Starting phenix.real_space_refine on Sun Feb 8 09:04:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i06_52552/02_2026/9i06_52552.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i06_52552/02_2026/9i06_52552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i06_52552/02_2026/9i06_52552.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i06_52552/02_2026/9i06_52552.map" model { file = "/net/cci-nas-00/data/ceres_data/9i06_52552/02_2026/9i06_52552.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i06_52552/02_2026/9i06_52552.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.061 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 176 5.16 5 C 27120 2.51 5 N 7480 2.21 5 O 8376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43184 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "B" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "C" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "D" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "E" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "F" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "G" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "H" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "I" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "J" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "K" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "L" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "O" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "P" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "Q" Number of atoms: 2766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2766 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain: "R" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2544 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 325} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.41, per 1000 atoms: 0.24 Number of scatterers: 43184 At special positions: 0 Unit cell: (187.867, 173.247, 106.726, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 176 16.00 P 32 15.00 O 8376 8.00 N 7480 7.00 C 27120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS E 349 " - pdb=" SG CYS E 358 " distance=2.03 Simple disulfide: pdb=" SG CYS G 349 " - pdb=" SG CYS G 358 " distance=2.02 Simple disulfide: pdb=" SG CYS I 349 " - pdb=" SG CYS I 358 " distance=2.03 Simple disulfide: pdb=" SG CYS K 349 " - pdb=" SG CYS K 358 " distance=2.02 Simple disulfide: pdb=" SG CYS O 349 " - pdb=" SG CYS O 358 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 349 " - pdb=" SG CYS Q 358 " distance=2.02 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 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.8 seconds 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10288 Finding SS restraints... Secondary structure from input PDB file: 214 helices and 50 sheets defined 36.3% alpha, 29.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.33 Creating SS restraints... Processing helix chain 'A' and resid 10 through 19 Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.928A pdb=" N LYS A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS A 108 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 148 through 165 Proline residue: A 156 - end of helix Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.612A pdb=" N LEU A 201 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN A 202 " --> pdb=" O ALA A 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 202' Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 251 through 265 Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 314 through 330 Processing helix chain 'A' and resid 343 through 352 removed outlier: 3.564A pdb=" N ASP A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 36 through 46 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.672A pdb=" N MET B 87 " --> pdb=" O PRO B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 removed outlier: 4.181A pdb=" N HIS B 108 " --> pdb=" O GLY B 104 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 109 " --> pdb=" O ALA B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 148 through 165 Proline residue: B 156 - end of helix removed outlier: 3.789A pdb=" N VAL B 160 " --> pdb=" O PRO B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 218 removed outlier: 5.725A pdb=" N ALA B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 216 " --> pdb=" O LYS B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 222 Processing helix chain 'B' and resid 251 through 266 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 34 through 46 removed outlier: 4.057A pdb=" N SER C 39 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 101 through 112 removed outlier: 3.790A pdb=" N LYS C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N HIS C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 148 through 165 Proline residue: C 156 - end of helix Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 209 through 214 Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 218 through 222 Processing helix chain 'C' and resid 251 through 265 Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 295 through 297 No H-bonds generated for 'chain 'C' and resid 295 through 297' Processing helix chain 'C' and resid 314 through 331 Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 36 through 46 Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.504A pdb=" N MET D 87 " --> pdb=" O PRO D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 112 removed outlier: 4.320A pdb=" N HIS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 148 through 165 Proline residue: D 156 - end of helix removed outlier: 3.594A pdb=" N VAL D 160 " --> pdb=" O PRO D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 218 removed outlier: 5.446A pdb=" N ALA D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 222 Processing helix chain 'D' and resid 251 through 266 Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 315 through 330 Processing helix chain 'E' and resid 10 through 19 Processing helix chain 'E' and resid 34 through 46 removed outlier: 4.308A pdb=" N SER E 39 " --> pdb=" O GLY E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 82 Processing helix chain 'E' and resid 83 through 88 Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 106 through 112 Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 148 through 165 Proline residue: E 156 - end of helix Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 198 through 202 removed outlier: 3.896A pdb=" N LEU E 201 " --> pdb=" O ALA E 198 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN E 202 " --> pdb=" O ALA E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 202' Processing helix chain 'E' and resid 211 through 217 Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 251 through 265 Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 314 through 330 Processing helix chain 'E' and resid 343 through 352 Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 36 through 46 Processing helix chain 'F' and resid 78 through 82 Processing helix chain 'F' and resid 83 through 88 removed outlier: 3.519A pdb=" N MET F 87 " --> pdb=" O PRO F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 112 removed outlier: 4.124A pdb=" N HIS F 108 " --> pdb=" O GLY F 104 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU F 109 " --> pdb=" O ALA F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 148 through 165 Proline residue: F 156 - end of helix removed outlier: 3.679A pdb=" N VAL F 160 " --> pdb=" O PRO F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 218 removed outlier: 5.755A pdb=" N ALA F 215 " --> pdb=" O ALA F 211 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU F 216 " --> pdb=" O LYS F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 222 Processing helix chain 'F' and resid 251 through 266 Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.653A pdb=" N ARG F 284 " --> pdb=" O ILE F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 330 Processing helix chain 'G' and resid 10 through 19 Processing helix chain 'G' and resid 34 through 45 removed outlier: 4.144A pdb=" N SER G 39 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 82 Processing helix chain 'G' and resid 101 through 112 removed outlier: 3.976A pdb=" N LYS G 107 " --> pdb=" O PRO G 103 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS G 108 " --> pdb=" O GLY G 104 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE G 109 " --> pdb=" O ALA G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 137 Processing helix chain 'G' and resid 148 through 165 Proline residue: G 156 - end of helix Processing helix chain 'G' and resid 209 through 214 Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 218 through 222 Processing helix chain 'G' and resid 251 through 265 Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 295 through 297 No H-bonds generated for 'chain 'G' and resid 295 through 297' Processing helix chain 'G' and resid 314 through 331 Processing helix chain 'G' and resid 343 through 352 Processing helix chain 'H' and resid 9 through 19 Processing helix chain 'H' and resid 36 through 46 Processing helix chain 'H' and resid 78 through 82 Processing helix chain 'H' and resid 101 through 112 removed outlier: 4.202A pdb=" N HIS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU H 109 " --> pdb=" O ALA H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 137 Processing helix chain 'H' and resid 148 through 166 Proline residue: H 156 - end of helix removed outlier: 3.620A pdb=" N VAL H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 218 removed outlier: 5.625A pdb=" N ALA H 215 " --> pdb=" O ALA H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 222 Processing helix chain 'H' and resid 251 through 266 Processing helix chain 'H' and resid 279 through 284 Processing helix chain 'H' and resid 295 through 297 No H-bonds generated for 'chain 'H' and resid 295 through 297' Processing helix chain 'H' and resid 314 through 330 Processing helix chain 'I' and resid 10 through 19 Processing helix chain 'I' and resid 36 through 46 Processing helix chain 'I' and resid 78 through 82 Processing helix chain 'I' and resid 101 through 112 removed outlier: 3.935A pdb=" N LYS I 107 " --> pdb=" O PRO I 103 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS I 108 " --> pdb=" O GLY I 104 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ILE I 109 " --> pdb=" O ALA I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 137 Processing helix chain 'I' and resid 148 through 165 Proline residue: I 156 - end of helix Processing helix chain 'I' and resid 198 through 202 removed outlier: 3.612A pdb=" N LEU I 201 " --> pdb=" O ALA I 198 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN I 202 " --> pdb=" O ALA I 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 198 through 202' Processing helix chain 'I' and resid 209 through 214 Processing helix chain 'I' and resid 218 through 222 Processing helix chain 'I' and resid 251 through 265 Processing helix chain 'I' and resid 279 through 284 Processing helix chain 'I' and resid 295 through 297 No H-bonds generated for 'chain 'I' and resid 295 through 297' Processing helix chain 'I' and resid 314 through 331 removed outlier: 3.641A pdb=" N LYS I 331 " --> pdb=" O LEU I 327 " (cutoff:3.500A) Processing helix chain 'I' and resid 343 through 350 Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 36 through 46 Processing helix chain 'J' and resid 78 through 82 Processing helix chain 'J' and resid 83 through 88 removed outlier: 3.689A pdb=" N MET J 87 " --> pdb=" O PRO J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 112 removed outlier: 4.187A pdb=" N HIS J 108 " --> pdb=" O GLY J 104 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU J 109 " --> pdb=" O ALA J 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'J' and resid 148 through 165 Proline residue: J 156 - end of helix removed outlier: 3.794A pdb=" N VAL J 160 " --> pdb=" O PRO J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 218 removed outlier: 5.762A pdb=" N ALA J 215 " --> pdb=" O ALA J 211 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU J 216 " --> pdb=" O LYS J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 219 through 222 Processing helix chain 'J' and resid 251 through 266 Processing helix chain 'J' and resid 279 through 284 Processing helix chain 'J' and resid 314 through 330 Processing helix chain 'K' and resid 10 through 19 Processing helix chain 'K' and resid 34 through 46 removed outlier: 4.014A pdb=" N SER K 39 " --> pdb=" O GLY K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 82 Processing helix chain 'K' and resid 101 through 112 removed outlier: 3.780A pdb=" N LYS K 107 " --> pdb=" O PRO K 103 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N HIS K 108 " --> pdb=" O GLY K 104 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 137 Processing helix chain 'K' and resid 148 through 165 Proline residue: K 156 - end of helix Processing helix chain 'K' and resid 193 through 197 Processing helix chain 'K' and resid 209 through 214 Processing helix chain 'K' and resid 215 through 217 No H-bonds generated for 'chain 'K' and resid 215 through 217' Processing helix chain 'K' and resid 218 through 222 Processing helix chain 'K' and resid 251 through 265 Processing helix chain 'K' and resid 279 through 284 Processing helix chain 'K' and resid 295 through 297 No H-bonds generated for 'chain 'K' and resid 295 through 297' Processing helix chain 'K' and resid 314 through 331 Processing helix chain 'K' and resid 343 through 352 Processing helix chain 'L' and resid 9 through 19 Processing helix chain 'L' and resid 36 through 46 Processing helix chain 'L' and resid 78 through 82 Processing helix chain 'L' and resid 83 through 88 Processing helix chain 'L' and resid 101 through 112 removed outlier: 4.320A pdb=" N HIS L 108 " --> pdb=" O GLY L 104 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU L 109 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 137 removed outlier: 3.502A pdb=" N GLY L 136 " --> pdb=" O ASN L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 165 Proline residue: L 156 - end of helix Processing helix chain 'L' and resid 209 through 218 removed outlier: 5.506A pdb=" N ALA L 215 " --> pdb=" O ALA L 211 " (cutoff:3.500A) Processing helix chain 'L' and resid 219 through 222 Processing helix chain 'L' and resid 251 through 266 Processing helix chain 'L' and resid 279 through 284 Processing helix chain 'L' and resid 315 through 330 Processing helix chain 'O' and resid 10 through 19 Processing helix chain 'O' and resid 34 through 46 removed outlier: 4.273A pdb=" N SER O 39 " --> pdb=" O GLY O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 82 Processing helix chain 'O' and resid 83 through 88 Processing helix chain 'O' and resid 101 through 106 Processing helix chain 'O' and resid 106 through 112 Processing helix chain 'O' and resid 133 through 137 Processing helix chain 'O' and resid 148 through 165 Proline residue: O 156 - end of helix Processing helix chain 'O' and resid 193 through 197 Processing helix chain 'O' and resid 198 through 202 removed outlier: 3.890A pdb=" N LEU O 201 " --> pdb=" O ALA O 198 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN O 202 " --> pdb=" O ALA O 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 198 through 202' Processing helix chain 'O' and resid 211 through 217 Processing helix chain 'O' and resid 218 through 222 Processing helix chain 'O' and resid 251 through 265 Processing helix chain 'O' and resid 279 through 284 Processing helix chain 'O' and resid 314 through 330 Processing helix chain 'O' and resid 343 through 352 Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 36 through 46 Processing helix chain 'P' and resid 78 through 82 Processing helix chain 'P' and resid 83 through 88 Processing helix chain 'P' and resid 101 through 112 removed outlier: 4.114A pdb=" N HIS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU P 109 " --> pdb=" O ALA P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 133 through 137 Processing helix chain 'P' and resid 148 through 165 Proline residue: P 156 - end of helix removed outlier: 3.673A pdb=" N VAL P 160 " --> pdb=" O PRO P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 209 through 218 removed outlier: 5.729A pdb=" N ALA P 215 " --> pdb=" O ALA P 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU P 216 " --> pdb=" O LYS P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 222 Processing helix chain 'P' and resid 251 through 266 Processing helix chain 'P' and resid 279 through 284 removed outlier: 3.685A pdb=" N ARG P 284 " --> pdb=" O ILE P 281 " (cutoff:3.500A) Processing helix chain 'P' and resid 314 through 330 Processing helix chain 'Q' and resid 10 through 19 Processing helix chain 'Q' and resid 34 through 45 removed outlier: 4.058A pdb=" N SER Q 39 " --> pdb=" O GLY Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 82 Processing helix chain 'Q' and resid 101 through 112 removed outlier: 3.983A pdb=" N LYS Q 107 " --> pdb=" O PRO Q 103 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N HIS Q 108 " --> pdb=" O GLY Q 104 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE Q 109 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 137 Processing helix chain 'Q' and resid 148 through 165 Proline residue: Q 156 - end of helix Processing helix chain 'Q' and resid 209 through 214 Processing helix chain 'Q' and resid 215 through 217 No H-bonds generated for 'chain 'Q' and resid 215 through 217' Processing helix chain 'Q' and resid 218 through 222 Processing helix chain 'Q' and resid 251 through 265 Processing helix chain 'Q' and resid 279 through 284 Processing helix chain 'Q' and resid 295 through 297 No H-bonds generated for 'chain 'Q' and resid 295 through 297' Processing helix chain 'Q' and resid 314 through 331 Processing helix chain 'Q' and resid 343 through 352 Processing helix chain 'R' and resid 9 through 19 Processing helix chain 'R' and resid 36 through 46 Processing helix chain 'R' and resid 78 through 82 Processing helix chain 'R' and resid 101 through 112 removed outlier: 4.204A pdb=" N HIS R 108 " --> pdb=" O GLY R 104 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU R 109 " --> pdb=" O ALA R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 137 Processing helix chain 'R' and resid 148 through 166 Proline residue: R 156 - end of helix removed outlier: 3.638A pdb=" N VAL R 160 " --> pdb=" O PRO R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 218 removed outlier: 5.616A pdb=" N ALA R 215 " --> pdb=" O ALA R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 219 through 222 Processing helix chain 'R' and resid 251 through 266 Processing helix chain 'R' and resid 279 through 284 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 314 through 330 Processing sheet with id=AA1, first strand: chain 'A' and resid 57 through 60 removed outlier: 5.638A pdb=" N VAL A 28 " --> pdb=" O PRO A 70 " (cutoff:3.500A) removed outlier: 9.992A pdb=" N LEU A 1 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N VAL A 29 " --> pdb=" O LEU A 1 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 3 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N ASN A 31 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 5 " --> pdb=" O ASN A 31 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS A 2 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ILE A 93 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA A 4 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 92 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 207 removed outlier: 9.455A pdb=" N ASN A 226 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY A 170 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ILE A 228 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET A 172 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU A 230 " --> pdb=" O MET A 172 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A 174 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A 232 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N HIS A 176 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 169 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL A 308 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ASP A 272 " --> pdb=" O ILE A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 207 removed outlier: 9.455A pdb=" N ASN A 226 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY A 170 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 8.890A pdb=" N ILE A 228 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET A 172 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LEU A 230 " --> pdb=" O MET A 172 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR A 174 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A 232 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N HIS A 176 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 169 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 58 removed outlier: 10.341A pdb=" N VAL B 70 " --> pdb=" O ASP B 26 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N VAL B 28 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 9.534A pdb=" N LEU B 1 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 9.159A pdb=" N VAL B 29 " --> pdb=" O LEU B 1 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL B 3 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ASN B 31 " --> pdb=" O VAL B 3 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ILE B 5 " --> pdb=" O ASN B 31 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 92 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 204 through 206 removed outlier: 9.561A pdb=" N ASN B 226 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY B 170 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ILE B 228 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N MET B 172 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU B 230 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR B 174 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL B 232 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS B 176 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 169 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE B 308 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N SER B 272 " --> pdb=" O ILE B 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 204 through 206 removed outlier: 9.561A pdb=" N ASN B 226 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY B 170 " --> pdb=" O ASN B 226 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ILE B 228 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N MET B 172 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LEU B 230 " --> pdb=" O MET B 172 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR B 174 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL B 232 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS B 176 " --> pdb=" O VAL B 232 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 169 " --> pdb=" O GLN B 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 57 through 60 removed outlier: 5.525A pdb=" N VAL C 28 " --> pdb=" O PRO C 70 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N LEU C 1 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N VAL C 29 " --> pdb=" O LEU C 1 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 3 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N ASN C 31 " --> pdb=" O VAL C 3 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE C 5 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS C 2 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE C 93 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA C 4 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 92 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 204 through 207 removed outlier: 9.484A pdb=" N ASN C 226 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY C 170 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ILE C 228 " --> pdb=" O GLY C 170 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET C 172 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU C 230 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR C 174 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS C 169 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL C 308 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 204 through 207 removed outlier: 9.484A pdb=" N ASN C 226 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY C 170 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ILE C 228 " --> pdb=" O GLY C 170 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N MET C 172 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N LEU C 230 " --> pdb=" O MET C 172 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR C 174 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS C 169 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 57 through 58 removed outlier: 10.461A pdb=" N VAL D 70 " --> pdb=" O ASP D 26 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL D 28 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE D 5 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE D 30 " --> pdb=" O ILE D 5 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL D 92 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 204 through 206 removed outlier: 9.291A pdb=" N ASN D 226 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY D 170 " --> pdb=" O ASN D 226 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ILE D 228 " --> pdb=" O GLY D 170 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET D 172 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU D 230 " --> pdb=" O MET D 172 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR D 174 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL D 232 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS D 176 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS D 169 " --> pdb=" O GLN D 245 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE D 308 " --> pdb=" O ASP D 293 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER D 272 " --> pdb=" O ILE D 292 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 204 through 206 removed outlier: 9.291A pdb=" N ASN D 226 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY D 170 " --> pdb=" O ASN D 226 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ILE D 228 " --> pdb=" O GLY D 170 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N MET D 172 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU D 230 " --> pdb=" O MET D 172 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR D 174 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL D 232 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS D 176 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS D 169 " --> pdb=" O GLN D 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 57 through 60 removed outlier: 9.341A pdb=" N ASP E 26 " --> pdb=" O PRO E 70 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N LYS E 72 " --> pdb=" O ASP E 26 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL E 28 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL E 74 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL E 30 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N LEU E 1 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N VAL E 29 " --> pdb=" O LEU E 1 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL E 3 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ASN E 31 " --> pdb=" O VAL E 3 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE E 5 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS E 2 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ILE E 93 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA E 4 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL E 92 " --> pdb=" O ILE E 117 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 204 through 207 removed outlier: 9.448A pdb=" N ASN E 226 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY E 170 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N ILE E 228 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N MET E 172 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU E 230 " --> pdb=" O MET E 172 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR E 174 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL E 232 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS E 176 " --> pdb=" O VAL E 232 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E 169 " --> pdb=" O ASN E 245 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VAL E 308 " --> pdb=" O ASP E 293 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 204 through 207 removed outlier: 9.448A pdb=" N ASN E 226 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY E 170 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N ILE E 228 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N MET E 172 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU E 230 " --> pdb=" O MET E 172 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR E 174 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL E 232 " --> pdb=" O THR E 174 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N HIS E 176 " --> pdb=" O VAL E 232 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS E 169 " --> pdb=" O ASN E 245 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 57 through 58 removed outlier: 10.317A pdb=" N VAL F 70 " --> pdb=" O ASP F 26 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL F 28 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU F 1 " --> pdb=" O ASP F 26 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL F 28 " --> pdb=" O LEU F 1 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL F 3 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE F 30 " --> pdb=" O VAL F 3 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE F 5 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS F 2 " --> pdb=" O LEU F 91 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE F 93 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA F 4 " --> pdb=" O ILE F 93 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL F 92 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 204 through 206 removed outlier: 8.988A pdb=" N ILE F 228 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N MET F 172 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU F 230 " --> pdb=" O MET F 172 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR F 174 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN F 245 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY F 170 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL F 243 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N MET F 172 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASP F 241 " --> pdb=" O MET F 172 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR F 174 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL F 239 " --> pdb=" O THR F 174 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE F 308 " --> pdb=" O ASP F 293 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N SER F 272 " --> pdb=" O ILE F 292 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 204 through 206 removed outlier: 8.988A pdb=" N ILE F 228 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N MET F 172 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU F 230 " --> pdb=" O MET F 172 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR F 174 " --> pdb=" O LEU F 230 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN F 245 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY F 170 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL F 243 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N MET F 172 " --> pdb=" O ASP F 241 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ASP F 241 " --> pdb=" O MET F 172 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR F 174 " --> pdb=" O VAL F 239 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL F 239 " --> pdb=" O THR F 174 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 57 through 60 removed outlier: 9.728A pdb=" N ASP G 26 " --> pdb=" O PRO G 70 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N LYS G 72 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL G 28 " --> pdb=" O LYS G 72 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL G 74 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL G 30 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N LEU G 1 " --> pdb=" O VAL G 27 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL G 29 " --> pdb=" O LEU G 1 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL G 3 " --> pdb=" O VAL G 29 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ASN G 31 " --> pdb=" O VAL G 3 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ILE G 5 " --> pdb=" O ASN G 31 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS G 2 " --> pdb=" O ILE G 91 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ILE G 93 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA G 4 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL G 92 " --> pdb=" O ILE G 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 46 through 47 Processing sheet with id=AC3, first strand: chain 'G' and resid 204 through 207 removed outlier: 9.465A pdb=" N ASN G 226 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY G 170 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ILE G 228 " --> pdb=" O GLY G 170 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET G 172 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU G 230 " --> pdb=" O MET G 172 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR G 174 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS G 169 " --> pdb=" O ASN G 245 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N VAL G 308 " --> pdb=" O ASP G 293 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASP G 272 " --> pdb=" O ILE G 292 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 204 through 207 removed outlier: 9.465A pdb=" N ASN G 226 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLY G 170 " --> pdb=" O ASN G 226 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N ILE G 228 " --> pdb=" O GLY G 170 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET G 172 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU G 230 " --> pdb=" O MET G 172 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR G 174 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS G 169 " --> pdb=" O ASN G 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 57 through 58 removed outlier: 10.390A pdb=" N VAL H 70 " --> pdb=" O ASP H 26 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL H 28 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N LEU H 1 " --> pdb=" O VAL H 27 " (cutoff:3.500A) removed outlier: 9.276A pdb=" N VAL H 29 " --> pdb=" O LEU H 1 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL H 3 " --> pdb=" O VAL H 29 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASN H 31 " --> pdb=" O VAL H 3 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE H 5 " --> pdb=" O ASN H 31 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL H 92 " --> pdb=" O LEU H 117 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 204 through 207 removed outlier: 9.330A pdb=" N ASN H 226 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY H 170 " --> pdb=" O ASN H 226 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ILE H 228 " --> pdb=" O GLY H 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N MET H 172 " --> pdb=" O ILE H 228 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU H 230 " --> pdb=" O MET H 172 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR H 174 " --> pdb=" O LEU H 230 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL H 232 " --> pdb=" O THR H 174 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS H 176 " --> pdb=" O VAL H 232 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS H 169 " --> pdb=" O GLN H 245 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE H 308 " --> pdb=" O ASP H 293 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER H 272 " --> pdb=" O ILE H 292 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 204 through 207 removed outlier: 9.330A pdb=" N ASN H 226 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY H 170 " --> pdb=" O ASN H 226 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N ILE H 228 " --> pdb=" O GLY H 170 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N MET H 172 " --> pdb=" O ILE H 228 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU H 230 " --> pdb=" O MET H 172 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR H 174 " --> pdb=" O LEU H 230 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL H 232 " --> pdb=" O THR H 174 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N HIS H 176 " --> pdb=" O VAL H 232 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS H 169 " --> pdb=" O GLN H 245 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 57 through 60 removed outlier: 5.612A pdb=" N VAL I 28 " --> pdb=" O PRO I 70 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N LEU I 1 " --> pdb=" O VAL I 27 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL I 29 " --> pdb=" O LEU I 1 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL I 3 " --> pdb=" O VAL I 29 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN I 31 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ILE I 5 " --> pdb=" O ASN I 31 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS I 2 " --> pdb=" O ILE I 91 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE I 93 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA I 4 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL I 92 " --> pdb=" O ILE I 117 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 204 through 207 removed outlier: 9.378A pdb=" N ASN I 226 " --> pdb=" O VAL I 168 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY I 170 " --> pdb=" O ASN I 226 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ILE I 228 " --> pdb=" O GLY I 170 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N MET I 172 " --> pdb=" O ILE I 228 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU I 230 " --> pdb=" O MET I 172 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR I 174 " --> pdb=" O LEU I 230 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL I 232 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N HIS I 176 " --> pdb=" O VAL I 232 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS I 169 " --> pdb=" O ASN I 245 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL I 308 " --> pdb=" O ASP I 293 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP I 272 " --> pdb=" O ILE I 292 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 204 through 207 removed outlier: 9.378A pdb=" N ASN I 226 " --> pdb=" O VAL I 168 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY I 170 " --> pdb=" O ASN I 226 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ILE I 228 " --> pdb=" O GLY I 170 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N MET I 172 " --> pdb=" O ILE I 228 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU I 230 " --> pdb=" O MET I 172 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR I 174 " --> pdb=" O LEU I 230 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N VAL I 232 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N HIS I 176 " --> pdb=" O VAL I 232 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS I 169 " --> pdb=" O ASN I 245 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 57 through 58 removed outlier: 10.279A pdb=" N VAL J 70 " --> pdb=" O ASP J 26 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL J 28 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N LEU J 1 " --> pdb=" O VAL J 27 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N VAL J 29 " --> pdb=" O LEU J 1 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL J 3 " --> pdb=" O VAL J 29 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASN J 31 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE J 5 " --> pdb=" O ASN J 31 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL J 92 " --> pdb=" O LEU J 117 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 204 through 206 removed outlier: 9.578A pdb=" N ASN J 226 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY J 170 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N ILE J 228 " --> pdb=" O GLY J 170 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET J 172 " --> pdb=" O ILE J 228 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU J 230 " --> pdb=" O MET J 172 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR J 174 " --> pdb=" O LEU J 230 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL J 232 " --> pdb=" O THR J 174 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS J 176 " --> pdb=" O VAL J 232 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS J 169 " --> pdb=" O GLN J 245 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ILE J 308 " --> pdb=" O ASP J 293 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER J 272 " --> pdb=" O ILE J 292 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 204 through 206 removed outlier: 9.578A pdb=" N ASN J 226 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY J 170 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N ILE J 228 " --> pdb=" O GLY J 170 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N MET J 172 " --> pdb=" O ILE J 228 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU J 230 " --> pdb=" O MET J 172 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR J 174 " --> pdb=" O LEU J 230 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL J 232 " --> pdb=" O THR J 174 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HIS J 176 " --> pdb=" O VAL J 232 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS J 169 " --> pdb=" O GLN J 245 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 57 through 60 removed outlier: 5.513A pdb=" N VAL K 28 " --> pdb=" O PRO K 70 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N LEU K 1 " --> pdb=" O VAL K 27 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N VAL K 29 " --> pdb=" O LEU K 1 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL K 3 " --> pdb=" O VAL K 29 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ASN K 31 " --> pdb=" O VAL K 3 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ILE K 5 " --> pdb=" O ASN K 31 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS K 2 " --> pdb=" O ILE K 91 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE K 93 " --> pdb=" O LYS K 2 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA K 4 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL K 92 " --> pdb=" O ILE K 117 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 204 through 207 removed outlier: 9.495A pdb=" N ASN K 226 " --> pdb=" O VAL K 168 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY K 170 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ILE K 228 " --> pdb=" O GLY K 170 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET K 172 " --> pdb=" O ILE K 228 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU K 230 " --> pdb=" O MET K 172 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR K 174 " --> pdb=" O LEU K 230 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS K 169 " --> pdb=" O ASN K 245 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N VAL K 308 " --> pdb=" O ASP K 293 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 204 through 207 removed outlier: 9.495A pdb=" N ASN K 226 " --> pdb=" O VAL K 168 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY K 170 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ILE K 228 " --> pdb=" O GLY K 170 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET K 172 " --> pdb=" O ILE K 228 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N LEU K 230 " --> pdb=" O MET K 172 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR K 174 " --> pdb=" O LEU K 230 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS K 169 " --> pdb=" O ASN K 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 57 through 58 removed outlier: 10.459A pdb=" N VAL L 70 " --> pdb=" O ASP L 26 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL L 28 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ILE L 5 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE L 30 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL L 92 " --> pdb=" O LEU L 117 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 204 through 206 removed outlier: 9.292A pdb=" N ASN L 226 " --> pdb=" O ILE L 168 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY L 170 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N ILE L 228 " --> pdb=" O GLY L 170 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET L 172 " --> pdb=" O ILE L 228 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU L 230 " --> pdb=" O MET L 172 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR L 174 " --> pdb=" O LEU L 230 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL L 232 " --> pdb=" O THR L 174 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS L 176 " --> pdb=" O VAL L 232 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS L 169 " --> pdb=" O GLN L 245 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE L 308 " --> pdb=" O ASP L 293 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER L 272 " --> pdb=" O ILE L 292 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 204 through 206 removed outlier: 9.292A pdb=" N ASN L 226 " --> pdb=" O ILE L 168 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY L 170 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N ILE L 228 " --> pdb=" O GLY L 170 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N MET L 172 " --> pdb=" O ILE L 228 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU L 230 " --> pdb=" O MET L 172 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR L 174 " --> pdb=" O LEU L 230 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL L 232 " --> pdb=" O THR L 174 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N HIS L 176 " --> pdb=" O VAL L 232 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS L 169 " --> pdb=" O GLN L 245 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 57 through 60 removed outlier: 9.338A pdb=" N ASP O 26 " --> pdb=" O PRO O 70 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N LYS O 72 " --> pdb=" O ASP O 26 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL O 28 " --> pdb=" O LYS O 72 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL O 74 " --> pdb=" O VAL O 28 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL O 30 " --> pdb=" O VAL O 74 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N LEU O 1 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N VAL O 29 " --> pdb=" O LEU O 1 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL O 3 " --> pdb=" O VAL O 29 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ASN O 31 " --> pdb=" O VAL O 3 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE O 5 " --> pdb=" O ASN O 31 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS O 2 " --> pdb=" O ILE O 91 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE O 93 " --> pdb=" O LYS O 2 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA O 4 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL O 92 " --> pdb=" O ILE O 117 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 204 through 207 removed outlier: 9.489A pdb=" N ASN O 226 " --> pdb=" O VAL O 168 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY O 170 " --> pdb=" O ASN O 226 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N ILE O 228 " --> pdb=" O GLY O 170 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET O 172 " --> pdb=" O ILE O 228 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU O 230 " --> pdb=" O MET O 172 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR O 174 " --> pdb=" O LEU O 230 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL O 232 " --> pdb=" O THR O 174 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N HIS O 176 " --> pdb=" O VAL O 232 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS O 169 " --> pdb=" O ASN O 245 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N VAL O 308 " --> pdb=" O ASP O 293 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 204 through 207 removed outlier: 9.489A pdb=" N ASN O 226 " --> pdb=" O VAL O 168 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLY O 170 " --> pdb=" O ASN O 226 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N ILE O 228 " --> pdb=" O GLY O 170 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N MET O 172 " --> pdb=" O ILE O 228 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU O 230 " --> pdb=" O MET O 172 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR O 174 " --> pdb=" O LEU O 230 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL O 232 " --> pdb=" O THR O 174 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N HIS O 176 " --> pdb=" O VAL O 232 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS O 169 " --> pdb=" O ASN O 245 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 57 through 58 removed outlier: 10.353A pdb=" N VAL P 70 " --> pdb=" O ASP P 26 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL P 28 " --> pdb=" O VAL P 70 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N LEU P 1 " --> pdb=" O VAL P 27 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N VAL P 29 " --> pdb=" O LEU P 1 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL P 3 " --> pdb=" O VAL P 29 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ASN P 31 " --> pdb=" O VAL P 3 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE P 5 " --> pdb=" O ASN P 31 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL P 92 " --> pdb=" O LEU P 117 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'P' and resid 204 through 206 removed outlier: 8.928A pdb=" N ILE P 228 " --> pdb=" O GLY P 170 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N MET P 172 " --> pdb=" O ILE P 228 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU P 230 " --> pdb=" O MET P 172 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR P 174 " --> pdb=" O LEU P 230 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS P 169 " --> pdb=" O GLN P 245 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL P 243 " --> pdb=" O THR P 171 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE P 308 " --> pdb=" O ASP P 293 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N SER P 272 " --> pdb=" O ILE P 292 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 204 through 206 removed outlier: 8.928A pdb=" N ILE P 228 " --> pdb=" O GLY P 170 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N MET P 172 " --> pdb=" O ILE P 228 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU P 230 " --> pdb=" O MET P 172 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR P 174 " --> pdb=" O LEU P 230 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS P 169 " --> pdb=" O GLN P 245 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL P 243 " --> pdb=" O THR P 171 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 57 through 60 removed outlier: 9.685A pdb=" N ASP Q 26 " --> pdb=" O PRO Q 70 " (cutoff:3.500A) removed outlier: 9.639A pdb=" N LYS Q 72 " --> pdb=" O ASP Q 26 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL Q 28 " --> pdb=" O LYS Q 72 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL Q 74 " --> pdb=" O VAL Q 28 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL Q 30 " --> pdb=" O VAL Q 74 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N LEU Q 1 " --> pdb=" O VAL Q 27 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N VAL Q 29 " --> pdb=" O LEU Q 1 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL Q 3 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASN Q 31 " --> pdb=" O VAL Q 3 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE Q 5 " --> pdb=" O ASN Q 31 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS Q 2 " --> pdb=" O ILE Q 91 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE Q 93 " --> pdb=" O LYS Q 2 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA Q 4 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL Q 92 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 46 through 47 Processing sheet with id=AF1, first strand: chain 'Q' and resid 204 through 207 removed outlier: 9.479A pdb=" N ASN Q 226 " --> pdb=" O VAL Q 168 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY Q 170 " --> pdb=" O ASN Q 226 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ILE Q 228 " --> pdb=" O GLY Q 170 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N MET Q 172 " --> pdb=" O ILE Q 228 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU Q 230 " --> pdb=" O MET Q 172 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR Q 174 " --> pdb=" O LEU Q 230 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS Q 169 " --> pdb=" O ASN Q 245 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N VAL Q 308 " --> pdb=" O ASP Q 293 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP Q 272 " --> pdb=" O ILE Q 292 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Q' and resid 204 through 207 removed outlier: 9.479A pdb=" N ASN Q 226 " --> pdb=" O VAL Q 168 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLY Q 170 " --> pdb=" O ASN Q 226 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N ILE Q 228 " --> pdb=" O GLY Q 170 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N MET Q 172 " --> pdb=" O ILE Q 228 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU Q 230 " --> pdb=" O MET Q 172 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR Q 174 " --> pdb=" O LEU Q 230 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS Q 169 " --> pdb=" O ASN Q 245 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 57 through 58 removed outlier: 10.397A pdb=" N VAL R 70 " --> pdb=" O ASP R 26 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL R 28 " --> pdb=" O VAL R 70 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N LEU R 1 " --> pdb=" O VAL R 27 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N VAL R 29 " --> pdb=" O LEU R 1 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL R 3 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ASN R 31 " --> pdb=" O VAL R 3 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE R 5 " --> pdb=" O ASN R 31 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL R 92 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 204 through 207 removed outlier: 9.326A pdb=" N ASN R 226 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY R 170 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ILE R 228 " --> pdb=" O GLY R 170 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET R 172 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU R 230 " --> pdb=" O MET R 172 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR R 174 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL R 232 " --> pdb=" O THR R 174 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N HIS R 176 " --> pdb=" O VAL R 232 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS R 169 " --> pdb=" O GLN R 245 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ILE R 308 " --> pdb=" O ASP R 293 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER R 272 " --> pdb=" O ILE R 292 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 204 through 207 removed outlier: 9.326A pdb=" N ASN R 226 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY R 170 " --> pdb=" O ASN R 226 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ILE R 228 " --> pdb=" O GLY R 170 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N MET R 172 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N LEU R 230 " --> pdb=" O MET R 172 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR R 174 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL R 232 " --> pdb=" O THR R 174 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N HIS R 176 " --> pdb=" O VAL R 232 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS R 169 " --> pdb=" O GLN R 245 " (cutoff:3.500A) 2071 hydrogen bonds defined for protein. 5403 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.99 Time building geometry restraints manager: 4.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11715 1.33 - 1.45: 7404 1.45 - 1.58: 24537 1.58 - 1.70: 64 1.70 - 1.82: 248 Bond restraints: 43968 Sorted by residual: bond pdb=" C PRO Q 277 " pdb=" O PRO Q 277 " ideal model delta sigma weight residual 1.235 1.212 0.023 7.90e-03 1.60e+04 8.39e+00 bond pdb=" C1D NAD K 400 " pdb=" O4D NAD K 400 " ideal model delta sigma weight residual 1.376 1.433 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" N PRO Q 277 " pdb=" CA PRO Q 277 " ideal model delta sigma weight residual 1.470 1.441 0.028 1.01e-02 9.80e+03 7.81e+00 bond pdb=" N LEU P 82 " pdb=" CA LEU P 82 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.29e-02 6.01e+03 7.01e+00 bond pdb=" O3 NAD G 400 " pdb=" PA NAD G 400 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 7.00e+00 ... (remaining 43963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 58808 2.15 - 4.29: 951 4.29 - 6.44: 73 6.44 - 8.58: 21 8.58 - 10.73: 11 Bond angle restraints: 59864 Sorted by residual: angle pdb=" N PRO Q 277 " pdb=" CA PRO Q 277 " pdb=" C PRO Q 277 " ideal model delta sigma weight residual 110.74 101.28 9.46 1.66e+00 3.63e-01 3.25e+01 angle pdb=" C TYR I 361 " pdb=" CA TYR I 361 " pdb=" CB TYR I 361 " ideal model delta sigma weight residual 116.63 110.14 6.49 1.16e+00 7.43e-01 3.13e+01 angle pdb=" N PRO P 83 " pdb=" CA PRO P 83 " pdb=" CB PRO P 83 " ideal model delta sigma weight residual 102.28 98.75 3.53 7.50e-01 1.78e+00 2.22e+01 angle pdb=" CA PRO H 156 " pdb=" N PRO H 156 " pdb=" CD PRO H 156 " ideal model delta sigma weight residual 112.00 106.09 5.91 1.40e+00 5.10e-01 1.78e+01 angle pdb=" C TRP A 332 " pdb=" CA TRP A 332 " pdb=" CB TRP A 332 " ideal model delta sigma weight residual 110.17 118.40 -8.23 1.97e+00 2.58e-01 1.75e+01 ... (remaining 59859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 23718 17.95 - 35.91: 2449 35.91 - 53.86: 536 53.86 - 71.81: 126 71.81 - 89.77: 35 Dihedral angle restraints: 26864 sinusoidal: 10848 harmonic: 16016 Sorted by residual: dihedral pdb=" CA TRP A 332 " pdb=" C TRP A 332 " pdb=" N PRO A 333 " pdb=" CA PRO A 333 " ideal model delta harmonic sigma weight residual 180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ASN K 245 " pdb=" C ASN K 245 " pdb=" N ILE K 246 " pdb=" CA ILE K 246 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ASN G 202 " pdb=" C ASN G 202 " pdb=" N ILE G 203 " pdb=" CA ILE G 203 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 26861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 6264 0.081 - 0.162: 808 0.162 - 0.243: 3 0.243 - 0.324: 2 0.324 - 0.405: 3 Chirality restraints: 7080 Sorted by residual: chirality pdb=" CA ASP I 343 " pdb=" N ASP I 343 " pdb=" C ASP I 343 " pdb=" CB ASP I 343 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA CYS A 358 " pdb=" N CYS A 358 " pdb=" C CYS A 358 " pdb=" CB CYS A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CA LEU A 335 " pdb=" N LEU A 335 " pdb=" C LEU A 335 " pdb=" CB LEU A 335 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 7077 not shown) Planarity restraints: 7608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1B NAD K 400 " -0.028 2.00e-02 2.50e+03 2.84e-02 2.22e+01 pdb=" C2A NAD K 400 " -0.010 2.00e-02 2.50e+03 pdb=" C4A NAD K 400 " 0.058 2.00e-02 2.50e+03 pdb=" C5A NAD K 400 " 0.052 2.00e-02 2.50e+03 pdb=" C6A NAD K 400 " -0.004 2.00e-02 2.50e+03 pdb=" C8A NAD K 400 " -0.023 2.00e-02 2.50e+03 pdb=" N1A NAD K 400 " -0.008 2.00e-02 2.50e+03 pdb=" N3A NAD K 400 " -0.020 2.00e-02 2.50e+03 pdb=" N6A NAD K 400 " -0.020 2.00e-02 2.50e+03 pdb=" N7A NAD K 400 " -0.013 2.00e-02 2.50e+03 pdb=" N9A NAD K 400 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 343 " -0.064 5.00e-02 4.00e+02 9.61e-02 1.48e+01 pdb=" N PRO C 344 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO C 344 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 344 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 155 " 0.058 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO R 156 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO R 156 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO R 156 " 0.047 5.00e-02 4.00e+02 ... (remaining 7605 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 537 2.56 - 3.14: 36819 3.14 - 3.73: 68731 3.73 - 4.31: 103755 4.31 - 4.90: 170975 Nonbonded interactions: 380817 Sorted by model distance: nonbonded pdb=" OE2 GLU J 94 " pdb=" OG1 THR J 96 " model vdw 1.970 3.040 nonbonded pdb=" OE2 GLU B 94 " pdb=" OG1 THR B 96 " model vdw 1.974 3.040 nonbonded pdb=" OE2 GLU H 94 " pdb=" OG1 THR H 96 " model vdw 1.980 3.040 nonbonded pdb=" OH TYR C 46 " pdb=" OE1 GLU D 276 " model vdw 1.987 3.040 nonbonded pdb=" OE2 GLU R 94 " pdb=" OG1 THR R 96 " model vdw 2.001 3.040 ... (remaining 380812 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'P' selection = chain 'R' } 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: 4.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 41.800 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.006 0.073 43976 Z= 0.264 Angle : 0.680 10.728 59880 Z= 0.351 Chirality : 0.050 0.405 7080 Planarity : 0.005 0.112 7608 Dihedral : 15.600 89.765 16552 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.28 % Favored : 93.13 % Rotamer: Outliers : 0.66 % Allowed : 17.75 % Favored : 81.58 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.11), residues: 5608 helix: 0.43 (0.13), residues: 1523 sheet: -0.48 (0.14), residues: 1221 loop : -1.16 (0.11), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 77 TYR 0.019 0.002 TYR G 178 PHE 0.020 0.002 PHE G 157 TRP 0.008 0.001 TRP O 84 HIS 0.006 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00589 (43968) covalent geometry : angle 0.68006 (59864) SS BOND : bond 0.00503 ( 8) SS BOND : angle 1.04095 ( 16) hydrogen bonds : bond 0.14537 ( 1774) hydrogen bonds : angle 7.03755 ( 5403) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 720 time to evaluate : 1.191 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 LYS cc_start: 0.7937 (mmtp) cc_final: 0.7499 (mmtp) REVERT: C 77 ARG cc_start: 0.7345 (mmt-90) cc_final: 0.7064 (mmt180) REVERT: D 116 VAL cc_start: 0.8046 (t) cc_final: 0.7830 (p) REVERT: E 58 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7449 (mmmm) REVERT: E 81 LYS cc_start: 0.8487 (mmtm) cc_final: 0.8088 (mppt) REVERT: E 84 TRP cc_start: 0.8180 (OUTLIER) cc_final: 0.7579 (m100) REVERT: J 87 MET cc_start: 0.7982 (mtp) cc_final: 0.7592 (mtp) REVERT: J 324 LEU cc_start: 0.7893 (tp) cc_final: 0.7679 (tp) REVERT: K 58 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7606 (mmtp) REVERT: L 116 VAL cc_start: 0.8040 (t) cc_final: 0.7840 (p) REVERT: O 58 LYS cc_start: 0.7879 (ttpt) cc_final: 0.7462 (mmmm) REVERT: R 300 MET cc_start: 0.5692 (ttt) cc_final: 0.5430 (ttt) outliers start: 31 outliers final: 20 residues processed: 738 average time/residue: 0.2320 time to fit residues: 289.6624 Evaluate side-chains 709 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 688 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 362 GLU Chi-restraints excluded: chain C residue 332 TRP Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 245 ASN Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain I residue 240 VAL Chi-restraints excluded: chain I residue 362 GLU Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 172 MET Chi-restraints excluded: chain K residue 357 GLU Chi-restraints excluded: chain K residue 361 TYR Chi-restraints excluded: chain O residue 162 ASP Chi-restraints excluded: chain Q residue 362 GLU Chi-restraints excluded: chain R residue 294 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 265 optimal weight: 0.8980 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 30.0000 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 0.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18BHIS A 61 ASN A 133 ASN A 176 HIS B 139 HIS ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 319 GLN C 42 HIS C 146 ASN C 176 HIS C 202 ASN D 146 ASN D 152 ASN E 146 ASN E 176 HIS E 245 ASN F 146 ASN F 202 ASN G 202 ASN H 42 HIS H 78 ASN H 81 ASN H 139 HIS H 146 ASN H 152 ASN I 61 ASN I 133 ASN I 146 ASN I 176 HIS ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 ASN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 ASN J 245 GLN J 319 GLN K 146 ASN K 176 HIS K 202 ASN L 139 HIS L 146 ASN L 152 ASN O 76 ASN O 142 ASN O 146 ASN O 176 HIS ** O 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 ASN P 152 ASN P 202 ASN P 319 GLN Q 202 ASN R 42 HIS R 78 ASN R 81 ASN R 139 HIS R 146 ASN R 152 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.166335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.128749 restraints weight = 48552.797| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.74 r_work: 0.3094 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 43976 Z= 0.174 Angle : 0.595 6.602 59880 Z= 0.317 Chirality : 0.048 0.168 7080 Planarity : 0.005 0.060 7608 Dihedral : 8.513 89.789 6888 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.35 % Favored : 94.06 % Rotamer: Outliers : 3.26 % Allowed : 16.60 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.11), residues: 5608 helix: 0.84 (0.13), residues: 1574 sheet: -0.52 (0.15), residues: 1167 loop : -0.87 (0.12), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 77 TYR 0.016 0.002 TYR I 178 PHE 0.018 0.002 PHE O 348 TRP 0.011 0.001 TRP P 84 HIS 0.005 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00415 (43968) covalent geometry : angle 0.59455 (59864) SS BOND : bond 0.00664 ( 8) SS BOND : angle 1.63995 ( 16) hydrogen bonds : bond 0.03656 ( 1774) hydrogen bonds : angle 5.31140 ( 5403) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 744 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 152 ASN cc_start: 0.8654 (m110) cc_final: 0.8299 (m110) REVERT: B 172 MET cc_start: 0.7760 (ttp) cc_final: 0.7418 (tmm) REVERT: B 224 LYS cc_start: 0.7440 (mtmm) cc_final: 0.7185 (mtmm) REVERT: C 46 TYR cc_start: 0.8133 (m-80) cc_final: 0.7233 (m-80) REVERT: C 58 LYS cc_start: 0.8277 (mmtp) cc_final: 0.8030 (mmtp) REVERT: C 191 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8020 (ptt180) REVERT: C 332 TRP cc_start: 0.7378 (OUTLIER) cc_final: 0.4858 (m-90) REVERT: D 116 VAL cc_start: 0.7989 (t) cc_final: 0.7742 (p) REVERT: E 58 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7591 (mmmm) REVERT: E 81 LYS cc_start: 0.8632 (mmtm) cc_final: 0.8149 (mppt) REVERT: E 94 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: E 128 TYR cc_start: 0.8584 (m-80) cc_final: 0.8341 (m-80) REVERT: F 54 ASP cc_start: 0.6713 (t0) cc_final: 0.6357 (t0) REVERT: F 216 LEU cc_start: 0.7171 (mm) cc_final: 0.6945 (mm) REVERT: G 58 LYS cc_start: 0.7626 (ttmt) cc_final: 0.7063 (ttpp) REVERT: G 62 GLU cc_start: 0.8264 (mp0) cc_final: 0.7681 (mp0) REVERT: G 245 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.7015 (m-40) REVERT: H 58 LYS cc_start: 0.7645 (tptp) cc_final: 0.6850 (ttmm) REVERT: I 360 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7589 (mp) REVERT: J 216 LEU cc_start: 0.8041 (mp) cc_final: 0.7804 (mp) REVERT: K 58 LYS cc_start: 0.8278 (mmtp) cc_final: 0.8024 (mmtp) REVERT: K 114 LYS cc_start: 0.8387 (mttt) cc_final: 0.8138 (mtmt) REVERT: K 191 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7566 (ptp-170) REVERT: K 330 ASN cc_start: 0.8118 (t0) cc_final: 0.7465 (m110) REVERT: K 332 TRP cc_start: 0.7800 (OUTLIER) cc_final: 0.3925 (m-90) REVERT: K 362 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8417 (tm-30) REVERT: L 76 ASP cc_start: 0.7533 (t70) cc_final: 0.7073 (t70) REVERT: L 116 VAL cc_start: 0.8036 (t) cc_final: 0.7808 (p) REVERT: O 58 LYS cc_start: 0.8250 (ttpt) cc_final: 0.7624 (mmmm) REVERT: O 94 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: O 128 TYR cc_start: 0.8581 (m-80) cc_final: 0.8326 (m-80) REVERT: O 163 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7248 (mm-30) REVERT: O 311 TYR cc_start: 0.8865 (p90) cc_final: 0.8642 (p90) REVERT: P 1 LEU cc_start: 0.6718 (mp) cc_final: 0.6194 (tp) REVERT: P 29 VAL cc_start: 0.6939 (OUTLIER) cc_final: 0.6677 (p) REVERT: P 54 ASP cc_start: 0.6774 (t0) cc_final: 0.6418 (t0) REVERT: P 212 LYS cc_start: 0.7044 (mtmt) cc_final: 0.6490 (mttp) REVERT: P 216 LEU cc_start: 0.7164 (mm) cc_final: 0.6940 (mm) REVERT: Q 58 LYS cc_start: 0.7646 (ttmt) cc_final: 0.7042 (ttpp) REVERT: Q 245 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.6913 (m-40) REVERT: Q 362 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7940 (tm-30) REVERT: R 58 LYS cc_start: 0.7669 (tptp) cc_final: 0.6919 (ttmm) outliers start: 152 outliers final: 79 residues processed: 838 average time/residue: 0.2440 time to fit residues: 342.1477 Evaluate side-chains 802 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 711 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 284 ARG Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 332 TRP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 245 ASN Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 295 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 61 ASN Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 292 ILE Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 172 MET Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 285 CYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 191 ARG Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 284 ARG Chi-restraints excluded: chain K residue 332 TRP Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain P residue 29 VAL Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 208 THR Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 188 SER Chi-restraints excluded: chain Q residue 202 ASN Chi-restraints excluded: chain Q residue 245 ASN Chi-restraints excluded: chain Q residue 362 GLU Chi-restraints excluded: chain R residue 92 VAL Chi-restraints excluded: chain R residue 261 GLU Chi-restraints excluded: chain R residue 295 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 119 optimal weight: 0.0470 chunk 244 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 23 optimal weight: 0.0070 chunk 548 optimal weight: 0.5980 chunk 549 optimal weight: 3.9990 chunk 501 optimal weight: 3.9990 chunk 249 optimal weight: 0.0870 chunk 349 optimal weight: 0.8980 chunk 493 optimal weight: 3.9990 chunk 357 optimal weight: 0.0670 overall best weight: 0.1612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 152 ASN F 319 GLN G 139 HIS ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 78 ASN H 81 ASN I 133 ASN ** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 HIS L 152 ASN O 76 ASN O 245 ASN P 226 ASN ** Q 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN R 319 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.172722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.136454 restraints weight = 48452.099| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.69 r_work: 0.3174 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 43976 Z= 0.101 Angle : 0.509 7.789 59880 Z= 0.271 Chirality : 0.046 0.289 7080 Planarity : 0.004 0.052 7608 Dihedral : 7.628 89.477 6862 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.26 % Favored : 95.15 % Rotamer: Outliers : 2.42 % Allowed : 17.65 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.12), residues: 5608 helix: 1.19 (0.14), residues: 1580 sheet: -0.51 (0.15), residues: 1170 loop : -0.64 (0.12), residues: 2858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 77 TYR 0.011 0.001 TYR F 317 PHE 0.015 0.001 PHE O 348 TRP 0.011 0.001 TRP P 84 HIS 0.003 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00230 (43968) covalent geometry : angle 0.50845 (59864) SS BOND : bond 0.00460 ( 8) SS BOND : angle 1.48276 ( 16) hydrogen bonds : bond 0.02781 ( 1774) hydrogen bonds : angle 4.82157 ( 5403) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 772 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7181 (m-40) cc_final: 0.6783 (m-40) REVERT: B 102 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7911 (mmm160) REVERT: B 152 ASN cc_start: 0.8499 (m-40) cc_final: 0.8165 (m110) REVERT: B 224 LYS cc_start: 0.7469 (mtmm) cc_final: 0.7194 (mtmm) REVERT: B 282 ASP cc_start: 0.8578 (m-30) cc_final: 0.8269 (m-30) REVERT: B 293 ASP cc_start: 0.8274 (t0) cc_final: 0.8074 (t0) REVERT: C 46 TYR cc_start: 0.7971 (m-80) cc_final: 0.7183 (m-80) REVERT: C 58 LYS cc_start: 0.8274 (mmtp) cc_final: 0.7946 (mmtp) REVERT: C 114 LYS cc_start: 0.8391 (mtpt) cc_final: 0.8180 (mtmt) REVERT: C 191 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8191 (ptt180) REVERT: C 332 TRP cc_start: 0.7119 (OUTLIER) cc_final: 0.4245 (m-90) REVERT: D 72 LYS cc_start: 0.6895 (ttpp) cc_final: 0.6257 (ttpt) REVERT: D 276 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6996 (mt-10) REVERT: E 38 LYS cc_start: 0.8245 (tptm) cc_final: 0.7902 (ttmm) REVERT: E 58 LYS cc_start: 0.8045 (ttpt) cc_final: 0.7522 (mmmm) REVERT: E 81 LYS cc_start: 0.8431 (mmtm) cc_final: 0.7949 (mppt) REVERT: E 84 TRP cc_start: 0.8151 (OUTLIER) cc_final: 0.7664 (m100) REVERT: E 94 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: E 253 GLU cc_start: 0.6892 (mp0) cc_final: 0.6358 (mp0) REVERT: F 1 LEU cc_start: 0.6093 (mp) cc_final: 0.5830 (tp) REVERT: F 54 ASP cc_start: 0.6628 (t0) cc_final: 0.6261 (t0) REVERT: F 114 LYS cc_start: 0.7615 (mptt) cc_final: 0.7264 (mmtm) REVERT: F 212 LYS cc_start: 0.7101 (mtmt) cc_final: 0.6333 (mtpt) REVERT: F 216 LEU cc_start: 0.7140 (mm) cc_final: 0.6911 (mm) REVERT: G 20 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7838 (mmm-85) REVERT: G 62 GLU cc_start: 0.8071 (mp0) cc_final: 0.7529 (mp0) REVERT: H 58 LYS cc_start: 0.7580 (tptp) cc_final: 0.6889 (ttmm) REVERT: I 350 LYS cc_start: 0.7722 (mmmt) cc_final: 0.7486 (tppt) REVERT: I 360 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7104 (mp) REVERT: J 224 LYS cc_start: 0.7517 (mtmm) cc_final: 0.7293 (mtmm) REVERT: J 282 ASP cc_start: 0.8601 (m-30) cc_final: 0.8295 (m-30) REVERT: J 293 ASP cc_start: 0.8235 (t0) cc_final: 0.8021 (t0) REVERT: J 299 VAL cc_start: 0.8514 (p) cc_final: 0.8302 (t) REVERT: K 58 LYS cc_start: 0.8229 (mmtp) cc_final: 0.7880 (mmtp) REVERT: K 114 LYS cc_start: 0.8171 (mttt) cc_final: 0.7970 (mtpt) REVERT: K 330 ASN cc_start: 0.7898 (t0) cc_final: 0.7390 (m110) REVERT: K 332 TRP cc_start: 0.7429 (OUTLIER) cc_final: 0.3929 (m-90) REVERT: L 76 ASP cc_start: 0.7245 (t70) cc_final: 0.6833 (t70) REVERT: L 90 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7128 (t70) REVERT: O 38 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7753 (ttmm) REVERT: O 58 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7532 (mmmm) REVERT: O 94 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.6893 (tm-30) REVERT: P 1 LEU cc_start: 0.6541 (mp) cc_final: 0.6191 (tp) REVERT: P 54 ASP cc_start: 0.6656 (t0) cc_final: 0.6294 (t0) REVERT: P 114 LYS cc_start: 0.7670 (mptt) cc_final: 0.7429 (mmtm) REVERT: P 216 LEU cc_start: 0.7159 (mm) cc_final: 0.6914 (mm) REVERT: Q 58 LYS cc_start: 0.7486 (ttmt) cc_final: 0.6972 (ttpp) REVERT: R 58 LYS cc_start: 0.7606 (tptp) cc_final: 0.6891 (ttmm) REVERT: R 259 PHE cc_start: 0.7852 (m-80) cc_final: 0.7588 (m-80) outliers start: 113 outliers final: 64 residues processed: 829 average time/residue: 0.2420 time to fit residues: 335.7424 Evaluate side-chains 794 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 721 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 332 TRP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 247 GLU Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain I residue 61 ASN Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 285 CYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 191 ARG Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 332 TRP Chi-restraints excluded: chain K residue 361 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain Q residue 202 ASN Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 261 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 15 optimal weight: 1.9990 chunk 307 optimal weight: 6.9990 chunk 418 optimal weight: 4.9990 chunk 441 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 487 optimal weight: 1.9990 chunk 335 optimal weight: 3.9990 chunk 281 optimal weight: 0.0870 chunk 505 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 133 optimal weight: 0.0270 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18BHIS D 152 ASN ** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN G 176 HIS H 81 ASN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 18BHIS J 139 HIS P 226 ASN Q 176 HIS R 81 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.170679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.134036 restraints weight = 48396.241| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.72 r_work: 0.3144 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 43976 Z= 0.118 Angle : 0.507 6.363 59880 Z= 0.270 Chirality : 0.046 0.206 7080 Planarity : 0.004 0.049 7608 Dihedral : 7.503 87.235 6854 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.62 % Favored : 94.79 % Rotamer: Outliers : 2.92 % Allowed : 18.27 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.12), residues: 5608 helix: 1.22 (0.14), residues: 1588 sheet: -0.50 (0.15), residues: 1170 loop : -0.58 (0.12), residues: 2850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 77 TYR 0.015 0.002 TYR O 311 PHE 0.022 0.002 PHE E 348 TRP 0.007 0.001 TRP B 310 HIS 0.004 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00278 (43968) covalent geometry : angle 0.50639 (59864) SS BOND : bond 0.00478 ( 8) SS BOND : angle 1.36477 ( 16) hydrogen bonds : bond 0.02798 ( 1774) hydrogen bonds : angle 4.69952 ( 5403) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 731 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7219 (m-40) cc_final: 0.6858 (m-40) REVERT: A 332 TRP cc_start: 0.6838 (OUTLIER) cc_final: 0.6124 (m100) REVERT: B 77 ARG cc_start: 0.7203 (mtt180) cc_final: 0.6947 (mmt90) REVERT: B 152 ASN cc_start: 0.8435 (m-40) cc_final: 0.8136 (m110) REVERT: B 224 LYS cc_start: 0.7454 (mtmm) cc_final: 0.7146 (mtmm) REVERT: B 293 ASP cc_start: 0.8253 (t0) cc_final: 0.8017 (t70) REVERT: C 46 TYR cc_start: 0.7991 (m-80) cc_final: 0.7101 (m-80) REVERT: C 58 LYS cc_start: 0.8278 (mmtp) cc_final: 0.7936 (mmtp) REVERT: C 248 LYS cc_start: 0.5533 (OUTLIER) cc_final: 0.4943 (tmtt) REVERT: C 332 TRP cc_start: 0.7277 (OUTLIER) cc_final: 0.4446 (m-90) REVERT: D 45 LYS cc_start: 0.8624 (tppt) cc_final: 0.8041 (tttp) REVERT: D 76 ASP cc_start: 0.7372 (t70) cc_final: 0.6924 (t70) REVERT: D 90 ASP cc_start: 0.7331 (t0) cc_final: 0.6986 (t70) REVERT: D 276 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7046 (mt-10) REVERT: E 38 LYS cc_start: 0.8234 (tptm) cc_final: 0.7885 (ttmm) REVERT: E 58 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7555 (mmmm) REVERT: E 81 LYS cc_start: 0.8465 (mmtm) cc_final: 0.7976 (mppt) REVERT: E 253 GLU cc_start: 0.6907 (mp0) cc_final: 0.6370 (mp0) REVERT: F 1 LEU cc_start: 0.6136 (mp) cc_final: 0.5810 (tp) REVERT: F 54 ASP cc_start: 0.6671 (t0) cc_final: 0.6291 (t0) REVERT: F 65 SER cc_start: 0.7502 (p) cc_final: 0.7093 (t) REVERT: F 114 LYS cc_start: 0.7600 (mptt) cc_final: 0.7278 (mmtt) REVERT: F 216 LEU cc_start: 0.7201 (mm) cc_final: 0.6973 (mm) REVERT: G 58 LYS cc_start: 0.7515 (ttmt) cc_final: 0.6977 (ttpp) REVERT: G 62 GLU cc_start: 0.8118 (mp0) cc_final: 0.7568 (mp0) REVERT: H 58 LYS cc_start: 0.7587 (tptp) cc_final: 0.6887 (ttmm) REVERT: H 259 PHE cc_start: 0.7853 (m-80) cc_final: 0.7519 (m-80) REVERT: I 350 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7478 (tppp) REVERT: J 224 LYS cc_start: 0.7464 (mtmm) cc_final: 0.7176 (mtmm) REVERT: J 299 VAL cc_start: 0.8501 (p) cc_final: 0.8280 (t) REVERT: K 58 LYS cc_start: 0.8244 (mmtp) cc_final: 0.7872 (mmtp) REVERT: K 114 LYS cc_start: 0.8223 (mttt) cc_final: 0.7960 (mtmt) REVERT: K 248 LYS cc_start: 0.5532 (OUTLIER) cc_final: 0.4905 (tmtt) REVERT: K 330 ASN cc_start: 0.7847 (t0) cc_final: 0.7366 (m110) REVERT: K 332 TRP cc_start: 0.7511 (OUTLIER) cc_final: 0.3939 (m-90) REVERT: L 45 LYS cc_start: 0.8620 (tppt) cc_final: 0.8208 (tttp) REVERT: L 76 ASP cc_start: 0.7211 (t70) cc_final: 0.6776 (t70) REVERT: L 90 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7092 (t70) REVERT: O 38 LYS cc_start: 0.8086 (tptm) cc_final: 0.7790 (ttmm) REVERT: O 58 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7571 (mmmm) REVERT: O 81 LYS cc_start: 0.8501 (mppt) cc_final: 0.8198 (mppt) REVERT: O 94 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.6908 (tm-30) REVERT: P 1 LEU cc_start: 0.6455 (mp) cc_final: 0.6092 (tp) REVERT: P 54 ASP cc_start: 0.6685 (t0) cc_final: 0.6325 (t0) REVERT: P 114 LYS cc_start: 0.7629 (mptt) cc_final: 0.7283 (mmtm) REVERT: P 216 LEU cc_start: 0.7177 (mm) cc_final: 0.6948 (mm) REVERT: Q 58 LYS cc_start: 0.7456 (ttmt) cc_final: 0.6949 (ttpp) REVERT: R 58 LYS cc_start: 0.7617 (tptp) cc_final: 0.6912 (ttmm) REVERT: R 259 PHE cc_start: 0.7871 (m-80) cc_final: 0.7575 (m-80) REVERT: R 287 ASP cc_start: 0.7619 (m-30) cc_final: 0.7344 (m-30) outliers start: 136 outliers final: 87 residues processed: 818 average time/residue: 0.2524 time to fit residues: 347.8349 Evaluate side-chains 804 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 710 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 332 TRP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 281 VAL Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 285 CYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 191 ARG Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 332 TRP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 TRP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain L residue 281 ILE Chi-restraints excluded: chain L residue 304 MET Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 171 THR Chi-restraints excluded: chain Q residue 188 SER Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 261 GLU Chi-restraints excluded: chain R residue 300 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 507 optimal weight: 0.7980 chunk 270 optimal weight: 0.0870 chunk 107 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 540 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 448 optimal weight: 20.0000 chunk 419 optimal weight: 4.9990 chunk 543 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN C 202 ASN D 139 HIS D 152 ASN F 139 HIS H 81 ASN I 133 ASN ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 352 ASN K 202 ASN ** P 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 78 ASN R 81 ASN R 146 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.168213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.130195 restraints weight = 48328.700| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.79 r_work: 0.3126 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 43976 Z= 0.151 Angle : 0.533 6.767 59880 Z= 0.283 Chirality : 0.047 0.203 7080 Planarity : 0.004 0.049 7608 Dihedral : 7.679 89.867 6854 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.01 % Favored : 94.42 % Rotamer: Outliers : 3.82 % Allowed : 17.60 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.12), residues: 5608 helix: 1.23 (0.14), residues: 1517 sheet: -0.50 (0.15), residues: 1163 loop : -0.67 (0.12), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 77 TYR 0.022 0.002 TYR G 178 PHE 0.017 0.002 PHE K 64 TRP 0.008 0.001 TRP B 310 HIS 0.004 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00361 (43968) covalent geometry : angle 0.53288 (59864) SS BOND : bond 0.00533 ( 8) SS BOND : angle 1.40874 ( 16) hydrogen bonds : bond 0.03024 ( 1774) hydrogen bonds : angle 4.76143 ( 5403) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 741 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 ASN cc_start: 0.7215 (m-40) cc_final: 0.6844 (m-40) REVERT: A 332 TRP cc_start: 0.7076 (OUTLIER) cc_final: 0.5340 (m-90) REVERT: B 77 ARG cc_start: 0.7284 (mtt180) cc_final: 0.7004 (mmt90) REVERT: B 152 ASN cc_start: 0.8573 (m-40) cc_final: 0.8256 (m110) REVERT: B 224 LYS cc_start: 0.7428 (mtmm) cc_final: 0.7116 (mtmm) REVERT: B 293 ASP cc_start: 0.8488 (t0) cc_final: 0.8211 (t0) REVERT: C 46 TYR cc_start: 0.8112 (m-80) cc_final: 0.7162 (m-80) REVERT: C 58 LYS cc_start: 0.8362 (mmtp) cc_final: 0.7929 (mmtp) REVERT: C 191 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8008 (ptt180) REVERT: C 248 LYS cc_start: 0.5560 (OUTLIER) cc_final: 0.4926 (tmtt) REVERT: C 257 ASN cc_start: 0.6934 (m110) cc_final: 0.6686 (m110) REVERT: C 332 TRP cc_start: 0.7509 (OUTLIER) cc_final: 0.4902 (m-90) REVERT: D 20 ARG cc_start: 0.7756 (mmt90) cc_final: 0.7466 (mmt90) REVERT: D 45 LYS cc_start: 0.8654 (tppt) cc_final: 0.8133 (tttp) REVERT: D 76 ASP cc_start: 0.7581 (t70) cc_final: 0.7109 (t70) REVERT: D 90 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.7052 (t70) REVERT: E 38 LYS cc_start: 0.8322 (tptm) cc_final: 0.7972 (ttmm) REVERT: E 58 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7589 (mmmm) REVERT: E 81 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8044 (mppt) REVERT: E 94 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7295 (tm-30) REVERT: E 163 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6446 (pt0) REVERT: F 1 LEU cc_start: 0.6185 (mp) cc_final: 0.5883 (tp) REVERT: F 54 ASP cc_start: 0.6842 (t0) cc_final: 0.6464 (t0) REVERT: F 65 SER cc_start: 0.7502 (p) cc_final: 0.7093 (t) REVERT: F 114 LYS cc_start: 0.7650 (mptt) cc_final: 0.7296 (mmtt) REVERT: F 216 LEU cc_start: 0.7201 (mm) cc_final: 0.6956 (mm) REVERT: G 58 LYS cc_start: 0.7578 (ttmt) cc_final: 0.6958 (ttpp) REVERT: G 62 GLU cc_start: 0.8333 (mp0) cc_final: 0.7746 (mp0) REVERT: H 58 LYS cc_start: 0.7655 (tptp) cc_final: 0.7087 (ttmm) REVERT: H 73 VAL cc_start: 0.8082 (m) cc_final: 0.7818 (t) REVERT: H 172 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6721 (ptt) REVERT: H 259 PHE cc_start: 0.7946 (m-80) cc_final: 0.7520 (m-80) REVERT: I 58 LYS cc_start: 0.7163 (ttpt) cc_final: 0.6541 (tppt) REVERT: J 1 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6590 (tt) REVERT: J 224 LYS cc_start: 0.7330 (mtmm) cc_final: 0.7075 (mtmm) REVERT: J 299 VAL cc_start: 0.8570 (p) cc_final: 0.8332 (t) REVERT: K 58 LYS cc_start: 0.8325 (mmtp) cc_final: 0.7901 (mmtp) REVERT: K 114 LYS cc_start: 0.8375 (mttt) cc_final: 0.8151 (mtmt) REVERT: K 158 VAL cc_start: 0.7521 (t) cc_final: 0.7310 (t) REVERT: K 191 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8013 (ptt180) REVERT: K 248 LYS cc_start: 0.5615 (OUTLIER) cc_final: 0.4949 (tmtt) REVERT: K 257 ASN cc_start: 0.6914 (m110) cc_final: 0.6676 (m110) REVERT: K 330 ASN cc_start: 0.8046 (t0) cc_final: 0.7503 (m110) REVERT: K 332 TRP cc_start: 0.7690 (OUTLIER) cc_final: 0.3744 (m-90) REVERT: K 362 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8474 (tm-30) REVERT: L 45 LYS cc_start: 0.8666 (tppt) cc_final: 0.8293 (tttp) REVERT: L 76 ASP cc_start: 0.7409 (t70) cc_final: 0.6969 (t70) REVERT: L 90 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7240 (t70) REVERT: L 207 SER cc_start: 0.8830 (p) cc_final: 0.8569 (m) REVERT: O 38 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7875 (ttmm) REVERT: O 58 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7607 (mmmm) REVERT: O 81 LYS cc_start: 0.8503 (mppt) cc_final: 0.8284 (mppt) REVERT: O 94 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7306 (tm-30) REVERT: P 1 LEU cc_start: 0.6390 (mp) cc_final: 0.5953 (tp) REVERT: P 54 ASP cc_start: 0.6832 (t0) cc_final: 0.6450 (t0) REVERT: P 114 LYS cc_start: 0.7716 (mptt) cc_final: 0.7317 (mmtm) REVERT: P 216 LEU cc_start: 0.7196 (mm) cc_final: 0.6941 (mm) REVERT: Q 58 LYS cc_start: 0.7567 (ttmt) cc_final: 0.6979 (ttpp) REVERT: Q 62 GLU cc_start: 0.8340 (mp0) cc_final: 0.7704 (mp0) REVERT: R 58 LYS cc_start: 0.7684 (tptp) cc_final: 0.7100 (ttmm) REVERT: R 73 VAL cc_start: 0.8111 (m) cc_final: 0.7853 (t) REVERT: R 259 PHE cc_start: 0.7848 (m-80) cc_final: 0.7311 (m-80) REVERT: R 261 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7716 (tm-30) REVERT: R 287 ASP cc_start: 0.7888 (m-30) cc_final: 0.7501 (m-30) outliers start: 178 outliers final: 108 residues processed: 849 average time/residue: 0.2410 time to fit residues: 346.6054 Evaluate side-chains 839 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 715 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 332 TRP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 313 ASN Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 238 SER Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 145 SER Chi-restraints excluded: chain J residue 172 MET Chi-restraints excluded: chain J residue 228 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 285 CYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 191 ARG Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 332 TRP Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 TRP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 38 LYS Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 281 ILE Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain P residue 297 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 188 SER Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 261 GLU Chi-restraints excluded: chain R residue 294 SER Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 53 optimal weight: 9.9990 chunk 405 optimal weight: 3.9990 chunk 505 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 272 optimal weight: 0.7980 chunk 501 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 371 optimal weight: 4.9990 chunk 482 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 133 ASN B 313 ASN D 152 ASN E 42 HIS G 202 ASN H 78 ASN H 81 ASN I 18BHIS I 61 ASN I 133 ASN ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 ASN ** P 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.164269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.127064 restraints weight = 48391.721| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.68 r_work: 0.3066 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 43976 Z= 0.239 Angle : 0.616 6.184 59880 Z= 0.326 Chirality : 0.050 0.203 7080 Planarity : 0.005 0.051 7608 Dihedral : 8.265 87.406 6854 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.57 % Allowed : 5.63 % Favored : 93.79 % Rotamer: Outliers : 4.10 % Allowed : 18.12 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.11), residues: 5608 helix: 0.86 (0.14), residues: 1514 sheet: -0.76 (0.15), residues: 1260 loop : -0.89 (0.12), residues: 2834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 77 TYR 0.029 0.003 TYR G 178 PHE 0.028 0.003 PHE I 348 TRP 0.010 0.001 TRP J 310 HIS 0.007 0.001 HIS G 139 Details of bonding type rmsd covalent geometry : bond 0.00566 (43968) covalent geometry : angle 0.61518 (59864) SS BOND : bond 0.00660 ( 8) SS BOND : angle 1.53423 ( 16) hydrogen bonds : bond 0.03674 ( 1774) hydrogen bonds : angle 5.03820 ( 5403) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 724 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 ARG cc_start: 0.8540 (ptt180) cc_final: 0.8253 (ptt180) REVERT: A 241 ASP cc_start: 0.7294 (OUTLIER) cc_final: 0.6929 (t70) REVERT: B 146 ASN cc_start: 0.7807 (t0) cc_final: 0.7570 (t0) REVERT: B 152 ASN cc_start: 0.8558 (m-40) cc_final: 0.8061 (m110) REVERT: B 224 LYS cc_start: 0.7399 (mtmm) cc_final: 0.7118 (mtmm) REVERT: B 292 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8361 (mm) REVERT: C 8 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8469 (t80) REVERT: C 46 TYR cc_start: 0.8218 (m-80) cc_final: 0.7186 (m-80) REVERT: C 58 LYS cc_start: 0.8339 (mmtp) cc_final: 0.8016 (mmtp) REVERT: C 191 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8491 (ptp-170) REVERT: C 248 LYS cc_start: 0.5737 (OUTLIER) cc_final: 0.5027 (tmtt) REVERT: C 332 TRP cc_start: 0.7841 (OUTLIER) cc_final: 0.5805 (m-90) REVERT: D 20 ARG cc_start: 0.7846 (mmt90) cc_final: 0.7584 (mmt90) REVERT: D 45 LYS cc_start: 0.8674 (tppt) cc_final: 0.8313 (tptm) REVERT: D 76 ASP cc_start: 0.7654 (t70) cc_final: 0.7137 (t70) REVERT: D 90 ASP cc_start: 0.7475 (OUTLIER) cc_final: 0.7201 (t70) REVERT: D 207 SER cc_start: 0.8909 (p) cc_final: 0.8624 (m) REVERT: D 276 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7308 (mt-10) REVERT: E 58 LYS cc_start: 0.8240 (ttpt) cc_final: 0.7600 (mmmm) REVERT: E 81 LYS cc_start: 0.8663 (mmtm) cc_final: 0.8196 (mppt) REVERT: E 94 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: E 152 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8744 (m-40) REVERT: E 163 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6408 (pt0) REVERT: F 1 LEU cc_start: 0.6138 (mp) cc_final: 0.5757 (tp) REVERT: F 54 ASP cc_start: 0.6836 (t0) cc_final: 0.6469 (t0) REVERT: F 114 LYS cc_start: 0.7593 (mptt) cc_final: 0.7349 (mptt) REVERT: F 216 LEU cc_start: 0.7276 (mm) cc_final: 0.7027 (mm) REVERT: G 58 LYS cc_start: 0.7679 (ttmt) cc_final: 0.7065 (ttpp) REVERT: G 62 GLU cc_start: 0.8387 (mp0) cc_final: 0.7770 (mp0) REVERT: G 246 ILE cc_start: 0.7892 (mm) cc_final: 0.7430 (pt) REVERT: H 58 LYS cc_start: 0.7693 (tptp) cc_final: 0.7061 (ttmm) REVERT: H 172 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6781 (ptt) REVERT: H 259 PHE cc_start: 0.7976 (m-80) cc_final: 0.7460 (m-80) REVERT: I 241 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6931 (t70) REVERT: I 357 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7167 (mm-30) REVERT: J 1 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6572 (tt) REVERT: J 224 LYS cc_start: 0.7464 (mtmm) cc_final: 0.7177 (mtmm) REVERT: J 292 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8318 (mm) REVERT: K 46 TYR cc_start: 0.8148 (m-80) cc_final: 0.7308 (m-80) REVERT: K 58 LYS cc_start: 0.8279 (mmtp) cc_final: 0.7954 (mmtp) REVERT: K 114 LYS cc_start: 0.8428 (mttt) cc_final: 0.8180 (mtmt) REVERT: K 248 LYS cc_start: 0.5814 (OUTLIER) cc_final: 0.5047 (tmtt) REVERT: K 300 MET cc_start: 0.6704 (tpt) cc_final: 0.6493 (tpt) REVERT: K 330 ASN cc_start: 0.8138 (t0) cc_final: 0.7602 (m110) REVERT: K 362 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8593 (tm-30) REVERT: L 76 ASP cc_start: 0.7556 (t70) cc_final: 0.7096 (t70) REVERT: L 90 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7309 (t70) REVERT: L 207 SER cc_start: 0.8905 (p) cc_final: 0.8640 (m) REVERT: L 300 MET cc_start: 0.7441 (mtp) cc_final: 0.7086 (ttm) REVERT: O 58 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7608 (mmmm) REVERT: O 81 LYS cc_start: 0.8545 (mppt) cc_final: 0.8292 (mppt) REVERT: O 94 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7308 (tm-30) REVERT: P 54 ASP cc_start: 0.6850 (t0) cc_final: 0.6507 (t0) REVERT: P 114 LYS cc_start: 0.7763 (mptt) cc_final: 0.7521 (mptt) REVERT: P 216 LEU cc_start: 0.7254 (mm) cc_final: 0.7000 (mm) REVERT: Q 58 LYS cc_start: 0.7684 (ttmt) cc_final: 0.7061 (ttpp) REVERT: Q 62 GLU cc_start: 0.8345 (mp0) cc_final: 0.7700 (mp0) REVERT: Q 222 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8309 (ttmm) REVERT: Q 246 ILE cc_start: 0.7853 (mm) cc_final: 0.7459 (pt) REVERT: R 58 LYS cc_start: 0.7738 (tptp) cc_final: 0.7153 (ttmm) REVERT: R 259 PHE cc_start: 0.7992 (m-80) cc_final: 0.7499 (m-80) REVERT: R 261 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7754 (tm-30) outliers start: 191 outliers final: 124 residues processed: 845 average time/residue: 0.2395 time to fit residues: 341.8184 Evaluate side-chains 842 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 699 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 8 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 332 TRP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 202 ASN Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 188 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 313 ASN Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 238 SER Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 172 MET Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 285 CYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 292 ILE Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 191 ARG Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 332 TRP Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 TRP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 281 ILE Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain P residue 297 THR Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 30 VAL Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 188 SER Chi-restraints excluded: chain Q residue 222 LYS Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 261 GLU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 294 SER Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 300 MET Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 69 optimal weight: 7.9990 chunk 211 optimal weight: 0.5980 chunk 479 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 414 optimal weight: 5.9990 chunk 445 optimal weight: 0.1980 chunk 538 optimal weight: 0.9980 chunk 428 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 443 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** G 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN I 133 ASN ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 ASN O 76 ASN ** P 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.169531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.132831 restraints weight = 47949.272| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.69 r_work: 0.3138 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43976 Z= 0.113 Angle : 0.514 7.876 59880 Z= 0.272 Chirality : 0.046 0.193 7080 Planarity : 0.004 0.064 7608 Dihedral : 7.646 88.785 6854 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.56 % Favored : 94.86 % Rotamer: Outliers : 3.00 % Allowed : 19.53 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.12), residues: 5608 helix: 1.26 (0.14), residues: 1525 sheet: -0.71 (0.15), residues: 1210 loop : -0.70 (0.12), residues: 2873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 77 TYR 0.013 0.002 TYR E 311 PHE 0.023 0.001 PHE I 348 TRP 0.011 0.001 TRP P 84 HIS 0.003 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00268 (43968) covalent geometry : angle 0.51357 (59864) SS BOND : bond 0.00477 ( 8) SS BOND : angle 1.50247 ( 16) hydrogen bonds : bond 0.02742 ( 1774) hydrogen bonds : angle 4.70794 ( 5403) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 734 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7141 (ttpt) cc_final: 0.6497 (tppt) REVERT: A 191 ARG cc_start: 0.8482 (ptt180) cc_final: 0.8142 (ptt180) REVERT: B 122 LYS cc_start: 0.7672 (tttm) cc_final: 0.7263 (ttmm) REVERT: B 152 ASN cc_start: 0.8533 (m-40) cc_final: 0.8061 (m110) REVERT: B 224 LYS cc_start: 0.7334 (mtmm) cc_final: 0.7101 (mtmm) REVERT: B 282 ASP cc_start: 0.8738 (m-30) cc_final: 0.8351 (m-30) REVERT: C 46 TYR cc_start: 0.8152 (m-80) cc_final: 0.7158 (m-80) REVERT: C 58 LYS cc_start: 0.8377 (mmtp) cc_final: 0.7915 (mmtp) REVERT: C 158 VAL cc_start: 0.7479 (t) cc_final: 0.7265 (t) REVERT: C 248 LYS cc_start: 0.5625 (OUTLIER) cc_final: 0.4934 (tmtt) REVERT: C 257 ASN cc_start: 0.7031 (m110) cc_final: 0.6604 (m110) REVERT: C 332 TRP cc_start: 0.7644 (OUTLIER) cc_final: 0.5485 (m-90) REVERT: D 20 ARG cc_start: 0.7761 (mmt90) cc_final: 0.7462 (mmt90) REVERT: D 45 LYS cc_start: 0.8685 (tppt) cc_final: 0.8162 (tttp) REVERT: D 90 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6977 (t70) REVERT: D 207 SER cc_start: 0.8863 (p) cc_final: 0.8584 (m) REVERT: D 276 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7243 (mt-10) REVERT: E 38 LYS cc_start: 0.8297 (tptm) cc_final: 0.7930 (ttmm) REVERT: E 58 LYS cc_start: 0.8174 (ttpt) cc_final: 0.7538 (mmmm) REVERT: E 81 LYS cc_start: 0.8562 (mmtm) cc_final: 0.8089 (mppt) REVERT: E 94 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7322 (tm-30) REVERT: E 152 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8698 (m-40) REVERT: E 163 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6488 (pt0) REVERT: F 1 LEU cc_start: 0.6053 (mp) cc_final: 0.5741 (tp) REVERT: F 54 ASP cc_start: 0.6827 (t0) cc_final: 0.6449 (t0) REVERT: F 65 SER cc_start: 0.7507 (p) cc_final: 0.7155 (t) REVERT: F 114 LYS cc_start: 0.7540 (mptt) cc_final: 0.7148 (mmtm) REVERT: F 216 LEU cc_start: 0.7253 (mm) cc_final: 0.7008 (mm) REVERT: G 58 LYS cc_start: 0.7642 (ttmt) cc_final: 0.6999 (ttpp) REVERT: G 62 GLU cc_start: 0.8362 (mp0) cc_final: 0.7750 (mp0) REVERT: H 58 LYS cc_start: 0.7660 (tptp) cc_final: 0.7073 (ttmm) REVERT: H 172 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6716 (ptt) REVERT: H 259 PHE cc_start: 0.7959 (m-80) cc_final: 0.7552 (m-80) REVERT: H 261 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7620 (tm-30) REVERT: I 58 LYS cc_start: 0.7033 (ttpt) cc_final: 0.6417 (tppt) REVERT: J 1 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6609 (tt) REVERT: J 122 LYS cc_start: 0.7666 (tttm) cc_final: 0.7265 (ttmm) REVERT: J 146 ASN cc_start: 0.8020 (OUTLIER) cc_final: 0.7609 (t0) REVERT: J 224 LYS cc_start: 0.7415 (mtmm) cc_final: 0.7127 (mtmm) REVERT: J 282 ASP cc_start: 0.8746 (m-30) cc_final: 0.8357 (m-30) REVERT: J 299 VAL cc_start: 0.8539 (p) cc_final: 0.8317 (t) REVERT: K 46 TYR cc_start: 0.8084 (m-80) cc_final: 0.7274 (m-80) REVERT: K 58 LYS cc_start: 0.8328 (mmtp) cc_final: 0.7860 (mmtp) REVERT: K 114 LYS cc_start: 0.8400 (mttt) cc_final: 0.8162 (mtmt) REVERT: K 248 LYS cc_start: 0.5695 (OUTLIER) cc_final: 0.4992 (tmtt) REVERT: K 257 ASN cc_start: 0.7035 (m110) cc_final: 0.6599 (m110) REVERT: K 330 ASN cc_start: 0.8041 (t0) cc_final: 0.7502 (m110) REVERT: K 332 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.3866 (m-90) REVERT: K 362 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: L 76 ASP cc_start: 0.7472 (t70) cc_final: 0.7039 (t70) REVERT: L 90 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7324 (t70) REVERT: L 300 MET cc_start: 0.7325 (mtp) cc_final: 0.7009 (ttm) REVERT: O 38 LYS cc_start: 0.8292 (tptm) cc_final: 0.7927 (ttmm) REVERT: O 58 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7542 (mmmm) REVERT: O 94 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: O 152 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8658 (m-40) REVERT: O 163 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6505 (pt0) REVERT: P 54 ASP cc_start: 0.6858 (t0) cc_final: 0.6482 (t0) REVERT: P 114 LYS cc_start: 0.7711 (mptt) cc_final: 0.7459 (mptt) REVERT: P 216 LEU cc_start: 0.7229 (mm) cc_final: 0.6982 (mm) REVERT: Q 58 LYS cc_start: 0.7603 (ttmt) cc_final: 0.6975 (ttpp) REVERT: Q 62 GLU cc_start: 0.8369 (mp0) cc_final: 0.7712 (mp0) REVERT: R 58 LYS cc_start: 0.7715 (tptp) cc_final: 0.7108 (ttmm) REVERT: R 73 VAL cc_start: 0.8087 (m) cc_final: 0.7777 (t) REVERT: R 259 PHE cc_start: 0.7877 (m-80) cc_final: 0.7512 (m-80) REVERT: R 261 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7770 (tm-30) outliers start: 140 outliers final: 99 residues processed: 824 average time/residue: 0.2459 time to fit residues: 340.9168 Evaluate side-chains 825 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 710 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 332 TRP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 186 ASP Chi-restraints excluded: chain F residue 208 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 191 ARG Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 271 LEU Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 146 ASN Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 285 CYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 191 ARG Chi-restraints excluded: chain K residue 202 ASN Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 332 TRP Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 152 ASN Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 188 SER Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 241 ASP Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 261 GLU Chi-restraints excluded: chain R residue 285 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 503 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 510 optimal weight: 2.9990 chunk 350 optimal weight: 5.9990 chunk 496 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 537 optimal weight: 0.4980 chunk 349 optimal weight: 0.7980 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 133 ASN B 220 ASN H 81 ASN I 133 ASN ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 202 ASN O 76 ASN P 139 HIS R 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.168750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.132049 restraints weight = 48324.020| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.69 r_work: 0.3138 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43976 Z= 0.132 Angle : 0.531 10.406 59880 Z= 0.280 Chirality : 0.047 0.401 7080 Planarity : 0.004 0.082 7608 Dihedral : 7.645 88.059 6854 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.81 % Favored : 94.61 % Rotamer: Outliers : 3.15 % Allowed : 19.96 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.12), residues: 5608 helix: 1.33 (0.14), residues: 1516 sheet: -0.67 (0.15), residues: 1228 loop : -0.70 (0.12), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 183 TYR 0.018 0.002 TYR G 178 PHE 0.015 0.002 PHE K 64 TRP 0.010 0.001 TRP E 310 HIS 0.004 0.001 HIS L 108 Details of bonding type rmsd covalent geometry : bond 0.00316 (43968) covalent geometry : angle 0.53060 (59864) SS BOND : bond 0.00519 ( 8) SS BOND : angle 1.43376 ( 16) hydrogen bonds : bond 0.02868 ( 1774) hydrogen bonds : angle 4.71052 ( 5403) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 717 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7102 (ttpt) cc_final: 0.6475 (tppt) REVERT: A 300 MET cc_start: 0.6644 (tpt) cc_final: 0.6295 (mmm) REVERT: B 77 ARG cc_start: 0.7178 (mtt180) cc_final: 0.6854 (mmt90) REVERT: B 122 LYS cc_start: 0.7661 (tttm) cc_final: 0.7246 (ttmm) REVERT: B 152 ASN cc_start: 0.8398 (m-40) cc_final: 0.8126 (m-40) REVERT: B 224 LYS cc_start: 0.7422 (mtmm) cc_final: 0.7131 (mtmm) REVERT: B 282 ASP cc_start: 0.8728 (m-30) cc_final: 0.8376 (m-30) REVERT: C 46 TYR cc_start: 0.8128 (m-80) cc_final: 0.7130 (m-80) REVERT: C 58 LYS cc_start: 0.8356 (mmtp) cc_final: 0.8027 (mmtp) REVERT: C 158 VAL cc_start: 0.7482 (t) cc_final: 0.7277 (t) REVERT: C 191 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7997 (ptt180) REVERT: C 248 LYS cc_start: 0.5577 (OUTLIER) cc_final: 0.4941 (tmtt) REVERT: C 257 ASN cc_start: 0.7063 (m110) cc_final: 0.6559 (m110) REVERT: C 332 TRP cc_start: 0.7619 (OUTLIER) cc_final: 0.5456 (m-90) REVERT: D 20 ARG cc_start: 0.7773 (mmt90) cc_final: 0.7453 (mmt90) REVERT: D 45 LYS cc_start: 0.8660 (tppt) cc_final: 0.8164 (tttp) REVERT: D 76 ASP cc_start: 0.7545 (t70) cc_final: 0.7059 (t70) REVERT: D 90 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7008 (t70) REVERT: D 276 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7245 (mt-10) REVERT: E 38 LYS cc_start: 0.8296 (tptm) cc_final: 0.7965 (ttmm) REVERT: E 58 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7538 (mmmm) REVERT: E 81 LYS cc_start: 0.8578 (mmtm) cc_final: 0.8118 (mppt) REVERT: E 94 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7277 (tm-30) REVERT: E 152 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8736 (m-40) REVERT: E 163 GLU cc_start: 0.7461 (mm-30) cc_final: 0.6535 (pt0) REVERT: F 1 LEU cc_start: 0.6045 (mp) cc_final: 0.5746 (tp) REVERT: F 54 ASP cc_start: 0.6830 (t0) cc_final: 0.6435 (t0) REVERT: F 65 SER cc_start: 0.7507 (p) cc_final: 0.7164 (t) REVERT: F 114 LYS cc_start: 0.7633 (mptt) cc_final: 0.7260 (mmtm) REVERT: F 216 LEU cc_start: 0.7239 (mm) cc_final: 0.6996 (mm) REVERT: G 58 LYS cc_start: 0.7653 (ttmt) cc_final: 0.7022 (ttpp) REVERT: G 62 GLU cc_start: 0.8334 (mp0) cc_final: 0.7722 (mp0) REVERT: H 58 LYS cc_start: 0.7651 (tptp) cc_final: 0.7097 (ttmm) REVERT: H 172 MET cc_start: 0.7187 (OUTLIER) cc_final: 0.6653 (ptt) REVERT: H 259 PHE cc_start: 0.7930 (m-80) cc_final: 0.7508 (m-80) REVERT: H 261 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: I 58 LYS cc_start: 0.7018 (ttpt) cc_final: 0.6429 (tppt) REVERT: J 1 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6609 (tt) REVERT: J 122 LYS cc_start: 0.7647 (tttm) cc_final: 0.7256 (ttmm) REVERT: J 146 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7564 (t0) REVERT: J 224 LYS cc_start: 0.7396 (mtmm) cc_final: 0.7061 (mtmm) REVERT: J 299 VAL cc_start: 0.8547 (p) cc_final: 0.8309 (t) REVERT: K 46 TYR cc_start: 0.8091 (m-80) cc_final: 0.7282 (m-80) REVERT: K 58 LYS cc_start: 0.8315 (mmtp) cc_final: 0.7832 (mmtp) REVERT: K 114 LYS cc_start: 0.8379 (mttt) cc_final: 0.8108 (mtmt) REVERT: K 191 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7993 (ptt180) REVERT: K 248 LYS cc_start: 0.5679 (OUTLIER) cc_final: 0.4895 (tmtt) REVERT: K 257 ASN cc_start: 0.7018 (m110) cc_final: 0.6577 (m110) REVERT: K 330 ASN cc_start: 0.8032 (t0) cc_final: 0.7507 (m110) REVERT: K 332 TRP cc_start: 0.7821 (OUTLIER) cc_final: 0.3829 (m-90) REVERT: K 362 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: L 76 ASP cc_start: 0.7471 (t70) cc_final: 0.7029 (t70) REVERT: L 90 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7307 (t70) REVERT: L 300 MET cc_start: 0.7348 (mtp) cc_final: 0.7050 (ttm) REVERT: O 38 LYS cc_start: 0.8253 (tptm) cc_final: 0.7903 (ttmm) REVERT: O 58 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7545 (mmmm) REVERT: O 81 LYS cc_start: 0.8397 (mppt) cc_final: 0.8101 (mppt) REVERT: O 152 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8661 (m-40) REVERT: O 163 GLU cc_start: 0.7530 (mm-30) cc_final: 0.6502 (pt0) REVERT: P 54 ASP cc_start: 0.6854 (t0) cc_final: 0.6459 (t0) REVERT: P 114 LYS cc_start: 0.7718 (mptt) cc_final: 0.7488 (mptt) REVERT: P 216 LEU cc_start: 0.7206 (mm) cc_final: 0.6974 (mm) REVERT: Q 58 LYS cc_start: 0.7628 (ttmt) cc_final: 0.6988 (ttpp) REVERT: Q 62 GLU cc_start: 0.8373 (mp0) cc_final: 0.7726 (mp0) REVERT: R 58 LYS cc_start: 0.7676 (tptp) cc_final: 0.7104 (ttmm) REVERT: R 73 VAL cc_start: 0.8086 (m) cc_final: 0.7767 (t) REVERT: R 259 PHE cc_start: 0.7849 (m-80) cc_final: 0.7466 (m-80) REVERT: R 261 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: R 287 ASP cc_start: 0.7913 (m-30) cc_final: 0.7649 (m-30) outliers start: 147 outliers final: 108 residues processed: 805 average time/residue: 0.2492 time to fit residues: 338.5093 Evaluate side-chains 836 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 711 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 332 TRP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 191 ARG Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 313 ASN Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 238 SER Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 146 ASN Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 285 CYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 191 ARG Chi-restraints excluded: chain K residue 202 ASN Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 332 TRP Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 TRP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 285 CYS Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 152 ASN Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 186 ASP Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 188 SER Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 242 LEU Chi-restraints excluded: chain R residue 261 GLU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 300 MET Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 424 optimal weight: 0.1980 chunk 37 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 417 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 355 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 354 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN H 81 ASN I 133 ASN ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 ASN K 202 ASN P 110 GLN ** Q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.169761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.132950 restraints weight = 48063.532| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.68 r_work: 0.3144 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43976 Z= 0.115 Angle : 0.520 10.997 59880 Z= 0.273 Chirality : 0.046 0.398 7080 Planarity : 0.004 0.061 7608 Dihedral : 7.530 89.119 6854 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.71 % Favored : 94.72 % Rotamer: Outliers : 2.96 % Allowed : 20.20 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.12), residues: 5608 helix: 1.34 (0.14), residues: 1536 sheet: -0.63 (0.15), residues: 1226 loop : -0.70 (0.12), residues: 2846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 183 TYR 0.014 0.002 TYR G 178 PHE 0.018 0.001 PHE E 348 TRP 0.009 0.001 TRP H 84 HIS 0.003 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00276 (43968) covalent geometry : angle 0.51924 (59864) SS BOND : bond 0.00477 ( 8) SS BOND : angle 1.41478 ( 16) hydrogen bonds : bond 0.02736 ( 1774) hydrogen bonds : angle 4.65808 ( 5403) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 721 time to evaluate : 1.577 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 58 LYS cc_start: 0.7103 (ttpt) cc_final: 0.6472 (tppt) REVERT: A 300 MET cc_start: 0.6608 (tpt) cc_final: 0.6321 (mmm) REVERT: A 330 ASN cc_start: 0.6827 (m-40) cc_final: 0.6464 (m-40) REVERT: B 77 ARG cc_start: 0.7176 (mtt180) cc_final: 0.6887 (mmt90) REVERT: B 122 LYS cc_start: 0.7643 (tttm) cc_final: 0.7225 (ttmm) REVERT: B 152 ASN cc_start: 0.8441 (m-40) cc_final: 0.8194 (m-40) REVERT: B 224 LYS cc_start: 0.7423 (mtmm) cc_final: 0.7129 (mtmm) REVERT: B 282 ASP cc_start: 0.8732 (m-30) cc_final: 0.8426 (m-30) REVERT: C 46 TYR cc_start: 0.8147 (m-80) cc_final: 0.7208 (m-80) REVERT: C 58 LYS cc_start: 0.8355 (mmtp) cc_final: 0.8053 (mmtp) REVERT: C 158 VAL cc_start: 0.7431 (t) cc_final: 0.7226 (t) REVERT: C 248 LYS cc_start: 0.5620 (OUTLIER) cc_final: 0.4984 (tmtt) REVERT: C 257 ASN cc_start: 0.6987 (m110) cc_final: 0.6490 (m110) REVERT: C 332 TRP cc_start: 0.7624 (OUTLIER) cc_final: 0.5363 (m-90) REVERT: D 20 ARG cc_start: 0.7757 (mmt90) cc_final: 0.7439 (mmt90) REVERT: D 45 LYS cc_start: 0.8670 (tppt) cc_final: 0.8160 (tttp) REVERT: D 76 ASP cc_start: 0.7536 (t70) cc_final: 0.7037 (t70) REVERT: D 90 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7047 (t70) REVERT: D 276 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7247 (mt-10) REVERT: E 38 LYS cc_start: 0.8305 (tptm) cc_final: 0.7977 (ttmm) REVERT: E 58 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7532 (mmmm) REVERT: E 81 LYS cc_start: 0.8537 (mmtm) cc_final: 0.8076 (mppt) REVERT: E 94 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7271 (tm-30) REVERT: E 152 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8718 (m-40) REVERT: E 163 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6498 (pt0) REVERT: F 1 LEU cc_start: 0.5997 (mp) cc_final: 0.5723 (tp) REVERT: F 54 ASP cc_start: 0.6835 (t0) cc_final: 0.6413 (t0) REVERT: F 65 SER cc_start: 0.7429 (p) cc_final: 0.7122 (t) REVERT: F 76 ASP cc_start: 0.6645 (t70) cc_final: 0.6429 (t0) REVERT: F 114 LYS cc_start: 0.7620 (mptt) cc_final: 0.7246 (mmtm) REVERT: F 216 LEU cc_start: 0.7254 (mm) cc_final: 0.7022 (mm) REVERT: G 58 LYS cc_start: 0.7639 (ttmt) cc_final: 0.6989 (ttpp) REVERT: G 62 GLU cc_start: 0.8335 (mp0) cc_final: 0.7714 (mp0) REVERT: H 58 LYS cc_start: 0.7634 (tptp) cc_final: 0.7074 (ttmm) REVERT: H 152 ASN cc_start: 0.8619 (m-40) cc_final: 0.8198 (m110) REVERT: H 172 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.6695 (ptt) REVERT: H 259 PHE cc_start: 0.7907 (m-80) cc_final: 0.7498 (m-80) REVERT: H 261 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: I 58 LYS cc_start: 0.7028 (ttpt) cc_final: 0.6405 (tppt) REVERT: I 300 MET cc_start: 0.6395 (tpt) cc_final: 0.6139 (mmm) REVERT: J 1 LEU cc_start: 0.6941 (OUTLIER) cc_final: 0.6602 (tt) REVERT: J 122 LYS cc_start: 0.7624 (tttm) cc_final: 0.7228 (ttmm) REVERT: J 146 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7556 (t0) REVERT: J 152 ASN cc_start: 0.8610 (m-40) cc_final: 0.8350 (m-40) REVERT: J 299 VAL cc_start: 0.8480 (p) cc_final: 0.8251 (t) REVERT: K 46 TYR cc_start: 0.8090 (m-80) cc_final: 0.7285 (m-80) REVERT: K 58 LYS cc_start: 0.8311 (mmtp) cc_final: 0.7825 (mmtp) REVERT: K 114 LYS cc_start: 0.8384 (mttt) cc_final: 0.8111 (mttt) REVERT: K 248 LYS cc_start: 0.5668 (OUTLIER) cc_final: 0.4913 (tmtt) REVERT: K 257 ASN cc_start: 0.6996 (m110) cc_final: 0.6641 (m110) REVERT: K 332 TRP cc_start: 0.7782 (OUTLIER) cc_final: 0.3760 (m-90) REVERT: K 362 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8392 (tm-30) REVERT: L 76 ASP cc_start: 0.7481 (t70) cc_final: 0.7039 (t70) REVERT: L 90 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7317 (t0) REVERT: L 300 MET cc_start: 0.7312 (mtp) cc_final: 0.7013 (ttm) REVERT: O 38 LYS cc_start: 0.8238 (tptm) cc_final: 0.7921 (ttmm) REVERT: O 58 LYS cc_start: 0.8140 (ttpt) cc_final: 0.7534 (mmmm) REVERT: O 81 LYS cc_start: 0.8595 (mppt) cc_final: 0.8313 (mppt) REVERT: O 152 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8662 (m-40) REVERT: O 163 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6507 (pt0) REVERT: P 54 ASP cc_start: 0.6877 (t0) cc_final: 0.6478 (t0) REVERT: P 114 LYS cc_start: 0.7650 (mptt) cc_final: 0.7394 (mptt) REVERT: Q 58 LYS cc_start: 0.7612 (ttmt) cc_final: 0.6956 (ttpp) REVERT: Q 62 GLU cc_start: 0.8401 (mp0) cc_final: 0.7753 (mp0) REVERT: R 58 LYS cc_start: 0.7671 (tptp) cc_final: 0.7092 (ttmm) REVERT: R 259 PHE cc_start: 0.7856 (m-80) cc_final: 0.7476 (m-80) REVERT: R 261 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: R 287 ASP cc_start: 0.7893 (m-30) cc_final: 0.7617 (m-30) outliers start: 138 outliers final: 112 residues processed: 802 average time/residue: 0.2546 time to fit residues: 343.5061 Evaluate side-chains 829 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 702 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 332 TRP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 146 ASN Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 285 CYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 191 ARG Chi-restraints excluded: chain K residue 202 ASN Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 332 TRP Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 TRP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 285 CYS Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain O residue 152 ASN Chi-restraints excluded: chain O residue 158 VAL Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 242 LEU Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 276 GLU Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 188 SER Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 261 GLU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 313 ASN Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 242 optimal weight: 0.8980 chunk 330 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 442 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 537 optimal weight: 0.0770 chunk 68 optimal weight: 0.9980 chunk 431 optimal weight: 6.9990 chunk 289 optimal weight: 0.9990 chunk 399 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN H 81 ASN I 133 ASN ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 152 ASN K 202 ASN ** Q 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.171069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.134633 restraints weight = 48187.969| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.69 r_work: 0.3161 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 43976 Z= 0.105 Angle : 0.510 11.228 59880 Z= 0.267 Chirality : 0.046 0.396 7080 Planarity : 0.004 0.047 7608 Dihedral : 7.376 89.384 6854 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.57 % Allowed : 4.78 % Favored : 94.65 % Rotamer: Outliers : 2.64 % Allowed : 20.71 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.12), residues: 5608 helix: 1.45 (0.14), residues: 1536 sheet: -0.57 (0.15), residues: 1232 loop : -0.68 (0.12), residues: 2840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 183 TYR 0.012 0.001 TYR E 311 PHE 0.014 0.001 PHE E 348 TRP 0.011 0.001 TRP H 84 HIS 0.003 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00249 (43968) covalent geometry : angle 0.50993 (59864) SS BOND : bond 0.00446 ( 8) SS BOND : angle 1.42108 ( 16) hydrogen bonds : bond 0.02607 ( 1774) hydrogen bonds : angle 4.58840 ( 5403) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11216 Ramachandran restraints generated. 5608 Oldfield, 0 Emsley, 5608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 722 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LYS cc_start: 0.7159 (ttpt) cc_final: 0.6475 (tppt) REVERT: A 330 ASN cc_start: 0.6880 (m-40) cc_final: 0.6505 (m-40) REVERT: B 77 ARG cc_start: 0.7201 (mtt180) cc_final: 0.6916 (mmt90) REVERT: B 122 LYS cc_start: 0.7660 (tttm) cc_final: 0.7246 (ttmm) REVERT: B 152 ASN cc_start: 0.8416 (m-40) cc_final: 0.8164 (m-40) REVERT: B 224 LYS cc_start: 0.7440 (mtmm) cc_final: 0.7149 (mtmm) REVERT: B 282 ASP cc_start: 0.8715 (m-30) cc_final: 0.8383 (m-30) REVERT: B 293 ASP cc_start: 0.8453 (t0) cc_final: 0.8204 (t0) REVERT: C 46 TYR cc_start: 0.8109 (m-80) cc_final: 0.7181 (m-80) REVERT: C 58 LYS cc_start: 0.8347 (mmtp) cc_final: 0.7893 (mmtp) REVERT: C 158 VAL cc_start: 0.7424 (t) cc_final: 0.7213 (t) REVERT: C 248 LYS cc_start: 0.5557 (OUTLIER) cc_final: 0.4986 (tmtt) REVERT: C 257 ASN cc_start: 0.6991 (m110) cc_final: 0.6753 (m-40) REVERT: C 332 TRP cc_start: 0.7562 (OUTLIER) cc_final: 0.5048 (m-90) REVERT: C 357 GLU cc_start: 0.8339 (pm20) cc_final: 0.8105 (pm20) REVERT: D 20 ARG cc_start: 0.7765 (mmt90) cc_final: 0.7452 (mmt90) REVERT: D 45 LYS cc_start: 0.8633 (tppt) cc_final: 0.8085 (tttp) REVERT: D 76 ASP cc_start: 0.7506 (t70) cc_final: 0.7010 (t70) REVERT: D 90 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6972 (t70) REVERT: D 276 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7209 (mt-10) REVERT: E 38 LYS cc_start: 0.8286 (tptm) cc_final: 0.7961 (ttmm) REVERT: E 58 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7503 (mmmm) REVERT: E 81 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8035 (mppt) REVERT: E 94 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: E 152 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8691 (m-40) REVERT: E 163 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6499 (pt0) REVERT: F 1 LEU cc_start: 0.5947 (mp) cc_final: 0.5735 (tt) REVERT: F 54 ASP cc_start: 0.6831 (t0) cc_final: 0.6409 (t0) REVERT: F 65 SER cc_start: 0.7426 (p) cc_final: 0.7152 (t) REVERT: F 76 ASP cc_start: 0.6637 (t70) cc_final: 0.6437 (t0) REVERT: F 114 LYS cc_start: 0.7597 (mptt) cc_final: 0.7220 (mmtm) REVERT: F 216 LEU cc_start: 0.7264 (mm) cc_final: 0.7029 (mm) REVERT: G 58 LYS cc_start: 0.7646 (ttmt) cc_final: 0.6975 (ttpp) REVERT: G 62 GLU cc_start: 0.8356 (mp0) cc_final: 0.7747 (mp0) REVERT: H 152 ASN cc_start: 0.8614 (m-40) cc_final: 0.8192 (m110) REVERT: H 172 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6650 (ptt) REVERT: H 259 PHE cc_start: 0.7841 (m-80) cc_final: 0.7450 (m-80) REVERT: H 261 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: I 58 LYS cc_start: 0.7084 (ttpt) cc_final: 0.6400 (tppt) REVERT: I 300 MET cc_start: 0.6292 (tpt) cc_final: 0.6058 (mmm) REVERT: J 1 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6582 (tt) REVERT: J 122 LYS cc_start: 0.7642 (tttm) cc_final: 0.7244 (ttmm) REVERT: J 146 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7482 (t0) REVERT: J 152 ASN cc_start: 0.8595 (m110) cc_final: 0.8301 (m-40) REVERT: J 172 MET cc_start: 0.7611 (ttp) cc_final: 0.7298 (ttm) REVERT: K 46 TYR cc_start: 0.8063 (m-80) cc_final: 0.7251 (m-80) REVERT: K 58 LYS cc_start: 0.8302 (mmtp) cc_final: 0.7822 (mmtp) REVERT: K 114 LYS cc_start: 0.8362 (mttt) cc_final: 0.8132 (mttt) REVERT: K 248 LYS cc_start: 0.5641 (OUTLIER) cc_final: 0.4956 (tmtt) REVERT: K 257 ASN cc_start: 0.6878 (m110) cc_final: 0.6409 (m110) REVERT: K 332 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.3800 (m-90) REVERT: K 362 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: L 76 ASP cc_start: 0.7480 (t70) cc_final: 0.7029 (t70) REVERT: L 90 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7306 (t0) REVERT: L 300 MET cc_start: 0.7305 (mtp) cc_final: 0.7029 (ttm) REVERT: O 38 LYS cc_start: 0.8212 (tptm) cc_final: 0.7920 (ttmm) REVERT: O 58 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7506 (mmmm) REVERT: O 81 LYS cc_start: 0.8532 (mppt) cc_final: 0.8195 (mppt) REVERT: O 94 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7177 (tm-30) REVERT: O 152 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8656 (m-40) REVERT: O 163 GLU cc_start: 0.7535 (mm-30) cc_final: 0.6538 (pt0) REVERT: P 54 ASP cc_start: 0.6868 (t0) cc_final: 0.6476 (t0) REVERT: P 76 ASP cc_start: 0.6574 (t70) cc_final: 0.6365 (t0) REVERT: P 114 LYS cc_start: 0.7615 (mptt) cc_final: 0.7348 (mptt) REVERT: Q 58 LYS cc_start: 0.7597 (ttmt) cc_final: 0.6928 (ttpp) REVERT: Q 62 GLU cc_start: 0.8405 (mp0) cc_final: 0.7754 (mp0) REVERT: R 58 LYS cc_start: 0.7669 (tptp) cc_final: 0.7089 (ttmm) REVERT: R 259 PHE cc_start: 0.7827 (m-80) cc_final: 0.7450 (m-80) REVERT: R 261 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7817 (tm-30) REVERT: R 287 ASP cc_start: 0.7883 (m-30) cc_final: 0.7596 (m-30) outliers start: 123 outliers final: 96 residues processed: 796 average time/residue: 0.2399 time to fit residues: 322.5112 Evaluate side-chains 814 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 702 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 332 TRP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 172 MET Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 84 TRP Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 191 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 241 ASP Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 332 TRP Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 304 MET Chi-restraints excluded: chain E residue 39 SER Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 84 TRP Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain F residue 276 GLU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 289 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 188 SER Chi-restraints excluded: chain G residue 308 VAL Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain H residue 144 ILE Chi-restraints excluded: chain H residue 172 MET Chi-restraints excluded: chain H residue 241 ASP Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 285 CYS Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 133 ASN Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 289 SER Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain J residue 1 LEU Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 146 ASN Chi-restraints excluded: chain J residue 161 LEU Chi-restraints excluded: chain J residue 241 ASP Chi-restraints excluded: chain J residue 285 CYS Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain K residue 30 VAL Chi-restraints excluded: chain K residue 84 TRP Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 158 VAL Chi-restraints excluded: chain K residue 191 ARG Chi-restraints excluded: chain K residue 239 VAL Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 248 LYS Chi-restraints excluded: chain K residue 332 TRP Chi-restraints excluded: chain K residue 343 ASP Chi-restraints excluded: chain K residue 362 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 73 VAL Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 84 TRP Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 60 ILE Chi-restraints excluded: chain O residue 63 THR Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain O residue 152 ASN Chi-restraints excluded: chain O residue 168 VAL Chi-restraints excluded: chain O residue 281 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain P residue 289 SER Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 63 THR Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Q residue 308 VAL Chi-restraints excluded: chain R residue 11 ILE Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 208 THR Chi-restraints excluded: chain R residue 261 GLU Chi-restraints excluded: chain R residue 285 CYS Chi-restraints excluded: chain R residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 273 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 331 optimal weight: 5.9990 chunk 383 optimal weight: 0.9990 chunk 378 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 332 optimal weight: 0.3980 chunk 455 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 146 ASN B 152 ASN H 78 ASN H 81 ASN H 313 ASN ** I 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN P 146 ASN R 81 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.167894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.130405 restraints weight = 48310.160| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.72 r_work: 0.3118 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 43976 Z= 0.159 Angle : 0.554 11.651 59880 Z= 0.290 Chirality : 0.048 0.387 7080 Planarity : 0.004 0.048 7608 Dihedral : 7.690 86.786 6854 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.19 % Favored : 94.26 % Rotamer: Outliers : 3.11 % Allowed : 20.54 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.12), residues: 5608 helix: 1.33 (0.14), residues: 1521 sheet: -0.63 (0.15), residues: 1231 loop : -0.71 (0.12), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 183 TYR 0.022 0.002 TYR G 178 PHE 0.017 0.002 PHE K 64 TRP 0.010 0.001 TRP E 310 HIS 0.004 0.001 HIS G 139 Details of bonding type rmsd covalent geometry : bond 0.00380 (43968) covalent geometry : angle 0.55372 (59864) SS BOND : bond 0.00520 ( 8) SS BOND : angle 1.36973 ( 16) hydrogen bonds : bond 0.03030 ( 1774) hydrogen bonds : angle 4.72132 ( 5403) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12581.23 seconds wall clock time: 216 minutes 26.35 seconds (12986.35 seconds total)