mp) REVERT: B 80 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.7480 (m-40) REVERT: B 157 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.7558 (mtp85) REVERT: C 60 MET cc_start: 0.5830 (OUTLIER) cc_final: 0.5377 (tmm) REVERT: D 2 GLU cc_start: 0.8204 (tt0) cc_final: 0.7559 (tt0) REVERT: D 54 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7580 (tmtm) REVERT: D 82 SER cc_start: 0.8917 (p) cc_final: 0.8578 (m) REVERT: D 143 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7742 (mtp180) REVERT: D 212 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.7098 (p0) REVERT: D 290 ARG cc_start: 0.8163 (mmm-85) cc_final: 0.7701 (mmt90) REVERT: D 349 GLU cc_start: 0.7222 (mp0) cc_final: 0.5951 (tm-30) REVERT: E 143 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: E 166 MET cc_start: 0.8893 (ptt) cc_final: 0.8505 (ptt) REVERT: E 296 SER cc_start: 0.8634 (t) cc_final: 0.8326 (m) REVERT: F 60 MET cc_start: 0.6219 (mtp) cc_final: 0.5892 (mtm) REVERT: G 47 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8107 (mt) REVERT: G 48 THR cc_start: 0.7953 (m) cc_final: 0.7580 (m) REVERT: G 95 PHE cc_start: 0.8757 (t80) cc_final: 0.8348 (t80) REVERT: G 164 ILE cc_start: 0.7930 (mm) cc_final: 0.7575 (mp) REVERT: G 421 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.4720 (t80) REVERT: H 224 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.7935 (tpp-160) REVERT: H 270 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7408 (mp0) REVERT: H 304 THR cc_start: 0.8068 (m) cc_final: 0.7679 (m) REVERT: I 140 THR cc_start: 0.7854 (m) cc_final: 0.7534 (p) REVERT: J 36 THR cc_start: 0.8345 (t) cc_final: 0.8059 (m) REVERT: J 289 THR cc_start: 0.7923 (OUTLIER) cc_final: 0.7584 (p) REVERT: J 303 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7447 (mtmt) REVERT: J 426 LEU cc_start: 0.7595 (mt) cc_final: 0.7333 (mm) REVERT: K 279 THR cc_start: 0.8953 (m) cc_final: 0.8677 (m) REVERT: K 302 ASN cc_start: 0.7565 (t0) cc_final: 0.7271 (m110) REVERT: K 310 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8086 (ptp90) REVERT: K 387 CYS cc_start: 0.6486 (m) cc_final: 0.6024 (m) outliers start: 98 outliers final: 64 residues processed: 424 average time/residue: 0.5718 time to fit residues: 292.9028 Evaluate side-chains 432 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 353 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 409 SER Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 310 ARG Chi-restraints excluded: chain K residue 324 GLU Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain K residue 393 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 209 optimal weight: 0.4980 chunk 180 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 188 optimal weight: 0.8980 chunk 397 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 126 optimal weight: 10.0000 chunk 319 optimal weight: 0.9990 chunk 318 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 358 ASN D 369 GLN E 102 GLN ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 346 HIS G 30 GLN ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 ASN H 302 ASN K 102 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.210486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.177044 restraints weight = 31688.650| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 1.43 r_work: 0.3775 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32180 Z= 0.107 Angle : 0.505 6.365 43912 Z= 0.267 Chirality : 0.045 0.197 4896 Planarity : 0.004 0.058 5624 Dihedral : 4.962 50.954 4520 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.42 % Allowed : 12.86 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.45 (0.13), residues: 4000 helix: 2.05 (0.24), residues: 480 sheet: 0.39 (0.14), residues: 1328 loop : -0.08 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 388 TYR 0.019 0.001 TYR J 309 PHE 0.021 0.001 PHE D 95 TRP 0.013 0.001 TRP I 134 HIS 0.004 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00241 (32112) covalent geometry : angle 0.49967 (43768) SS BOND : bond 0.00275 ( 60) SS BOND : angle 1.10796 ( 120) hydrogen bonds : bond 0.03266 ( 1264) hydrogen bonds : angle 5.25680 ( 3378) link_NAG-ASN : bond 0.00261 ( 8) link_NAG-ASN : angle 2.38174 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 378 time to evaluate : 1.061 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 20 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: A 99 GLU cc_start: 0.6835 (tt0) cc_final: 0.6423 (tt0) REVERT: A 105 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8143 (mt-10) REVERT: A 246 LYS cc_start: 0.8041 (mttp) cc_final: 0.7197 (mmtm) REVERT: A 399 PHE cc_start: 0.7157 (t80) cc_final: 0.6510 (t80) REVERT: B 62 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7440 (mp) REVERT: B 80 ASN cc_start: 0.7953 (OUTLIER) cc_final: 0.7436 (m-40) REVERT: B 157 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7499 (mtp85) REVERT: B 198 TYR cc_start: 0.7477 (t80) cc_final: 0.7027 (t80) REVERT: D 2 GLU cc_start: 0.8142 (tt0) cc_final: 0.7428 (tt0) REVERT: D 82 SER cc_start: 0.8878 (p) cc_final: 0.8544 (m) REVERT: D 144 SER cc_start: 0.8717 (p) cc_final: 0.8478 (t) REVERT: D 212 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.7072 (p0) REVERT: D 290 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7742 (mmt90) REVERT: D 349 GLU cc_start: 0.7197 (mp0) cc_final: 0.5944 (tm-30) REVERT: D 367 LYS cc_start: 0.7959 (tmtt) cc_final: 0.7721 (tptm) REVERT: E 143 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: E 166 MET cc_start: 0.8834 (ptt) cc_final: 0.8591 (ptt) REVERT: F 60 MET cc_start: 0.6116 (mtp) cc_final: 0.5888 (mtm) REVERT: G 48 THR cc_start: 0.7858 (m) cc_final: 0.7484 (m) REVERT: G 95 PHE cc_start: 0.8710 (t80) cc_final: 0.8322 (t80) REVERT: G 164 ILE cc_start: 0.7750 (mm) cc_final: 0.7366 (mp) REVERT: G 421 PHE cc_start: 0.5732 (OUTLIER) cc_final: 0.4802 (t80) REVERT: H 35 GLU cc_start: 0.8375 (tt0) cc_final: 0.8032 (tt0) REVERT: H 221 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7542 (pmtt) REVERT: H 224 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8000 (tpp-160) REVERT: H 270 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7313 (mp0) REVERT: H 304 THR cc_start: 0.8195 (m) cc_final: 0.7835 (m) REVERT: I 140 THR cc_start: 0.7704 (m) cc_final: 0.7438 (p) REVERT: J 143 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.6816 (mtp180) REVERT: J 289 THR cc_start: 0.7928 (OUTLIER) cc_final: 0.7605 (p) REVERT: J 303 LYS cc_start: 0.7674 (mmtt) cc_final: 0.7334 (mtmt) REVERT: J 426 LEU cc_start: 0.7604 (mt) cc_final: 0.7367 (mm) REVERT: K 64 TYR cc_start: 0.8281 (m-80) cc_final: 0.7662 (m-80) REVERT: K 279 THR cc_start: 0.8889 (m) cc_final: 0.8671 (m) REVERT: K 296 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8528 (m) REVERT: K 310 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8106 (ptp90) REVERT: K 387 CYS cc_start: 0.6365 (m) cc_final: 0.6038 (m) REVERT: L 52 GLU cc_start: 0.7763 (tt0) cc_final: 0.7505 (mt-10) outliers start: 83 outliers final: 55 residues processed: 427 average time/residue: 0.5532 time to fit residues: 283.9222 Evaluate side-chains 428 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 362 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 310 ARG Chi-restraints excluded: chain K residue 393 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 170 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 304 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 288 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 312 optimal weight: 0.9980 chunk 61 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 358 ASN D 369 GLN E 102 GLN E 236 ASN E 302 ASN E 346 HIS ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 ASN K 102 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.202215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.167362 restraints weight = 32307.673| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.68 r_work: 0.3620 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32180 Z= 0.131 Angle : 0.523 6.419 43912 Z= 0.275 Chirality : 0.046 0.194 4896 Planarity : 0.004 0.056 5624 Dihedral : 4.956 50.714 4520 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.32 % Rotamer: Outliers : 2.25 % Allowed : 13.16 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.47 (0.13), residues: 4000 helix: 2.18 (0.24), residues: 480 sheet: 0.41 (0.14), residues: 1288 loop : -0.09 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 388 TYR 0.021 0.001 TYR J 309 PHE 0.022 0.001 PHE D 95 TRP 0.012 0.001 TRP B 327 HIS 0.005 0.001 HIS K 41 Details of bonding type rmsd covalent geometry : bond 0.00308 (32112) covalent geometry : angle 0.51577 (43768) SS BOND : bond 0.00314 ( 60) SS BOND : angle 1.38416 ( 120) hydrogen bonds : bond 0.03317 ( 1264) hydrogen bonds : angle 5.23206 ( 3378) link_NAG-ASN : bond 0.00237 ( 8) link_NAG-ASN : angle 2.34108 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 371 time to evaluate : 1.172 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 20 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7589 (mt-10) REVERT: A 99 GLU cc_start: 0.6711 (tt0) cc_final: 0.6280 (tt0) REVERT: A 105 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8039 (mt-10) REVERT: A 141 SER cc_start: 0.8281 (p) cc_final: 0.7760 (t) REVERT: A 246 LYS cc_start: 0.7991 (mttp) cc_final: 0.7127 (mmtm) REVERT: A 378 LYS cc_start: 0.7023 (mtmt) cc_final: 0.6746 (mtpm) REVERT: A 399 PHE cc_start: 0.7088 (t80) cc_final: 0.6450 (t80) REVERT: B 62 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7406 (mp) REVERT: B 80 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7430 (m-40) REVERT: B 157 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7431 (mtp85) REVERT: B 198 TYR cc_start: 0.7436 (t80) cc_final: 0.6949 (t80) REVERT: D 2 GLU cc_start: 0.8064 (tt0) cc_final: 0.7363 (tt0) REVERT: D 82 SER cc_start: 0.8894 (p) cc_final: 0.8542 (m) REVERT: D 144 SER cc_start: 0.8680 (p) cc_final: 0.8425 (t) REVERT: D 212 ASN cc_start: 0.7550 (OUTLIER) cc_final: 0.7061 (p0) REVERT: D 290 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7676 (mmt90) REVERT: D 349 GLU cc_start: 0.7111 (mp0) cc_final: 0.5869 (tm-30) REVERT: E 143 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: F 60 MET cc_start: 0.6063 (mtp) cc_final: 0.5851 (mtm) REVERT: G 48 THR cc_start: 0.7849 (m) cc_final: 0.7454 (m) REVERT: G 95 PHE cc_start: 0.8633 (t80) cc_final: 0.8243 (t80) REVERT: G 164 ILE cc_start: 0.7763 (mm) cc_final: 0.7393 (mp) REVERT: G 421 PHE cc_start: 0.5721 (OUTLIER) cc_final: 0.4764 (t80) REVERT: H 35 GLU cc_start: 0.8371 (tt0) cc_final: 0.8033 (tt0) REVERT: H 221 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7454 (pmtt) REVERT: H 224 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.7930 (tpp-160) REVERT: H 270 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7260 (mp0) REVERT: H 304 THR cc_start: 0.7966 (m) cc_final: 0.7598 (m) REVERT: I 140 THR cc_start: 0.7661 (m) cc_final: 0.7337 (p) REVERT: J 143 ARG cc_start: 0.7285 (ttm-80) cc_final: 0.6718 (mtp180) REVERT: J 217 ASN cc_start: 0.8745 (t0) cc_final: 0.8495 (t0) REVERT: J 289 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7530 (p) REVERT: J 303 LYS cc_start: 0.7654 (mmtt) cc_final: 0.7293 (mtmt) REVERT: J 426 LEU cc_start: 0.7426 (mt) cc_final: 0.7191 (mm) REVERT: K 279 THR cc_start: 0.8857 (m) cc_final: 0.8626 (m) REVERT: K 296 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8467 (m) REVERT: K 310 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7988 (ptp90) REVERT: K 387 CYS cc_start: 0.6259 (m) cc_final: 0.5761 (m) REVERT: L 52 GLU cc_start: 0.7642 (tt0) cc_final: 0.7405 (mt-10) outliers start: 77 outliers final: 56 residues processed: 418 average time/residue: 0.5727 time to fit residues: 288.7687 Evaluate side-chains 426 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 359 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 310 ARG Chi-restraints excluded: chain K residue 393 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 238 optimal weight: 3.9990 chunk 334 optimal weight: 0.9990 chunk 243 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 396 optimal weight: 8.9990 chunk 216 optimal weight: 0.9990 chunk 121 optimal weight: 0.0070 chunk 150 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 314 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 358 ASN D 30 GLN E 102 GLN ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN E 302 ASN E 346 HIS G 223 GLN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 ASN J 79 GLN L 84 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.203156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.168582 restraints weight = 32040.989| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 1.61 r_work: 0.3633 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32180 Z= 0.131 Angle : 0.529 9.663 43912 Z= 0.277 Chirality : 0.046 0.190 4896 Planarity : 0.004 0.057 5624 Dihedral : 4.954 50.306 4520 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.22 % Allowed : 13.54 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.47 (0.13), residues: 4000 helix: 2.20 (0.24), residues: 480 sheet: 0.38 (0.14), residues: 1288 loop : -0.09 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 152 TYR 0.021 0.001 TYR J 309 PHE 0.023 0.001 PHE D 95 TRP 0.011 0.001 TRP B 327 HIS 0.005 0.001 HIS B 41 Details of bonding type rmsd covalent geometry : bond 0.00310 (32112) covalent geometry : angle 0.52024 (43768) SS BOND : bond 0.00331 ( 60) SS BOND : angle 1.58269 ( 120) hydrogen bonds : bond 0.03301 ( 1264) hydrogen bonds : angle 5.21416 ( 3378) link_NAG-ASN : bond 0.00233 ( 8) link_NAG-ASN : angle 2.30624 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8000 Ramachandran restraints generated. 4000 Oldfield, 0 Emsley, 4000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 362 time to evaluate : 1.434 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 20 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: A 99 GLU cc_start: 0.6679 (tt0) cc_final: 0.6255 (tt0) REVERT: A 105 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8000 (mt-10) REVERT: A 141 SER cc_start: 0.8286 (p) cc_final: 0.7778 (t) REVERT: A 246 LYS cc_start: 0.7978 (mttp) cc_final: 0.7130 (mmtm) REVERT: A 378 LYS cc_start: 0.7011 (mtmt) cc_final: 0.6742 (mtpm) REVERT: A 399 PHE cc_start: 0.7084 (t80) cc_final: 0.6448 (t80) REVERT: B 62 LEU cc_start: 0.7672 (OUTLIER) cc_final: 0.7339 (mp) REVERT: B 157 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7431 (mtp85) REVERT: B 198 TYR cc_start: 0.7327 (t80) cc_final: 0.6864 (t80) REVERT: D 2 GLU cc_start: 0.8054 (tt0) cc_final: 0.7361 (tt0) REVERT: D 82 SER cc_start: 0.8877 (p) cc_final: 0.8530 (m) REVERT: D 144 SER cc_start: 0.8676 (p) cc_final: 0.8406 (t) REVERT: D 212 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.7004 (p0) REVERT: D 290 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7686 (mmt90) REVERT: D 349 GLU cc_start: 0.7088 (mp0) cc_final: 0.5873 (tm-30) REVERT: E 143 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: E 166 MET cc_start: 0.8971 (ptp) cc_final: 0.8529 (ptt) REVERT: F 60 MET cc_start: 0.6061 (mtp) cc_final: 0.5845 (mtm) REVERT: G 47 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8114 (mt) REVERT: G 48 THR cc_start: 0.7824 (m) cc_final: 0.7434 (m) REVERT: G 95 PHE cc_start: 0.8638 (t80) cc_final: 0.8241 (t80) REVERT: G 99 GLU cc_start: 0.7411 (mp0) cc_final: 0.6871 (tp30) REVERT: G 164 ILE cc_start: 0.7749 (mm) cc_final: 0.7380 (mp) REVERT: G 421 PHE cc_start: 0.5743 (OUTLIER) cc_final: 0.4760 (t80) REVERT: H 35 GLU cc_start: 0.8330 (tt0) cc_final: 0.8013 (tt0) REVERT: H 221 LYS cc_start: 0.8101 (mtmm) cc_final: 0.7443 (pmtt) REVERT: H 224 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.7963 (tpp-160) REVERT: H 270 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7285 (mp0) REVERT: H 304 THR cc_start: 0.8106 (m) cc_final: 0.7749 (m) REVERT: I 140 THR cc_start: 0.7682 (m) cc_final: 0.7368 (p) REVERT: J 143 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.6723 (mtp180) REVERT: J 217 ASN cc_start: 0.8730 (t0) cc_final: 0.8478 (t0) REVERT: J 289 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7522 (p) REVERT: J 303 LYS cc_start: 0.7633 (mmtt) cc_final: 0.7302 (mtmt) REVERT: J 426 LEU cc_start: 0.7431 (mt) cc_final: 0.7197 (mm) REVERT: K 168 GLN cc_start: 0.8402 (tt0) cc_final: 0.8033 (tt0) REVERT: K 279 THR cc_start: 0.8855 (m) cc_final: 0.8622 (m) REVERT: K 296 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8439 (m) REVERT: K 310 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8022 (ptp90) REVERT: K 387 CYS cc_start: 0.6252 (m) cc_final: 0.5769 (m) REVERT: L 52 GLU cc_start: 0.7605 (tt0) cc_final: 0.7398 (mt-10) outliers start: 76 outliers final: 58 residues processed: 410 average time/residue: 0.5927 time to fit residues: 291.7154 Evaluate side-chains 427 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 358 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 212 ASN Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 308 THR Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain G residue 97 ASP Chi-restraints excluded: chain G residue 136 THR Chi-restraints excluded: chain G residue 144 SER Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 224 ARG Chi-restraints excluded: chain H residue 272 LEU Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 112 GLU Chi-restraints excluded: chain J residue 172 SER Chi-restraints excluded: chain J residue 209 SER Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 274 VAL Chi-restraints excluded: chain J residue 289 THR Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 371 CYS Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 296 SER Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain K residue 310 ARG Chi-restraints excluded: chain K residue 393 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 214 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 389 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 362 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 286 optimal weight: 7.9990 chunk 283 optimal weight: 0.9990 chunk 371 optimal weight: 5.9990 chunk 315 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN B 358 ASN E 102 GLN E 302 ASN E 346 HIS ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 ASN J 79 GLN K 102 GLN L 84 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.166031 restraints weight = 32379.772| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.70 r_work: 0.3600 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32180 Z= 0.164 Angle : 0.554 9.405 43912 Z= 0.290 Chirality : 0.047 0.190 4896 Planarity : 0.004 0.057 5624 Dihedral : 5.052 50.489 4520 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.08 % Rotamer: Outliers : 2.36 % Allowed : 13.39 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 aren not related in a simple way. whole: 0.39 (0.13), residues: 4000 helix: 2.12 (0.24), residues: 480 sheet: 0.34 (0.14), residues: 1288 loop : -0.14 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 152 TYR 0.022 0.002 TYR J 309 PHE 0.018 0.002 PHE A 421 TRP 0.011 0.001 TRP I 134 HIS 0.005 0.001 HIS D 28 Details of bonding type rmsd covalent geometry : bond 0.00396 (32112) covalent geometry : angle 0.54485 (43768) SS BOND : bond 0.00371 ( 60) SS BOND : angle 1.66320 ( 120) hydrogen bonds : bond 0.03438 ( 1264) hydrogen bonds : angle 5.29118 ( 3378) link_NAG-ASN : bond 0.00249 ( 8) link_NAG-ASN : angle 2.32311 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11162.69 seconds wall clock time: 190 minutes 45.22 seconds (11445.22 seconds total)