Starting phenix.real_space_refine on Thu Jun 26 15:17:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ufa_42188/06_2025/8ufa_42188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ufa_42188/06_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_42188/06_2025/8ufa_42188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ufa_42188/06_2025/8ufa_42188.map" model { file = "/net/cci-nas-00/data/ceres_data/8ufa_42188/06_2025/8ufa_42188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ufa_42188/06_2025/8ufa_42188.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.79, per 1000 atoms: 0.54 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: 6.75 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 5.07 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: 12.86 Time building geometry restraints manager: 8.16 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: 0.03 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.160 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 67.240 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.200 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:12.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.370 ------------------------------------------------------------------------------- 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 : 1.20 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.003 TRP F 134 HIS 0.010 0.002 HIS L 79 PHE 0.014 0.002 PHE G 421 TYR 0.033 0.005 TYR F 67 ARG 0.027 0.003 ARG E 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 8) link_NAG-ASN : angle 2.33883 ( 24) hydrogen bonds : bond 0.20336 ( 1264) hydrogen bonds : angle 8.59425 ( 3378) SS BOND : bond 0.00327 ( 60) SS BOND : angle 1.22796 ( 120) covalent geometry : bond 0.00357 (32112) covalent geometry : angle 0.68384 (43768) *********************** 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 : 3.363 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: 1.3501 time to fit residues: 1034.6978 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 : 3.046 ------------------------------------------------------------------------------- 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 337 optimal weight: 6.9990 chunk 303 optimal weight: 0.5980 chunk 168 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 204 optimal weight: 0.5980 chunk 161 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 233 optimal weight: 0.9980 chunk 363 optimal weight: 10.0000 overall best weight: 3.2384 ------------------------------------------------------------------------------- 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 HIS K 21 ASN K 102 GLN K 114 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.208351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.174611 restraints weight = 31517.274| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 1.46 r_work: 0.3724 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 32180 Z= 0.257 Angle : 0.693 12.762 43912 Z= 0.369 Chirality : 0.051 0.218 4896 Planarity : 0.005 0.047 5624 Dihedral : 5.579 57.683 4522 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.57 % Allowed : 8.17 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.13), residues: 4000 helix: 1.38 (0.23), residues: 468 sheet: 0.49 (0.14), residues: 1300 loop : 0.13 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 327 HIS 0.014 0.002 HIS B 175 PHE 0.018 0.002 PHE G 421 TYR 0.026 0.002 TYR J 309 ARG 0.007 0.001 ARG J 37 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 8) link_NAG-ASN : angle 2.45735 ( 24) hydrogen bonds : bond 0.04986 ( 1264) hydrogen bonds : angle 6.23659 ( 3378) SS BOND : bond 0.00654 ( 60) SS BOND : angle 2.28282 ( 120) covalent geometry : bond 0.00631 (32112) covalent geometry : angle 0.68155 (43768) *********************** 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 496 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 408 time to evaluate : 3.584 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: 0.8554 (OUTLIER) cc_final: 0.7791 (mt-10) REVERT: A 105 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 246 LYS cc_start: 0.8092 (mttp) cc_final: 0.7241 (mmtt) REVERT: A 399 PHE cc_start: 0.7070 (t80) cc_final: 0.6530 (t80) REVERT: B 80 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7492 (m-40) REVERT: D 54 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7346 (tmtm) REVERT: D 82 SER cc_start: 0.8887 (p) cc_final: 0.8616 (m) REVERT: D 189 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8419 (t70) REVERT: D 398 SER cc_start: 0.8359 (m) cc_final: 0.8149 (t) REVERT: E 37 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8753 (mmp-170) REVERT: E 166 MET cc_start: 0.8933 (ptt) cc_final: 0.8555 (ptt) REVERT: F 60 MET cc_start: 0.6260 (mtp) cc_final: 0.5894 (mtm) REVERT: G 32 GLN cc_start: 0.8907 (tt0) cc_final: 0.8624 (tt0) REVERT: G 164 ILE cc_start: 0.7910 (mm) cc_final: 0.7576 (mp) REVERT: G 412 LYS cc_start: 0.6580 (mttt) cc_final: 0.5728 (mtmt) REVERT: H 35 GLU cc_start: 0.8448 (tt0) cc_final: 0.8096 (tt0) REVERT: H 276 LYS cc_start: 0.8775 (mtmm) cc_final: 0.8538 (mtmt) REVERT: I 140 THR cc_start: 0.7880 (m) cc_final: 0.7450 (p) REVERT: J 88 MET cc_start: 0.8184 (mmm) cc_final: 0.7744 (mmm) REVERT: J 143 ARG cc_start: 0.7504 (ttm-80) cc_final: 0.6891 (mtp180) REVERT: J 289 THR cc_start: 0.7437 (m) cc_final: 0.7197 (t) REVERT: J 303 LYS cc_start: 0.7703 (mmtt) cc_final: 0.6988 (mmmt) REVERT: K 28 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: K 119 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7178 (mmt90) REVERT: K 139 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8298 (mtt-85) REVERT: K 351 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7758 (mt-10) outliers start: 88 outliers final: 42 residues processed: 451 average time/residue: 1.3559 time to fit residues: 729.5509 Evaluate side-chains 424 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 374 time to evaluate : 3.209 ------------------------------------------------------------------------------- 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 A residue 274 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 396 THR 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 4 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 F residue 131 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 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 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 139 ARG 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 169 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 315 optimal weight: 6.9990 chunk 180 optimal weight: 7.9990 chunk 373 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 354 optimal weight: 0.7980 chunk 395 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 358 ASN D 369 GLN E 102 GLN E 346 HIS G 30 GLN G 223 GLN ** G 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 160 GLN H 302 ASN I 79 HIS K 102 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.208810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.174959 restraints weight = 31641.658| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 1.43 r_work: 0.3741 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3629 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32180 Z= 0.182 Angle : 0.587 6.105 43912 Z= 0.312 Chirality : 0.048 0.211 4896 Planarity : 0.005 0.049 5624 Dihedral : 5.405 59.040 4520 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.54 % Allowed : 9.54 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.13), residues: 4000 helix: 1.50 (0.23), residues: 476 sheet: 0.34 (0.14), residues: 1300 loop : 0.04 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 327 HIS 0.005 0.001 HIS E 41 PHE 0.017 0.002 PHE G 421 TYR 0.024 0.002 TYR J 309 ARG 0.009 0.001 ARG K 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 8) link_NAG-ASN : angle 2.36852 ( 24) hydrogen bonds : bond 0.04274 ( 1264) hydrogen bonds : angle 5.79644 ( 3378) SS BOND : bond 0.00379 ( 60) SS BOND : angle 1.40086 ( 120) covalent geometry : bond 0.00437 (32112) covalent geometry : angle 0.58034 (43768) *********************** 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 469 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 382 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7838 (mt-10) REVERT: A 105 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8167 (mt-10) REVERT: A 135 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8641 (pt) REVERT: A 246 LYS cc_start: 0.8083 (mttp) cc_final: 0.7263 (mmtt) REVERT: A 399 PHE cc_start: 0.7220 (t80) cc_final: 0.6637 (t80) REVERT: B 13 ARG cc_start: 0.8370 (ptt-90) cc_final: 0.8129 (ppt170) REVERT: B 80 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7495 (m-40) REVERT: B 102 GLN cc_start: 0.8434 (mt0) cc_final: 0.8077 (mt0) REVERT: B 157 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7555 (mtp85) REVERT: D 82 SER cc_start: 0.8965 (p) cc_final: 0.8665 (m) REVERT: D 143 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7783 (mtp180) REVERT: D 212 ASN cc_start: 0.7419 (OUTLIER) cc_final: 0.6956 (p0) REVERT: D 349 GLU cc_start: 0.7299 (mp0) cc_final: 0.5970 (tm-30) REVERT: E 143 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: E 166 MET cc_start: 0.8896 (ptt) cc_final: 0.8522 (ptt) REVERT: F 60 MET cc_start: 0.6312 (mtp) cc_final: 0.5980 (mtm) REVERT: G 32 GLN cc_start: 0.8875 (tt0) cc_final: 0.8553 (tt0) REVERT: G 48 THR cc_start: 0.7854 (m) cc_final: 0.7461 (m) REVERT: G 130 GLN cc_start: 0.8492 (mt0) cc_final: 0.8260 (mt0) REVERT: G 164 ILE cc_start: 0.7945 (mm) cc_final: 0.7599 (mp) REVERT: G 412 LYS cc_start: 0.6573 (mttt) cc_final: 0.5681 (mtmt) REVERT: H 35 GLU cc_start: 0.8416 (tt0) cc_final: 0.8057 (tt0) REVERT: H 276 LYS cc_start: 0.8747 (mtmm) cc_final: 0.8539 (mtmt) REVERT: I 140 THR cc_start: 0.7856 (m) cc_final: 0.7444 (p) REVERT: J 143 ARG cc_start: 0.7411 (ttm-80) cc_final: 0.6792 (mtp180) REVERT: J 303 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7411 (mtmt) REVERT: J 378 LYS cc_start: 0.8306 (OUTLIER) cc_final: 0.7781 (mtpp) REVERT: K 139 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8283 (mtt-85) REVERT: K 279 THR cc_start: 0.8949 (m) cc_final: 0.8718 (m) REVERT: K 310 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8082 (ptp90) REVERT: K 351 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7821 (mt-10) outliers start: 87 outliers final: 46 residues processed: 425 average time/residue: 1.3420 time to fit residues: 689.6397 Evaluate side-chains 416 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 360 time to evaluate : 3.379 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain A residue 282 ASP 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 99 GLU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 212 ASN 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 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 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 27 CYS Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 304 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 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 324 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 313 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 338 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 chunk 335 optimal weight: 4.9990 chunk 264 optimal weight: 20.0000 chunk 139 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN C 88 ASN D 369 GLN E 236 ASN E 302 ASN E 346 HIS F 79 HIS G 30 GLN ** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 GLN ** G 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 HIS ** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.203492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.168864 restraints weight = 31747.710| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.45 r_work: 0.3431 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.085 32180 Z= 0.384 Angle : 0.760 8.787 43912 Z= 0.401 Chirality : 0.055 0.243 4896 Planarity : 0.006 0.058 5624 Dihedral : 6.007 58.514 4520 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.35 % Favored : 96.60 % Rotamer: Outliers : 3.56 % Allowed : 10.71 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 4000 helix: 0.96 (0.23), residues: 480 sheet: -0.06 (0.14), residues: 1300 loop : -0.42 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP I 134 HIS 0.011 0.002 HIS E 41 PHE 0.022 0.003 PHE E 113 TYR 0.031 0.003 TYR J 309 ARG 0.009 0.001 ARG K 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00511 ( 8) link_NAG-ASN : angle 2.66140 ( 24) hydrogen bonds : bond 0.04747 ( 1264) hydrogen bonds : angle 6.16792 ( 3378) SS BOND : bond 0.00665 ( 60) SS BOND : angle 1.84343 ( 120) covalent geometry : bond 0.00950 (32112) covalent geometry : angle 0.75286 (43768) *********************** 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 486 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 364 time to evaluate : 3.108 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: 0.8506 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: A 99 GLU cc_start: 0.6876 (tt0) cc_final: 0.6611 (tt0) REVERT: A 105 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8118 (mt-10) REVERT: A 246 LYS cc_start: 0.8039 (mttp) cc_final: 0.7109 (mmtt) REVERT: A 293 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7033 (mt-10) REVERT: A 367 LYS cc_start: 0.8481 (tttt) cc_final: 0.8178 (ttpp) REVERT: A 378 LYS cc_start: 0.6768 (mttm) cc_final: 0.6550 (mtmt) REVERT: A 399 PHE cc_start: 0.7174 (t80) cc_final: 0.6537 (t80) REVERT: B 13 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7901 (ptt-90) REVERT: B 62 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7392 (mp) REVERT: B 80 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7467 (m-40) REVERT: B 102 GLN cc_start: 0.8418 (mt0) cc_final: 0.8083 (mt0) REVERT: B 274 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8232 (mt-10) REVERT: D 54 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7426 (tmtm) REVERT: D 82 SER cc_start: 0.8939 (p) cc_final: 0.8563 (m) REVERT: D 109 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: D 143 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7574 (mtp180) REVERT: D 189 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8376 (t70) REVERT: D 290 ARG cc_start: 0.8097 (mmm-85) cc_final: 0.7581 (mmt90) REVERT: D 349 GLU cc_start: 0.7233 (mp0) cc_final: 0.5864 (tm-30) REVERT: E 143 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8020 (tt0) REVERT: E 166 MET cc_start: 0.8919 (ptt) cc_final: 0.8476 (ptt) REVERT: E 296 SER cc_start: 0.8677 (t) cc_final: 0.8308 (m) REVERT: F 60 MET cc_start: 0.6269 (mtp) cc_final: 0.5965 (mtm) REVERT: G 32 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8569 (tt0) REVERT: G 95 PHE cc_start: 0.8670 (t80) cc_final: 0.8425 (t80) REVERT: G 164 ILE cc_start: 0.8037 (mm) cc_final: 0.7667 (mp) REVERT: G 382 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8405 (mppt) REVERT: G 412 LYS cc_start: 0.6373 (mttt) cc_final: 0.5382 (mtmt) REVERT: H 37 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7547 (mmp80) REVERT: I 85 TYR cc_start: 0.6225 (t80) cc_final: 0.5905 (t80) REVERT: I 140 THR cc_start: 0.7762 (m) cc_final: 0.7365 (p) REVERT: J 13 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8395 (mm) REVERT: J 376 THR cc_start: 0.8796 (t) cc_final: 0.8248 (m) REVERT: J 378 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7795 (mtpp) REVERT: K 119 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8149 (mmt90) REVERT: K 139 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8113 (mtt-85) REVERT: K 231 LYS cc_start: 0.7923 (tptm) cc_final: 0.7062 (mtpp) REVERT: K 279 THR cc_start: 0.9042 (m) cc_final: 0.8720 (m) REVERT: K 310 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7895 (ptp90) outliers start: 122 outliers final: 72 residues processed: 433 average time/residue: 1.2641 time to fit residues: 659.3884 Evaluate side-chains 421 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 332 time to evaluate : 3.234 ------------------------------------------------------------------------------- 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 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 A residue 296 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 13 ARG 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 379 CYS 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 109 GLU Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 261 SER 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 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 215 THR Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 304 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain G residue 32 GLN Chi-restraints excluded: chain G residue 36 THR 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 135 ILE 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 H residue 4 THR Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 41 HIS Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain I residue 112 ARG 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 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 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 52 MET 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 Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain L residue 131 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 399 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 344 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 chunk 221 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 150 ASN B 358 ASN D 369 GLN E 102 GLN ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 HIS G 30 GLN G 223 GLN ** G 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 114 HIS H 236 ASN H 302 ASN K 102 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.209342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.175745 restraints weight = 31571.813| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.43 r_work: 0.3758 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2449 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= 0.113 Angle : 0.533 6.242 43912 Z= 0.284 Chirality : 0.046 0.193 4896 Planarity : 0.004 0.057 5624 Dihedral : 5.479 58.913 4520 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.78 % Rotamer: Outliers : 2.25 % Allowed : 12.54 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.13), residues: 4000 helix: 1.55 (0.24), residues: 480 sheet: 0.10 (0.14), residues: 1308 loop : -0.22 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 134 HIS 0.004 0.001 HIS A 395 PHE 0.017 0.001 PHE A 421 TYR 0.021 0.001 TYR J 309 ARG 0.005 0.000 ARG K 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 8) link_NAG-ASN : angle 2.45162 ( 24) hydrogen bonds : bond 0.03595 ( 1264) hydrogen bonds : angle 5.60831 ( 3378) SS BOND : bond 0.00280 ( 60) SS BOND : angle 1.15574 ( 120) covalent geometry : bond 0.00246 (32112) covalent geometry : angle 0.52757 (43768) *********************** 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 443 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 366 time to evaluate : 3.313 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: 0.8471 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: A 82 SER cc_start: 0.8926 (OUTLIER) cc_final: 0.8708 (m) REVERT: A 99 GLU cc_start: 0.6848 (tt0) cc_final: 0.6498 (tt0) REVERT: A 105 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8058 (mt-10) REVERT: A 246 LYS cc_start: 0.8056 (mttp) cc_final: 0.7218 (mmtt) REVERT: A 293 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: A 399 PHE cc_start: 0.7187 (t80) cc_final: 0.6538 (t80) REVERT: B 13 ARG cc_start: 0.8380 (ptt-90) cc_final: 0.8101 (ppt170) REVERT: B 80 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7481 (m-40) REVERT: B 102 GLN cc_start: 0.8479 (mt0) cc_final: 0.8108 (mt0) REVERT: B 157 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7602 (mtp85) REVERT: B 186 LYS cc_start: 0.7486 (tttt) cc_final: 0.7044 (tttm) REVERT: B 198 TYR cc_start: 0.7474 (t80) cc_final: 0.7216 (t80) REVERT: C 60 MET cc_start: 0.5920 (OUTLIER) cc_final: 0.5372 (tmm) REVERT: D 2 GLU cc_start: 0.8211 (tt0) cc_final: 0.7562 (tt0) REVERT: D 82 SER cc_start: 0.8802 (p) cc_final: 0.8457 (m) REVERT: D 189 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8354 (t70) REVERT: D 212 ASN cc_start: 0.7503 (OUTLIER) cc_final: 0.7081 (p0) REVERT: D 290 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7676 (mmt90) REVERT: D 349 GLU cc_start: 0.7205 (mp0) cc_final: 0.5978 (tm-30) REVERT: E 143 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7958 (tt0) REVERT: E 166 MET cc_start: 0.8848 (ptt) cc_final: 0.8589 (ptt) REVERT: F 60 MET cc_start: 0.6341 (mtp) cc_final: 0.6037 (mtm) REVERT: G 7 MET cc_start: 0.8461 (ptm) cc_final: 0.8049 (ptp) REVERT: G 32 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8549 (tt0) REVERT: G 47 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.8116 (mt) REVERT: G 48 THR cc_start: 0.7808 (m) cc_final: 0.7393 (m) REVERT: G 164 ILE cc_start: 0.7777 (mm) cc_final: 0.7395 (mp) REVERT: G 421 PHE cc_start: 0.5701 (OUTLIER) cc_final: 0.4718 (t80) REVERT: H 135 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8928 (mtm180) REVERT: H 270 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7381 (mp0) REVERT: I 140 THR cc_start: 0.7787 (m) cc_final: 0.7442 (p) REVERT: J 36 THR cc_start: 0.8294 (t) cc_final: 0.7982 (m) REVERT: J 397 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: J 426 LEU cc_start: 0.7457 (mt) cc_final: 0.7205 (mm) REVERT: K 28 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7808 (m-30) REVERT: K 139 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8246 (mtt-85) REVERT: K 279 THR cc_start: 0.8912 (m) cc_final: 0.8635 (m) REVERT: K 296 SER cc_start: 0.8864 (p) cc_final: 0.8601 (m) REVERT: K 310 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8017 (ptp90) outliers start: 77 outliers final: 36 residues processed: 414 average time/residue: 1.2883 time to fit residues: 646.9258 Evaluate side-chains 397 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 344 time to evaluate : 3.396 ------------------------------------------------------------------------------- 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 261 SER 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 80 ASN Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 189 ASP 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 299 SER Chi-restraints excluded: chain F residue 23 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 47 ILE Chi-restraints excluded: chain G residue 97 ASP 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 H residue 27 CYS 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 209 SER Chi-restraints excluded: chain J residue 212 ASN Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 397 GLU Chi-restraints excluded: chain J residue 409 SER Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain K residue 310 ARG Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain K residue 393 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 259 optimal weight: 7.9990 chunk 326 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 367 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 378 optimal weight: 9.9990 chunk 375 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 69 optimal weight: 0.0870 overall best weight: 2.5162 ------------------------------------------------------------------------------- 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 236 ASN E 302 ASN E 346 HIS ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** 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 = 0.4292 r_free = 0.4292 target = 0.206786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.172841 restraints weight = 31646.132| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 1.43 r_work: 0.3714 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3600 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 0.048 32180 Z= 0.201 Angle : 0.589 7.062 43912 Z= 0.311 Chirality : 0.048 0.191 4896 Planarity : 0.005 0.059 5624 Dihedral : 5.495 54.144 4520 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.73 % Rotamer: Outliers : 3.00 % Allowed : 12.19 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.13), residues: 4000 helix: 1.56 (0.24), residues: 480 sheet: 0.08 (0.14), residues: 1328 loop : -0.32 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 134 HIS 0.006 0.001 HIS D 28 PHE 0.017 0.002 PHE D 95 TYR 0.026 0.002 TYR J 309 ARG 0.005 0.000 ARG K 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 8) link_NAG-ASN : angle 2.43465 ( 24) hydrogen bonds : bond 0.03801 ( 1264) hydrogen bonds : angle 5.64462 ( 3378) SS BOND : bond 0.00427 ( 60) SS BOND : angle 1.45051 ( 120) covalent geometry : bond 0.00489 (32112) covalent geometry : angle 0.58240 (43768) *********************** 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 462 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 359 time to evaluate : 3.097 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: 0.8527 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: A 99 GLU cc_start: 0.6888 (tt0) cc_final: 0.6511 (tt0) REVERT: A 105 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8272 (mt-10) REVERT: A 221 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8066 (mtpp) REVERT: A 246 LYS cc_start: 0.8094 (mttp) cc_final: 0.7237 (mmtt) REVERT: A 293 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: A 399 PHE cc_start: 0.7175 (t80) cc_final: 0.6523 (t80) REVERT: B 68 MET cc_start: 0.7691 (mmm) cc_final: 0.7073 (mmt) REVERT: B 80 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7526 (m-40) REVERT: B 102 GLN cc_start: 0.8494 (mt0) cc_final: 0.8126 (mt0) REVERT: B 186 LYS cc_start: 0.7479 (tttt) cc_final: 0.7035 (tttm) REVERT: C 60 MET cc_start: 0.5831 (OUTLIER) cc_final: 0.5413 (tmm) REVERT: D 82 SER cc_start: 0.8936 (p) cc_final: 0.8592 (m) REVERT: D 189 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8418 (t70) REVERT: D 212 ASN cc_start: 0.7571 (OUTLIER) cc_final: 0.7134 (p0) REVERT: D 290 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7679 (mmt90) REVERT: D 349 GLU cc_start: 0.7191 (mp0) cc_final: 0.5970 (tm-30) REVERT: E 143 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8045 (tt0) REVERT: E 166 MET cc_start: 0.8912 (ptt) cc_final: 0.8509 (ptt) REVERT: E 296 SER cc_start: 0.8681 (t) cc_final: 0.8358 (m) REVERT: F 60 MET cc_start: 0.6303 (mtp) cc_final: 0.6009 (mtm) REVERT: G 164 ILE cc_start: 0.7903 (mm) cc_final: 0.7546 (mp) REVERT: G 412 LYS cc_start: 0.6472 (mttt) cc_final: 0.5604 (mtmt) REVERT: G 421 PHE cc_start: 0.5745 (OUTLIER) cc_final: 0.4731 (t80) REVERT: H 37 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7808 (mmp80) REVERT: H 270 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7391 (mp0) REVERT: I 140 THR cc_start: 0.7877 (m) cc_final: 0.7543 (p) REVERT: J 36 THR cc_start: 0.8309 (t) cc_final: 0.7977 (m) REVERT: J 376 THR cc_start: 0.8771 (t) cc_final: 0.8228 (m) REVERT: J 378 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7869 (mtpp) REVERT: J 426 LEU cc_start: 0.7596 (mt) cc_final: 0.7334 (mm) REVERT: K 139 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8252 (mtt-85) REVERT: K 279 THR cc_start: 0.8966 (m) cc_final: 0.8696 (m) REVERT: K 310 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8062 (ptp90) outliers start: 103 outliers final: 65 residues processed: 422 average time/residue: 1.3115 time to fit residues: 666.7712 Evaluate side-chains 413 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 336 time to evaluate : 3.379 ------------------------------------------------------------------------------- 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 82 SER 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 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 C residue 60 MET Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 208 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 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 F residue 113 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 126 THR 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 413 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 91 LEU 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 I residue 3 THR 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 291 ILE Chi-restraints excluded: chain J residue 378 LYS Chi-restraints excluded: chain J residue 409 SER Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 52 MET 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 K residue 393 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 148 optimal weight: 0.0670 chunk 127 optimal weight: 2.9990 chunk 241 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 323 optimal weight: 5.9990 chunk 329 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 395 optimal weight: 0.9980 chunk 278 optimal weight: 7.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN E 102 GLN ** E 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 346 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.209307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.175629 restraints weight = 31668.931| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.43 r_work: 0.3763 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32180 Z= 0.124 Angle : 0.518 6.276 43912 Z= 0.274 Chirality : 0.045 0.172 4896 Planarity : 0.004 0.063 5624 Dihedral : 5.194 55.980 4520 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.48 % Allowed : 12.89 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 4000 helix: 1.83 (0.24), residues: 480 sheet: 0.26 (0.14), residues: 1260 loop : -0.23 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 134 HIS 0.004 0.001 HIS B 175 PHE 0.019 0.001 PHE D 95 TYR 0.021 0.001 TYR J 309 ARG 0.008 0.000 ARG K 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 8) link_NAG-ASN : angle 2.31495 ( 24) hydrogen bonds : bond 0.03396 ( 1264) hydrogen bonds : angle 5.39337 ( 3378) SS BOND : bond 0.00278 ( 60) SS BOND : angle 1.12290 ( 120) covalent geometry : bond 0.00287 (32112) covalent geometry : angle 0.51267 (43768) *********************** 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 448 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 363 time to evaluate : 3.191 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: 0.8411 (OUTLIER) cc_final: 0.7717 (mt-10) REVERT: A 99 GLU cc_start: 0.6797 (tt0) cc_final: 0.6417 (tt0) REVERT: A 105 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8114 (mt-10) REVERT: A 246 LYS cc_start: 0.8063 (mttp) cc_final: 0.7190 (mmtm) REVERT: A 293 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: A 399 PHE cc_start: 0.7161 (t80) cc_final: 0.6510 (t80) REVERT: B 68 MET cc_start: 0.7698 (mmm) cc_final: 0.6982 (mmt) REVERT: B 80 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7467 (m-40) REVERT: B 157 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7562 (mtp85) REVERT: B 186 LYS cc_start: 0.7398 (tttt) cc_final: 0.6892 (tttm) REVERT: B 198 TYR cc_start: 0.7525 (t80) cc_final: 0.7179 (t80) REVERT: D 82 SER cc_start: 0.8907 (p) cc_final: 0.8566 (m) REVERT: D 290 ARG cc_start: 0.8157 (mmm160) cc_final: 0.7692 (mmt90) REVERT: D 349 GLU cc_start: 0.7167 (mp0) cc_final: 0.5949 (tm-30) REVERT: E 143 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: E 166 MET cc_start: 0.8858 (ptt) cc_final: 0.8528 (ptt) REVERT: F 60 MET cc_start: 0.6262 (mtp) cc_final: 0.5965 (mtm) REVERT: G 48 THR cc_start: 0.7831 (m) cc_final: 0.7401 (m) REVERT: G 99 GLU cc_start: 0.7642 (mp0) cc_final: 0.6945 (tp30) REVERT: G 164 ILE cc_start: 0.7783 (mm) cc_final: 0.7402 (mp) REVERT: G 421 PHE cc_start: 0.5790 (OUTLIER) cc_final: 0.4735 (t80) REVERT: H 37 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7738 (mmp80) REVERT: H 221 LYS cc_start: 0.8105 (mtmm) cc_final: 0.7705 (pmtt) REVERT: H 270 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7366 (mp0) REVERT: H 304 THR cc_start: 0.7995 (m) cc_final: 0.7614 (m) REVERT: I 140 THR cc_start: 0.7719 (m) cc_final: 0.7437 (p) REVERT: J 36 THR cc_start: 0.8232 (t) cc_final: 0.7925 (m) REVERT: J 306 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7579 (tp30) REVERT: J 378 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7826 (mtpp) REVERT: J 426 LEU cc_start: 0.7478 (mt) cc_final: 0.7215 (mm) REVERT: K 64 TYR cc_start: 0.8273 (m-80) cc_final: 0.7696 (m-80) REVERT: K 139 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8252 (mtt-85) REVERT: K 279 THR cc_start: 0.8894 (m) cc_final: 0.8680 (m) REVERT: K 296 SER cc_start: 0.8838 (p) cc_final: 0.8567 (m) REVERT: K 310 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8030 (ptp90) outliers start: 85 outliers final: 55 residues processed: 416 average time/residue: 1.2282 time to fit residues: 622.2264 Evaluate side-chains 414 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 348 time to evaluate : 3.475 ------------------------------------------------------------------------------- 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 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 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 99 GLU 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 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 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 80 VAL Chi-restraints excluded: chain G residue 97 ASP 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 413 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 91 LEU 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 I residue 3 THR Chi-restraints excluded: chain J residue 101 THR Chi-restraints excluded: chain J residue 112 GLU 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 291 ILE Chi-restraints excluded: chain J residue 306 GLU Chi-restraints excluded: chain J residue 378 LYS Chi-restraints excluded: chain J residue 409 SER Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain K residue 310 ARG 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 58 optimal weight: 5.9990 chunk 267 optimal weight: 7.9990 chunk 324 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 360 optimal weight: 5.9990 chunk 336 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 189 optimal weight: 0.8980 chunk 238 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 236 ASN E 302 ASN E 346 HIS ** G 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 302 ASN J 79 GLN K 102 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.206338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.172360 restraints weight = 31686.344| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.43 r_work: 0.3710 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3596 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 32180 Z= 0.224 Angle : 0.600 6.330 43912 Z= 0.316 Chirality : 0.049 0.208 4896 Planarity : 0.005 0.062 5624 Dihedral : 5.425 57.693 4520 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.92 % Allowed : 12.89 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.13), residues: 4000 helix: 1.68 (0.24), residues: 480 sheet: 0.10 (0.14), residues: 1336 loop : -0.32 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 142 HIS 0.006 0.001 HIS D 28 PHE 0.020 0.002 PHE D 95 TYR 0.026 0.002 TYR J 309 ARG 0.007 0.000 ARG K 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 8) link_NAG-ASN : angle 2.59176 ( 24) hydrogen bonds : bond 0.03789 ( 1264) hydrogen bonds : angle 5.58476 ( 3378) SS BOND : bond 0.00476 ( 60) SS BOND : angle 1.37408 ( 120) covalent geometry : bond 0.00548 (32112) covalent geometry : angle 0.59394 (43768) *********************** 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 455 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 355 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: A 99 GLU cc_start: 0.6862 (tt0) cc_final: 0.6463 (tt0) REVERT: A 105 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8188 (mt-10) REVERT: A 246 LYS cc_start: 0.8113 (mttp) cc_final: 0.7285 (mmtt) REVERT: A 293 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: A 399 PHE cc_start: 0.7193 (t80) cc_final: 0.6536 (t80) REVERT: B 68 MET cc_start: 0.7752 (mmm) cc_final: 0.7220 (mmt) REVERT: B 80 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7553 (m-40) REVERT: B 102 GLN cc_start: 0.8483 (mt0) cc_final: 0.8109 (mt0) REVERT: B 186 LYS cc_start: 0.7386 (tttt) cc_final: 0.6871 (tttm) REVERT: C 60 MET cc_start: 0.5818 (OUTLIER) cc_final: 0.5367 (tmm) REVERT: D 54 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7587 (tmtm) REVERT: D 82 SER cc_start: 0.8927 (p) cc_final: 0.8560 (m) REVERT: D 212 ASN cc_start: 0.7650 (OUTLIER) cc_final: 0.7283 (p0) REVERT: D 290 ARG cc_start: 0.8175 (mmm160) cc_final: 0.7700 (mmt90) REVERT: D 349 GLU cc_start: 0.7184 (mp0) cc_final: 0.5971 (tm-30) REVERT: E 143 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: E 166 MET cc_start: 0.8929 (ptt) cc_final: 0.8537 (ptt) REVERT: E 296 SER cc_start: 0.8673 (t) cc_final: 0.8348 (m) REVERT: F 60 MET cc_start: 0.6279 (mtp) cc_final: 0.5966 (mtm) REVERT: G 99 GLU cc_start: 0.7728 (mp0) cc_final: 0.6933 (tp30) REVERT: G 164 ILE cc_start: 0.7970 (mm) cc_final: 0.7610 (mp) REVERT: G 421 PHE cc_start: 0.5766 (OUTLIER) cc_final: 0.4761 (t80) REVERT: H 221 LYS cc_start: 0.8099 (mtmm) cc_final: 0.7619 (pmtt) REVERT: H 270 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7465 (mp0) REVERT: H 304 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7647 (m) REVERT: I 140 THR cc_start: 0.7912 (m) cc_final: 0.7567 (p) REVERT: J 36 THR cc_start: 0.8282 (t) cc_final: 0.7972 (m) REVERT: J 376 THR cc_start: 0.8780 (t) cc_final: 0.8231 (m) REVERT: J 378 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7865 (mtpp) REVERT: J 426 LEU cc_start: 0.7535 (mt) cc_final: 0.7309 (mm) REVERT: K 139 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8245 (mtt-85) REVERT: K 279 THR cc_start: 0.8962 (m) cc_final: 0.8698 (m) REVERT: K 310 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8051 (ptp90) outliers start: 100 outliers final: 67 residues processed: 417 average time/residue: 1.2368 time to fit residues: 624.4872 Evaluate side-chains 423 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 344 time to evaluate : 3.356 ------------------------------------------------------------------------------- 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 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 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 C residue 60 MET 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 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 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 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 396 THR Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain G residue 413 VAL Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain I residue 3 THR 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 291 ILE Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 378 LYS Chi-restraints excluded: chain J residue 409 SER Chi-restraints excluded: chain J residue 432 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 115 optimal weight: 0.0970 chunk 70 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 157 optimal weight: 0.0980 chunk 277 optimal weight: 0.6980 chunk 155 optimal weight: 0.3980 chunk 368 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 375 optimal weight: 0.8980 chunk 322 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 302 ASN E 346 HIS ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 ASN H 302 ASN J 79 GLN K 102 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.211045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.177966 restraints weight = 31702.424| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.41 r_work: 0.3775 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3665 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 32180 Z= 0.094 Angle : 0.501 8.619 43912 Z= 0.265 Chirality : 0.045 0.185 4896 Planarity : 0.004 0.057 5624 Dihedral : 4.982 50.410 4520 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.93 % Allowed : 14.24 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.13), residues: 4000 helix: 2.04 (0.24), residues: 480 sheet: 0.30 (0.14), residues: 1260 loop : -0.19 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 142 HIS 0.004 0.001 HIS B 175 PHE 0.016 0.001 PHE A 421 TYR 0.019 0.001 TYR J 309 ARG 0.008 0.000 ARG K 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 8) link_NAG-ASN : angle 2.29344 ( 24) hydrogen bonds : bond 0.03192 ( 1264) hydrogen bonds : angle 5.22890 ( 3378) SS BOND : bond 0.00296 ( 60) SS BOND : angle 1.18069 ( 120) covalent geometry : bond 0.00202 (32112) covalent geometry : angle 0.49555 (43768) *********************** 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 441 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 375 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: A 99 GLU cc_start: 0.6638 (tt0) cc_final: 0.6234 (tt0) REVERT: A 105 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8051 (mt-10) REVERT: A 246 LYS cc_start: 0.8041 (mttp) cc_final: 0.7189 (mmtm) REVERT: A 399 PHE cc_start: 0.7139 (t80) cc_final: 0.6491 (t80) REVERT: B 157 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7496 (mtp85) REVERT: B 186 LYS cc_start: 0.7382 (tttt) cc_final: 0.6853 (tttm) REVERT: C 60 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5366 (tmm) REVERT: D 82 SER cc_start: 0.8846 (p) cc_final: 0.8481 (m) REVERT: D 212 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.6993 (p0) REVERT: D 290 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7786 (mmt90) REVERT: D 349 GLU cc_start: 0.7154 (mp0) cc_final: 0.5870 (tm-30) REVERT: E 143 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: F 60 MET cc_start: 0.6205 (mtp) cc_final: 0.5907 (mtm) REVERT: G 99 GLU cc_start: 0.7657 (mp0) cc_final: 0.6998 (tp30) REVERT: G 164 ILE cc_start: 0.7721 (mm) cc_final: 0.7333 (mp) REVERT: G 421 PHE cc_start: 0.5729 (OUTLIER) cc_final: 0.4718 (t80) REVERT: H 37 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7688 (mmp80) REVERT: H 135 ARG cc_start: 0.9184 (OUTLIER) cc_final: 0.8832 (mtm180) REVERT: H 221 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7651 (pmtt) REVERT: H 270 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7313 (mp0) REVERT: H 304 THR cc_start: 0.7982 (m) cc_final: 0.7618 (m) REVERT: I 140 THR cc_start: 0.7704 (m) cc_final: 0.7414 (p) REVERT: J 36 THR cc_start: 0.8187 (t) cc_final: 0.7884 (m) REVERT: J 143 ARG cc_start: 0.7420 (ttm-80) cc_final: 0.6836 (mtp180) REVERT: J 426 LEU cc_start: 0.7558 (mt) cc_final: 0.7342 (mm) REVERT: K 64 TYR cc_start: 0.8264 (m-80) cc_final: 0.7682 (m-80) REVERT: K 168 GLN cc_start: 0.8456 (tt0) cc_final: 0.8094 (tt0) REVERT: K 231 LYS cc_start: 0.7828 (tptm) cc_final: 0.7044 (mtpp) REVERT: K 296 SER cc_start: 0.8786 (p) cc_final: 0.8567 (m) REVERT: K 387 CYS cc_start: 0.6226 (m) cc_final: 0.5968 (m) outliers start: 66 outliers final: 43 residues processed: 415 average time/residue: 1.3744 time to fit residues: 697.6713 Evaluate side-chains 411 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 360 time to evaluate : 3.834 ------------------------------------------------------------------------------- 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 261 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain C residue 60 MET 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 352 SER 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 143 GLU Chi-restraints excluded: chain E residue 179 SER 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 144 SER Chi-restraints excluded: chain G residue 211 SER Chi-restraints excluded: chain G residue 421 PHE Chi-restraints excluded: chain G residue 432 VAL Chi-restraints excluded: chain H residue 27 CYS Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 228 ILE Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain I residue 3 THR 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 274 VAL Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 329 CYS Chi-restraints excluded: chain J residue 432 VAL Chi-restraints excluded: chain K residue 27 CYS Chi-restraints excluded: chain K residue 304 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 175 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 319 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 364 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 307 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 65 optimal weight: 50.0000 chunk 56 optimal weight: 5.9990 chunk 286 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 346 HIS ** G 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN H 302 ASN J 79 GLN K 102 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.203398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.169243 restraints weight = 32264.837| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.65 r_work: 0.3630 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32180 Z= 0.115 Angle : 0.513 8.669 43912 Z= 0.269 Chirality : 0.045 0.184 4896 Planarity : 0.004 0.057 5624 Dihedral : 4.933 50.012 4520 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.58 % Allowed : 14.94 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.13), residues: 4000 helix: 2.21 (0.24), residues: 480 sheet: 0.30 (0.14), residues: 1356 loop : -0.14 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 142 HIS 0.004 0.001 HIS A 395 PHE 0.021 0.001 PHE D 95 TYR 0.020 0.001 TYR J 309 ARG 0.007 0.000 ARG K 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00178 ( 8) link_NAG-ASN : angle 2.27181 ( 24) hydrogen bonds : bond 0.03224 ( 1264) hydrogen bonds : angle 5.19606 ( 3378) SS BOND : bond 0.00281 ( 60) SS BOND : angle 1.04646 ( 120) covalent geometry : bond 0.00265 (32112) covalent geometry : angle 0.50771 (43768) ********************** 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 419 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 365 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: A 99 GLU cc_start: 0.6516 (tt0) cc_final: 0.6123 (tt0) REVERT: A 105 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8008 (mt-10) REVERT: A 246 LYS cc_start: 0.7985 (mttp) cc_final: 0.7129 (mmtm) REVERT: A 247 ASP cc_start: 0.7420 (m-30) cc_final: 0.6870 (p0) REVERT: A 399 PHE cc_start: 0.7063 (t80) cc_final: 0.6418 (t80) REVERT: B 13 ARG cc_start: 0.8623 (ptm-80) cc_final: 0.8300 (ttp80) REVERT: B 68 MET cc_start: 0.7628 (mmt) cc_final: 0.7107 (mmt) REVERT: B 157 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7525 (mtp85) REVERT: B 186 LYS cc_start: 0.7334 (tttt) cc_final: 0.6868 (tttm) REVERT: C 60 MET cc_start: 0.5785 (OUTLIER) cc_final: 0.5316 (tmm) REVERT: D 82 SER cc_start: 0.8841 (p) cc_final: 0.8461 (m) REVERT: D 212 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.6943 (p0) REVERT: D 290 ARG cc_start: 0.8082 (mmm160) cc_final: 0.7711 (mmt90) REVERT: D 349 GLU cc_start: 0.7121 (mp0) cc_final: 0.5841 (tm-30) REVERT: E 143 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7944 (tt0) REVERT: E 166 MET cc_start: 0.8934 (ptt) cc_final: 0.8428 (ptt) REVERT: F 60 MET cc_start: 0.6112 (mtp) cc_final: 0.5831 (mtm) REVERT: G 99 GLU cc_start: 0.7509 (mp0) cc_final: 0.6966 (tp30) REVERT: G 164 ILE cc_start: 0.7765 (mm) cc_final: 0.7366 (mp) REVERT: G 421 PHE cc_start: 0.5698 (OUTLIER) cc_final: 0.4646 (t80) REVERT: H 37 ARG cc_start: 0.8649 (OUTLIER) cc_final: 0.7663 (mmp80) REVERT: H 221 LYS cc_start: 0.8087 (mtmm) cc_final: 0.7573 (pmtt) REVERT: H 270 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7295 (mp0) REVERT: H 304 THR cc_start: 0.7932 (m) cc_final: 0.7575 (m) REVERT: I 140 THR cc_start: 0.7605 (m) cc_final: 0.7271 (p) REVERT: J 36 THR cc_start: 0.8130 (t) cc_final: 0.7830 (m) REVERT: J 143 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.6744 (mtp180) REVERT: J 426 LEU cc_start: 0.7407 (mt) cc_final: 0.7195 (mm) REVERT: K 168 GLN cc_start: 0.8404 (tt0) cc_final: 0.8042 (tt0) REVERT: K 231 LYS cc_start: 0.7834 (tptm) cc_final: 0.7045 (mtpp) REVERT: K 296 SER cc_start: 0.8742 (OUTLIER) cc_final: 0.8485 (m) REVERT: K 387 CYS cc_start: 0.6073 (m) cc_final: 0.5818 (m) outliers start: 54 outliers final: 40 residues processed: 399 average time/residue: 1.5844 time to fit residues: 762.5653 Evaluate side-chains 414 residues out of total 3428 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 366 time to evaluate : 3.531 ------------------------------------------------------------------------------- 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 82 SER Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 157 ARG Chi-restraints excluded: chain C residue 60 MET 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 350 SER 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 143 GLU Chi-restraints excluded: chain E residue 179 SER 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 144 SER Chi-restraints excluded: chain G residue 211 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 27 CYS Chi-restraints excluded: chain H residue 37 ARG Chi-restraints excluded: chain H residue 135 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 3 THR 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 274 VAL Chi-restraints excluded: chain J residue 277 ILE Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 329 CYS 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 324 GLU Chi-restraints excluded: chain K residue 354 VAL 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 188 optimal weight: 8.9990 chunk 367 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 324 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 215 optimal weight: 0.2980 chunk 259 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- 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 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4225 r_free = 0.4225 target = 0.201086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.165220 restraints weight = 32293.291| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.56 r_work: 0.3659 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32180 Z= 0.158 Angle : 0.545 7.959 43912 Z= 0.285 Chirality : 0.046 0.189 4896 Planarity : 0.005 0.057 5624 Dihedral : 5.039 50.067 4520 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.08 % Rotamer: Outliers : 1.84 % Allowed : 14.79 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.13), residues: 4000 helix: 2.04 (0.24), residues: 480 sheet: 0.26 (0.14), residues: 1320 loop : -0.16 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 142 HIS 0.004 0.001 HIS D 28 PHE 0.022 0.002 PHE D 95 TYR 0.022 0.002 TYR J 309 ARG 0.007 0.000 ARG K 388 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 8) link_NAG-ASN : angle 2.30986 ( 24) hydrogen bonds : bond 0.03405 ( 1264) hydrogen bonds : angle 5.28959 ( 3378) SS BOND : bond 0.00324 ( 60) SS BOND : angle 1.19187 ( 120) covalent geometry : bond 0.00379 (32112) covalent geometry : angle 0.53965 (43768) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25544.22 seconds wall clock time: 438 minutes 25.26 seconds (26305.26 seconds total)