Starting phenix.real_space_refine on Sat Feb 7 10:52:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qr6_53317/02_2026/9qr6_53317.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qr6_53317/02_2026/9qr6_53317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qr6_53317/02_2026/9qr6_53317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qr6_53317/02_2026/9qr6_53317.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qr6_53317/02_2026/9qr6_53317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qr6_53317/02_2026/9qr6_53317.map" } resolution = 3.05 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= 0.002 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 20443 2.51 5 N 5413 2.21 5 O 6121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s 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: 32133 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2675 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2680 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2680 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2680 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2675 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2675 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2675 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 2675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2675 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2676 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2682 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "K" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2680 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2680 Classifications: {'peptide': 350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 337} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 7.38, per 1000 atoms: 0.23 Number of scatterers: 32133 At special positions: 0 Unit cell: (154.635, 145.485, 139.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 6121 8.00 N 5413 7.00 C 20443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.07 Conformation dependent library (CDL) restraints added in 1.4 seconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7584 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 36 sheets defined 40.3% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 20 through 32 Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 114 through 118 removed outlier: 3.562A pdb=" N ARG A 117 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.924A pdb=" N THR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 140 through 147 Processing helix chain 'A' and resid 173 through 192 removed outlier: 7.882A pdb=" N GLY A 179 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 removed outlier: 3.605A pdb=" N VAL A 209 " --> pdb=" O GLN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 222 Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 268 through 283 Processing helix chain 'A' and resid 296 through 302 removed outlier: 4.390A pdb=" N ALA A 300 " --> pdb=" O THR A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 346 Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 20 through 35 removed outlier: 4.345A pdb=" N LYS B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.800A pdb=" N ILE B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 93 " --> pdb=" O ASP B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 88 through 93' Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.856A pdb=" N THR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 140 through 147 Processing helix chain 'B' and resid 173 through 192 removed outlier: 7.827A pdb=" N GLY B 179 " --> pdb=" O ASP B 175 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLU B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 210 removed outlier: 3.611A pdb=" N VAL B 209 " --> pdb=" O GLN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 268 through 283 Processing helix chain 'B' and resid 296 through 303 removed outlier: 4.416A pdb=" N ALA B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 346 Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 88 through 93 Processing helix chain 'C' and resid 114 through 118 removed outlier: 3.521A pdb=" N ARG C 117 " --> pdb=" O PRO C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 removed outlier: 3.786A pdb=" N THR C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'C' and resid 173 through 191 removed outlier: 7.815A pdb=" N GLY C 179 " --> pdb=" O ASP C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 210 removed outlier: 3.543A pdb=" N VAL C 209 " --> pdb=" O GLN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 268 through 283 Processing helix chain 'C' and resid 296 through 302 removed outlier: 4.396A pdb=" N ALA C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 345 Processing helix chain 'D' and resid 2 through 13 removed outlier: 3.520A pdb=" N TYR D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 13 " --> pdb=" O LYS D 9 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 Processing helix chain 'D' and resid 88 through 93 Processing helix chain 'D' and resid 114 through 118 Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.828A pdb=" N THR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 173 through 191 removed outlier: 7.838A pdb=" N GLY D 179 " --> pdb=" O ASP D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 210 removed outlier: 3.566A pdb=" N VAL D 209 " --> pdb=" O GLN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 268 through 283 Processing helix chain 'D' and resid 297 through 303 Processing helix chain 'D' and resid 329 through 345 Processing helix chain 'E' and resid 2 through 13 removed outlier: 3.829A pdb=" N LYS E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 32 Processing helix chain 'E' and resid 88 through 93 Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 121 through 125 removed outlier: 3.826A pdb=" N THR E 124 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 132 Processing helix chain 'E' and resid 140 through 147 Processing helix chain 'E' and resid 173 through 191 removed outlier: 7.828A pdb=" N GLY E 179 " --> pdb=" O ASP E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 210 removed outlier: 3.538A pdb=" N VAL E 209 " --> pdb=" O GLN E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 222 Processing helix chain 'E' and resid 241 through 245 Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 268 through 283 Processing helix chain 'E' and resid 296 through 302 removed outlier: 4.276A pdb=" N ALA E 300 " --> pdb=" O THR E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 346 Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 20 through 32 Processing helix chain 'F' and resid 88 through 93 removed outlier: 3.793A pdb=" N ILE F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU F 93 " --> pdb=" O ASP F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 114 through 118 Processing helix chain 'F' and resid 119 through 124 removed outlier: 3.839A pdb=" N THR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 132 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 173 through 191 removed outlier: 7.839A pdb=" N GLY F 179 " --> pdb=" O ASP F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 222 Processing helix chain 'F' and resid 241 through 245 Processing helix chain 'F' and resid 259 through 263 Processing helix chain 'F' and resid 268 through 283 Processing helix chain 'F' and resid 296 through 302 removed outlier: 4.375A pdb=" N ALA F 300 " --> pdb=" O THR F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 345 Processing helix chain 'F' and resid 346 through 349 Processing helix chain 'G' and resid 2 through 12 Processing helix chain 'G' and resid 20 through 32 Processing helix chain 'G' and resid 88 through 93 removed outlier: 3.824A pdb=" N ILE G 92 " --> pdb=" O TYR G 88 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU G 93 " --> pdb=" O ASP G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 88 through 93' Processing helix chain 'G' and resid 114 through 118 Processing helix chain 'G' and resid 119 through 124 removed outlier: 3.532A pdb=" N THR G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 132 Processing helix chain 'G' and resid 140 through 147 Processing helix chain 'G' and resid 173 through 191 removed outlier: 7.893A pdb=" N GLY G 179 " --> pdb=" O ASP G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 210 removed outlier: 3.588A pdb=" N VAL G 209 " --> pdb=" O GLN G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 222 Processing helix chain 'G' and resid 241 through 245 Processing helix chain 'G' and resid 259 through 263 Processing helix chain 'G' and resid 268 through 283 Processing helix chain 'G' and resid 297 through 302 Processing helix chain 'G' and resid 329 through 346 Processing helix chain 'G' and resid 347 through 349 No H-bonds generated for 'chain 'G' and resid 347 through 349' Processing helix chain 'H' and resid 2 through 13 removed outlier: 3.538A pdb=" N TYR H 6 " --> pdb=" O SER H 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU H 13 " --> pdb=" O LYS H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 35 removed outlier: 4.316A pdb=" N LYS H 33 " --> pdb=" O LYS H 29 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR H 34 " --> pdb=" O GLU H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 114 through 118 Processing helix chain 'H' and resid 119 through 124 removed outlier: 3.879A pdb=" N THR H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 132 Processing helix chain 'H' and resid 140 through 147 Processing helix chain 'H' and resid 173 through 191 removed outlier: 7.895A pdb=" N GLY H 179 " --> pdb=" O ASP H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 210 removed outlier: 3.523A pdb=" N VAL H 209 " --> pdb=" O GLN H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 222 Processing helix chain 'H' and resid 241 through 245 Processing helix chain 'H' and resid 259 through 263 Processing helix chain 'H' and resid 268 through 283 Processing helix chain 'H' and resid 296 through 302 removed outlier: 4.310A pdb=" N ALA H 300 " --> pdb=" O THR H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 345 Processing helix chain 'I' and resid 2 through 13 removed outlier: 3.845A pdb=" N LYS I 12 " --> pdb=" O LYS I 8 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU I 13 " --> pdb=" O LYS I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 32 Processing helix chain 'I' and resid 88 through 93 Processing helix chain 'I' and resid 114 through 118 Processing helix chain 'I' and resid 119 through 124 removed outlier: 3.539A pdb=" N THR I 124 " --> pdb=" O GLU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 132 Processing helix chain 'I' and resid 140 through 147 Processing helix chain 'I' and resid 173 through 191 removed outlier: 7.902A pdb=" N GLY I 179 " --> pdb=" O ASP I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 210 removed outlier: 3.601A pdb=" N VAL I 209 " --> pdb=" O GLN I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 222 Processing helix chain 'I' and resid 259 through 263 Processing helix chain 'I' and resid 268 through 283 Processing helix chain 'I' and resid 297 through 302 Processing helix chain 'I' and resid 329 through 346 Processing helix chain 'I' and resid 347 through 349 No H-bonds generated for 'chain 'I' and resid 347 through 349' Processing helix chain 'J' and resid 2 through 12 Processing helix chain 'J' and resid 20 through 32 Processing helix chain 'J' and resid 88 through 93 Processing helix chain 'J' and resid 114 through 118 Processing helix chain 'J' and resid 119 through 124 removed outlier: 4.026A pdb=" N THR J 124 " --> pdb=" O GLU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 132 Processing helix chain 'J' and resid 140 through 147 Processing helix chain 'J' and resid 173 through 191 removed outlier: 7.847A pdb=" N GLY J 179 " --> pdb=" O ASP J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 210 removed outlier: 3.626A pdb=" N VAL J 209 " --> pdb=" O GLN J 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 222 Processing helix chain 'J' and resid 241 through 245 Processing helix chain 'J' and resid 259 through 263 Processing helix chain 'J' and resid 268 through 283 Processing helix chain 'J' and resid 296 through 303 removed outlier: 4.341A pdb=" N ALA J 300 " --> pdb=" O THR J 296 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU J 303 " --> pdb=" O THR J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 329 through 346 Processing helix chain 'K' and resid 2 through 12 Processing helix chain 'K' and resid 20 through 32 Processing helix chain 'K' and resid 88 through 93 removed outlier: 3.821A pdb=" N ILE K 92 " --> pdb=" O TYR K 88 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU K 93 " --> pdb=" O ASP K 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 88 through 93' Processing helix chain 'K' and resid 114 through 118 Processing helix chain 'K' and resid 119 through 124 Processing helix chain 'K' and resid 128 through 132 Processing helix chain 'K' and resid 140 through 147 Processing helix chain 'K' and resid 173 through 191 removed outlier: 7.810A pdb=" N GLY K 179 " --> pdb=" O ASP K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 210 removed outlier: 3.574A pdb=" N VAL K 209 " --> pdb=" O GLN K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 222 Processing helix chain 'K' and resid 241 through 245 Processing helix chain 'K' and resid 259 through 263 Processing helix chain 'K' and resid 268 through 283 Processing helix chain 'K' and resid 296 through 302 removed outlier: 4.376A pdb=" N ALA K 300 " --> pdb=" O THR K 296 " (cutoff:3.500A) Processing helix chain 'K' and resid 329 through 346 Processing helix chain 'K' and resid 347 through 349 No H-bonds generated for 'chain 'K' and resid 347 through 349' Processing helix chain 'L' and resid 2 through 12 Processing helix chain 'L' and resid 20 through 32 Processing helix chain 'L' and resid 88 through 93 Processing helix chain 'L' and resid 114 through 118 Processing helix chain 'L' and resid 121 through 125 removed outlier: 3.860A pdb=" N THR L 124 " --> pdb=" O GLU L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 132 Processing helix chain 'L' and resid 140 through 147 Processing helix chain 'L' and resid 173 through 191 removed outlier: 7.862A pdb=" N GLY L 179 " --> pdb=" O ASP L 175 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 210 removed outlier: 3.634A pdb=" N VAL L 209 " --> pdb=" O GLN L 206 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 222 Processing helix chain 'L' and resid 259 through 263 Processing helix chain 'L' and resid 268 through 283 Processing helix chain 'L' and resid 297 through 302 Processing helix chain 'L' and resid 329 through 346 Processing helix chain 'L' and resid 347 through 349 No H-bonds generated for 'chain 'L' and resid 347 through 349' Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.713A pdb=" N ILE A 57 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A 202 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE A 59 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR A 204 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 61 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A 56 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE A 227 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET A 58 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU A 229 " --> pdb=" O MET A 58 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A 60 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N VAL A 231 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 10.794A pdb=" N HIS A 62 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 15.265A pdb=" N ILE A 233 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 226 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE A 313 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA A 228 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 315 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP A 230 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ALA A 317 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N THR A 232 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP A 328 " --> pdb=" O PRO A 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.713A pdb=" N ILE A 57 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A 202 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE A 59 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR A 204 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 61 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LYS A 56 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE A 227 " --> pdb=" O LYS A 56 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N MET A 58 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU A 229 " --> pdb=" O MET A 58 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA A 60 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N VAL A 231 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 10.794A pdb=" N HIS A 62 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 15.265A pdb=" N ILE A 233 " --> pdb=" O HIS A 62 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA A 226 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE A 313 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA A 228 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 315 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP A 230 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ALA A 317 " --> pdb=" O ASP A 230 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N THR A 232 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 13.459A pdb=" N THR A 310 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N VAL A 258 " --> pdb=" O THR A 310 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL A 312 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 73 removed outlier: 5.345A pdb=" N LEU A 68 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 84 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N VAL A 70 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR A 82 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TRP A 154 " --> pdb=" O HIS A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.667A pdb=" N LYS B 56 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE B 227 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N MET B 58 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU B 229 " --> pdb=" O MET B 58 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 60 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N VAL B 231 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N HIS B 62 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 15.301A pdb=" N ILE B 233 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA B 226 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE B 313 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA B 228 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL B 315 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP B 230 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ALA B 317 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR B 232 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASP B 328 " --> pdb=" O PRO B 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.667A pdb=" N LYS B 56 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ILE B 227 " --> pdb=" O LYS B 56 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N MET B 58 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU B 229 " --> pdb=" O MET B 58 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA B 60 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N VAL B 231 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 10.721A pdb=" N HIS B 62 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 15.301A pdb=" N ILE B 233 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA B 226 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE B 313 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA B 228 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL B 315 " --> pdb=" O ALA B 228 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ASP B 230 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ALA B 317 " --> pdb=" O ASP B 230 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR B 232 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 13.347A pdb=" N THR B 310 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N VAL B 258 " --> pdb=" O THR B 310 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL B 312 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 73 removed outlier: 5.376A pdb=" N LEU B 68 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B 84 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL B 70 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR B 82 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP B 154 " --> pdb=" O HIS B 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.782A pdb=" N ILE C 57 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL C 202 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE C 59 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N THR C 204 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 61 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LYS C 56 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE C 227 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N MET C 58 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU C 229 " --> pdb=" O MET C 58 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA C 60 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N VAL C 231 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N HIS C 62 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 15.235A pdb=" N ILE C 233 " --> pdb=" O HIS C 62 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA C 226 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE C 313 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ALA C 228 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N VAL C 315 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP C 230 " --> pdb=" O VAL C 315 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA C 317 " --> pdb=" O ASP C 230 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N THR C 232 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 13.387A pdb=" N THR C 310 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N VAL C 258 " --> pdb=" O THR C 310 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N VAL C 312 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 67 through 73 removed outlier: 5.305A pdb=" N LEU C 68 " --> pdb=" O ILE C 84 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE C 84 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL C 70 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR C 82 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N TRP C 154 " --> pdb=" O HIS C 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 162 through 164 Processing sheet with id=AB1, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.625A pdb=" N LYS D 56 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE D 227 " --> pdb=" O LYS D 56 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N MET D 58 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU D 229 " --> pdb=" O MET D 58 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA D 60 " --> pdb=" O LEU D 229 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N VAL D 231 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N HIS D 62 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 15.214A pdb=" N ILE D 233 " --> pdb=" O HIS D 62 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA D 226 " --> pdb=" O GLY D 311 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE D 313 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA D 228 " --> pdb=" O ILE D 313 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL D 315 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP D 230 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA D 317 " --> pdb=" O ASP D 230 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N THR D 232 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 13.474A pdb=" N THR D 310 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N VAL D 258 " --> pdb=" O THR D 310 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL D 312 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 67 through 73 removed outlier: 5.383A pdb=" N LEU D 68 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE D 84 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL D 70 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR D 82 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TRP D 154 " --> pdb=" O HIS D 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 162 through 164 Processing sheet with id=AB4, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.753A pdb=" N ILE E 57 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL E 202 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE E 59 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR E 204 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA E 61 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS E 56 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE E 227 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET E 58 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU E 229 " --> pdb=" O MET E 58 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA E 60 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N VAL E 231 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 10.733A pdb=" N HIS E 62 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 15.186A pdb=" N ILE E 233 " --> pdb=" O HIS E 62 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA E 226 " --> pdb=" O GLY E 311 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE E 313 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA E 228 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL E 315 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP E 230 " --> pdb=" O VAL E 315 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ALA E 317 " --> pdb=" O ASP E 230 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR E 232 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASP E 328 " --> pdb=" O PRO E 316 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.753A pdb=" N ILE E 57 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL E 202 " --> pdb=" O ILE E 57 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE E 59 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR E 204 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA E 61 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS E 56 " --> pdb=" O VAL E 225 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N ILE E 227 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET E 58 " --> pdb=" O ILE E 227 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU E 229 " --> pdb=" O MET E 58 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA E 60 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N VAL E 231 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 10.733A pdb=" N HIS E 62 " --> pdb=" O VAL E 231 " (cutoff:3.500A) removed outlier: 15.186A pdb=" N ILE E 233 " --> pdb=" O HIS E 62 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ALA E 226 " --> pdb=" O GLY E 311 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ILE E 313 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ALA E 228 " --> pdb=" O ILE E 313 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N VAL E 315 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ASP E 230 " --> pdb=" O VAL E 315 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ALA E 317 " --> pdb=" O ASP E 230 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N THR E 232 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 13.387A pdb=" N THR E 310 " --> pdb=" O VAL E 258 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N VAL E 258 " --> pdb=" O THR E 310 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N VAL E 312 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 67 through 73 removed outlier: 5.310A pdb=" N LEU E 68 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE E 84 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL E 70 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N THR E 82 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TRP E 154 " --> pdb=" O HIS E 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.564A pdb=" N LYS F 56 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ILE F 227 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET F 58 " --> pdb=" O ILE F 227 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU F 229 " --> pdb=" O MET F 58 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA F 60 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N VAL F 231 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 10.739A pdb=" N HIS F 62 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 15.284A pdb=" N ILE F 233 " --> pdb=" O HIS F 62 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA F 226 " --> pdb=" O GLY F 311 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE F 313 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA F 228 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL F 315 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP F 230 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ALA F 317 " --> pdb=" O ASP F 230 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N THR F 232 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ASP F 328 " --> pdb=" O PRO F 316 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.564A pdb=" N LYS F 56 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N ILE F 227 " --> pdb=" O LYS F 56 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N MET F 58 " --> pdb=" O ILE F 227 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU F 229 " --> pdb=" O MET F 58 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA F 60 " --> pdb=" O LEU F 229 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N VAL F 231 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 10.739A pdb=" N HIS F 62 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 15.284A pdb=" N ILE F 233 " --> pdb=" O HIS F 62 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA F 226 " --> pdb=" O GLY F 311 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE F 313 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA F 228 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N VAL F 315 " --> pdb=" O ALA F 228 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP F 230 " --> pdb=" O VAL F 315 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ALA F 317 " --> pdb=" O ASP F 230 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N THR F 232 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 13.426A pdb=" N THR F 310 " --> pdb=" O VAL F 258 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL F 258 " --> pdb=" O THR F 310 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL F 312 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 67 through 73 removed outlier: 5.338A pdb=" N LEU F 68 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE F 84 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL F 70 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N THR F 82 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TRP F 154 " --> pdb=" O HIS F 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 37 through 40 removed outlier: 6.755A pdb=" N ILE G 57 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL G 202 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE G 59 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR G 204 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA G 61 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS G 56 " --> pdb=" O VAL G 225 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE G 227 " --> pdb=" O LYS G 56 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N MET G 58 " --> pdb=" O ILE G 227 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU G 229 " --> pdb=" O MET G 58 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA G 60 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N VAL G 231 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N HIS G 62 " --> pdb=" O VAL G 231 " (cutoff:3.500A) removed outlier: 15.251A pdb=" N ILE G 233 " --> pdb=" O HIS G 62 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA G 226 " --> pdb=" O GLY G 311 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE G 313 " --> pdb=" O ALA G 226 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA G 228 " --> pdb=" O ILE G 313 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL G 315 " --> pdb=" O ALA G 228 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP G 230 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA G 317 " --> pdb=" O ASP G 230 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N THR G 232 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ASP G 328 " --> pdb=" O PRO G 316 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 37 through 40 removed outlier: 6.755A pdb=" N ILE G 57 " --> pdb=" O TYR G 200 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL G 202 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE G 59 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR G 204 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ALA G 61 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LYS G 56 " --> pdb=" O VAL G 225 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE G 227 " --> pdb=" O LYS G 56 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N MET G 58 " --> pdb=" O ILE G 227 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU G 229 " --> pdb=" O MET G 58 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA G 60 " --> pdb=" O LEU G 229 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N VAL G 231 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 10.504A pdb=" N HIS G 62 " --> pdb=" O VAL G 231 " (cutoff:3.500A) removed outlier: 15.251A pdb=" N ILE G 233 " --> pdb=" O HIS G 62 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ALA G 226 " --> pdb=" O GLY G 311 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE G 313 " --> pdb=" O ALA G 226 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ALA G 228 " --> pdb=" O ILE G 313 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL G 315 " --> pdb=" O ALA G 228 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP G 230 " --> pdb=" O VAL G 315 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA G 317 " --> pdb=" O ASP G 230 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N THR G 232 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 13.329A pdb=" N THR G 310 " --> pdb=" O VAL G 258 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N VAL G 258 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N VAL G 312 " --> pdb=" O GLY G 256 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 67 through 73 removed outlier: 5.313A pdb=" N LEU G 68 " --> pdb=" O ILE G 84 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE G 84 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL G 70 " --> pdb=" O THR G 82 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR G 82 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N TRP G 154 " --> pdb=" O HIS G 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 37 through 40 removed outlier: 6.183A pdb=" N LYS H 55 " --> pdb=" O GLN H 198 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR H 200 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE H 57 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL H 202 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE H 59 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR H 204 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA H 61 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS H 56 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ILE H 227 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET H 58 " --> pdb=" O ILE H 227 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU H 229 " --> pdb=" O MET H 58 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA H 60 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N VAL H 231 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 10.704A pdb=" N HIS H 62 " --> pdb=" O VAL H 231 " (cutoff:3.500A) removed outlier: 15.432A pdb=" N ILE H 233 " --> pdb=" O HIS H 62 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA H 226 " --> pdb=" O GLY H 311 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE H 313 " --> pdb=" O ALA H 226 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ALA H 228 " --> pdb=" O ILE H 313 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL H 315 " --> pdb=" O ALA H 228 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP H 230 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA H 317 " --> pdb=" O ASP H 230 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N THR H 232 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP H 328 " --> pdb=" O PRO H 316 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 37 through 40 removed outlier: 6.183A pdb=" N LYS H 55 " --> pdb=" O GLN H 198 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR H 200 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE H 57 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL H 202 " --> pdb=" O ILE H 57 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE H 59 " --> pdb=" O VAL H 202 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR H 204 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA H 61 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS H 56 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ILE H 227 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET H 58 " --> pdb=" O ILE H 227 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU H 229 " --> pdb=" O MET H 58 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA H 60 " --> pdb=" O LEU H 229 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N VAL H 231 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 10.704A pdb=" N HIS H 62 " --> pdb=" O VAL H 231 " (cutoff:3.500A) removed outlier: 15.432A pdb=" N ILE H 233 " --> pdb=" O HIS H 62 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA H 226 " --> pdb=" O GLY H 311 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE H 313 " --> pdb=" O ALA H 226 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ALA H 228 " --> pdb=" O ILE H 313 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL H 315 " --> pdb=" O ALA H 228 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP H 230 " --> pdb=" O VAL H 315 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ALA H 317 " --> pdb=" O ASP H 230 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N THR H 232 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 13.462A pdb=" N THR H 310 " --> pdb=" O VAL H 258 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N VAL H 258 " --> pdb=" O THR H 310 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL H 312 " --> pdb=" O GLY H 256 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 67 through 73 removed outlier: 5.278A pdb=" N LEU H 68 " --> pdb=" O ILE H 84 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE H 84 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL H 70 " --> pdb=" O THR H 82 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR H 82 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N TRP H 154 " --> pdb=" O HIS H 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 37 through 40 removed outlier: 6.799A pdb=" N ILE I 57 " --> pdb=" O TYR I 200 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL I 202 " --> pdb=" O ILE I 57 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE I 59 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR I 204 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA I 61 " --> pdb=" O THR I 204 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LYS I 56 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE I 227 " --> pdb=" O LYS I 56 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N MET I 58 " --> pdb=" O ILE I 227 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU I 229 " --> pdb=" O MET I 58 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA I 60 " --> pdb=" O LEU I 229 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N VAL I 231 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 10.671A pdb=" N HIS I 62 " --> pdb=" O VAL I 231 " (cutoff:3.500A) removed outlier: 15.281A pdb=" N ILE I 233 " --> pdb=" O HIS I 62 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA I 226 " --> pdb=" O GLY I 311 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE I 313 " --> pdb=" O ALA I 226 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ALA I 228 " --> pdb=" O ILE I 313 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL I 315 " --> pdb=" O ALA I 228 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP I 230 " --> pdb=" O VAL I 315 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N ALA I 317 " --> pdb=" O ASP I 230 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N THR I 232 " --> pdb=" O ALA I 317 " (cutoff:3.500A) removed outlier: 13.371A pdb=" N THR I 310 " --> pdb=" O VAL I 258 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N VAL I 258 " --> pdb=" O THR I 310 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL I 312 " --> pdb=" O GLY I 256 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 67 through 73 removed outlier: 5.373A pdb=" N LEU I 68 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ILE I 84 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL I 70 " --> pdb=" O THR I 82 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N THR I 82 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N TRP I 154 " --> pdb=" O HIS I 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 162 through 164 Processing sheet with id=AD1, first strand: chain 'J' and resid 37 through 40 removed outlier: 6.714A pdb=" N ILE J 57 " --> pdb=" O TYR J 200 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL J 202 " --> pdb=" O ILE J 57 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE J 59 " --> pdb=" O VAL J 202 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR J 204 " --> pdb=" O ILE J 59 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ALA J 61 " --> pdb=" O THR J 204 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS J 56 " --> pdb=" O VAL J 225 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ILE J 227 " --> pdb=" O LYS J 56 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N MET J 58 " --> pdb=" O ILE J 227 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU J 229 " --> pdb=" O MET J 58 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA J 60 " --> pdb=" O LEU J 229 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N VAL J 231 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 10.798A pdb=" N HIS J 62 " --> pdb=" O VAL J 231 " (cutoff:3.500A) removed outlier: 15.510A pdb=" N ILE J 233 " --> pdb=" O HIS J 62 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA J 226 " --> pdb=" O GLY J 311 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE J 313 " --> pdb=" O ALA J 226 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ALA J 228 " --> pdb=" O ILE J 313 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL J 315 " --> pdb=" O ALA J 228 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ASP J 230 " --> pdb=" O VAL J 315 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA J 317 " --> pdb=" O ASP J 230 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N THR J 232 " --> pdb=" O ALA J 317 " (cutoff:3.500A) removed outlier: 13.361A pdb=" N THR J 310 " --> pdb=" O VAL J 258 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N VAL J 258 " --> pdb=" O THR J 310 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL J 312 " --> pdb=" O GLY J 256 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 67 through 73 removed outlier: 5.358A pdb=" N LEU J 68 " --> pdb=" O ILE J 84 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE J 84 " --> pdb=" O LEU J 68 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL J 70 " --> pdb=" O THR J 82 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR J 82 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP J 154 " --> pdb=" O HIS J 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 162 through 164 Processing sheet with id=AD4, first strand: chain 'K' and resid 37 through 40 removed outlier: 6.718A pdb=" N LYS K 56 " --> pdb=" O VAL K 225 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ILE K 227 " --> pdb=" O LYS K 56 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N MET K 58 " --> pdb=" O ILE K 227 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU K 229 " --> pdb=" O MET K 58 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA K 60 " --> pdb=" O LEU K 229 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N VAL K 231 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N HIS K 62 " --> pdb=" O VAL K 231 " (cutoff:3.500A) removed outlier: 15.104A pdb=" N ILE K 233 " --> pdb=" O HIS K 62 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA K 226 " --> pdb=" O GLY K 311 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE K 313 " --> pdb=" O ALA K 226 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA K 228 " --> pdb=" O ILE K 313 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL K 315 " --> pdb=" O ALA K 228 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP K 230 " --> pdb=" O VAL K 315 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA K 317 " --> pdb=" O ASP K 230 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N THR K 232 " --> pdb=" O ALA K 317 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASP K 328 " --> pdb=" O PRO K 316 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 37 through 40 removed outlier: 6.718A pdb=" N LYS K 56 " --> pdb=" O VAL K 225 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ILE K 227 " --> pdb=" O LYS K 56 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N MET K 58 " --> pdb=" O ILE K 227 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LEU K 229 " --> pdb=" O MET K 58 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA K 60 " --> pdb=" O LEU K 229 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N VAL K 231 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N HIS K 62 " --> pdb=" O VAL K 231 " (cutoff:3.500A) removed outlier: 15.104A pdb=" N ILE K 233 " --> pdb=" O HIS K 62 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA K 226 " --> pdb=" O GLY K 311 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE K 313 " --> pdb=" O ALA K 226 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA K 228 " --> pdb=" O ILE K 313 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N VAL K 315 " --> pdb=" O ALA K 228 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP K 230 " --> pdb=" O VAL K 315 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA K 317 " --> pdb=" O ASP K 230 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N THR K 232 " --> pdb=" O ALA K 317 " (cutoff:3.500A) removed outlier: 13.518A pdb=" N THR K 310 " --> pdb=" O VAL K 258 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N VAL K 258 " --> pdb=" O THR K 310 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL K 312 " --> pdb=" O GLY K 256 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 67 through 73 removed outlier: 5.356A pdb=" N LEU K 68 " --> pdb=" O ILE K 84 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE K 84 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL K 70 " --> pdb=" O THR K 82 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR K 82 " --> pdb=" O VAL K 70 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TRP K 154 " --> pdb=" O HIS K 100 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 37 through 40 removed outlier: 6.684A pdb=" N LYS L 56 " --> pdb=" O VAL L 225 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ILE L 227 " --> pdb=" O LYS L 56 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N MET L 58 " --> pdb=" O ILE L 227 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU L 229 " --> pdb=" O MET L 58 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA L 60 " --> pdb=" O LEU L 229 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N VAL L 231 " --> pdb=" O ALA L 60 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N HIS L 62 " --> pdb=" O VAL L 231 " (cutoff:3.500A) removed outlier: 15.191A pdb=" N ILE L 233 " --> pdb=" O HIS L 62 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA L 226 " --> pdb=" O GLY L 311 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE L 313 " --> pdb=" O ALA L 226 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ALA L 228 " --> pdb=" O ILE L 313 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL L 315 " --> pdb=" O ALA L 228 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP L 230 " --> pdb=" O VAL L 315 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ALA L 317 " --> pdb=" O ASP L 230 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N THR L 232 " --> pdb=" O ALA L 317 " (cutoff:3.500A) removed outlier: 13.438A pdb=" N THR L 310 " --> pdb=" O VAL L 258 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N VAL L 258 " --> pdb=" O THR L 310 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N VAL L 312 " --> pdb=" O GLY L 256 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 67 through 73 removed outlier: 5.385A pdb=" N LEU L 68 " --> pdb=" O ILE L 84 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ILE L 84 " --> pdb=" O LEU L 68 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL L 70 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N THR L 82 " --> pdb=" O VAL L 70 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TRP L 154 " --> pdb=" O HIS L 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 162 through 164 1616 hydrogen bonds defined for protein. 4116 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: 8.53 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10641 1.34 - 1.45: 4059 1.45 - 1.57: 17668 1.57 - 1.69: 0 1.69 - 1.80: 264 Bond restraints: 32632 Sorted by residual: bond pdb=" C ALA H 245 " pdb=" N PRO H 246 " ideal model delta sigma weight residual 1.334 1.309 0.024 8.40e-03 1.42e+04 8.24e+00 bond pdb=" C ALA D 245 " pdb=" N PRO D 246 " ideal model delta sigma weight residual 1.334 1.310 0.024 8.40e-03 1.42e+04 7.84e+00 bond pdb=" C ALA G 245 " pdb=" N PRO G 246 " ideal model delta sigma weight residual 1.334 1.311 0.023 8.40e-03 1.42e+04 7.43e+00 bond pdb=" N TYR A 319 " pdb=" CA TYR A 319 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.45e-02 4.76e+03 4.76e+00 bond pdb=" C THR C 322 " pdb=" N PRO C 323 " ideal model delta sigma weight residual 1.334 1.317 0.017 8.40e-03 1.42e+04 4.12e+00 ... (remaining 32627 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 42454 1.42 - 2.85: 1372 2.85 - 4.27: 163 4.27 - 5.70: 18 5.70 - 7.12: 4 Bond angle restraints: 44011 Sorted by residual: angle pdb=" C ARG E 305 " pdb=" CA ARG E 305 " pdb=" CB ARG E 305 " ideal model delta sigma weight residual 116.54 110.76 5.78 1.15e+00 7.56e-01 2.53e+01 angle pdb=" N GLU E 306 " pdb=" CA GLU E 306 " pdb=" C GLU E 306 " ideal model delta sigma weight residual 113.19 117.66 -4.47 1.19e+00 7.06e-01 1.41e+01 angle pdb=" CA ARG E 305 " pdb=" C ARG E 305 " pdb=" N GLU E 306 " ideal model delta sigma weight residual 119.52 117.07 2.45 7.90e-01 1.60e+00 9.61e+00 angle pdb=" CB LYS E 128 " pdb=" CG LYS E 128 " pdb=" CD LYS E 128 " ideal model delta sigma weight residual 111.30 118.42 -7.12 2.30e+00 1.89e-01 9.58e+00 angle pdb=" N VAL F 209 " pdb=" CA VAL F 209 " pdb=" CB VAL F 209 " ideal model delta sigma weight residual 111.94 108.45 3.49 1.30e+00 5.92e-01 7.21e+00 ... (remaining 44006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 17416 17.77 - 35.54: 1804 35.54 - 53.32: 468 53.32 - 71.09: 106 71.09 - 88.86: 17 Dihedral angle restraints: 19811 sinusoidal: 7919 harmonic: 11892 Sorted by residual: dihedral pdb=" CA LEU J 265 " pdb=" C LEU J 265 " pdb=" N ILE J 266 " pdb=" CA ILE J 266 " ideal model delta harmonic sigma weight residual 180.00 161.88 18.12 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LEU B 265 " pdb=" C LEU B 265 " pdb=" N ILE B 266 " pdb=" CA ILE B 266 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA LEU D 265 " pdb=" C LEU D 265 " pdb=" N ILE D 266 " pdb=" CA ILE D 266 " ideal model delta harmonic sigma weight residual 180.00 162.56 17.44 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 19808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 3206 0.040 - 0.081: 1316 0.081 - 0.121: 508 0.121 - 0.162: 31 0.162 - 0.202: 4 Chirality restraints: 5065 Sorted by residual: chirality pdb=" CA GLU G 208 " pdb=" N GLU G 208 " pdb=" C GLU G 208 " pdb=" CB GLU G 208 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA GLU F 208 " pdb=" N GLU F 208 " pdb=" C GLU F 208 " pdb=" CB GLU F 208 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA GLU E 306 " pdb=" N GLU E 306 " pdb=" C GLU E 306 " pdb=" CB GLU E 306 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.40e-01 ... (remaining 5062 not shown) Planarity restraints: 5647 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN J 347 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C ASN J 347 " -0.028 2.00e-02 2.50e+03 pdb=" O ASN J 347 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN J 348 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 114 " -0.026 5.00e-02 4.00e+02 3.95e-02 2.50e+00 pdb=" N PRO A 115 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 114 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO F 115 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 115 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 115 " -0.022 5.00e-02 4.00e+02 ... (remaining 5644 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 588 2.66 - 3.22: 31405 3.22 - 3.78: 51279 3.78 - 4.34: 70814 4.34 - 4.90: 118977 Nonbonded interactions: 273063 Sorted by model distance: nonbonded pdb=" O ASP F 131 " pdb=" OD1 ASP F 131 " model vdw 2.101 3.040 nonbonded pdb=" OG SER E 191 " pdb=" OE1 GLU E 192 " model vdw 2.119 3.040 nonbonded pdb=" O ASP K 196 " pdb=" OD1 ASP K 196 " model vdw 2.169 3.040 nonbonded pdb=" O PHE H 219 " pdb=" NH1 ARG H 305 " model vdw 2.225 3.120 nonbonded pdb=" N GLU J 192 " pdb=" OE1 GLU J 192 " model vdw 2.230 3.120 ... (remaining 273058 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 124 or (resid 125 and (name N or name CA or name \ C or name O or name CB )) or resid 126 through 350)) selection = (chain 'B' and (resid 1 through 115 or (resid 116 through 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 350)) selection = (chain 'C' and (resid 1 through 115 or (resid 116 through 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 350)) selection = (chain 'D' and (resid 1 through 115 or (resid 116 through 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 350)) selection = (chain 'E' and (resid 1 through 124 or (resid 125 and (name N or name CA or name \ C or name O or name CB )) or resid 126 through 350)) selection = (chain 'F' and (resid 1 through 124 or (resid 125 and (name N or name CA or name \ C or name O or name CB )) or resid 126 through 350)) selection = (chain 'G' and (resid 1 through 124 or (resid 125 and (name N or name CA or name \ C or name O or name CB )) or resid 126 through 350)) selection = (chain 'H' and (resid 1 through 124 or (resid 125 and (name N or name CA or name \ C or name O or name CB )) or resid 126 through 350)) selection = (chain 'I' and (resid 1 through 115 or (resid 116 through 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 350)) selection = (chain 'J' and (resid 1 through 115 or (resid 116 through 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 350)) selection = (chain 'K' and (resid 1 through 115 or (resid 116 through 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 350)) selection = (chain 'L' and (resid 1 through 115 or (resid 116 through 125 and (name N or nam \ e CA or name C or name O or name CB )) or resid 126 through 350)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 32.280 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5181 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 : 0.008 0.047 32632 Z= 0.374 Angle : 0.614 7.119 44011 Z= 0.344 Chirality : 0.048 0.202 5065 Planarity : 0.003 0.039 5647 Dihedral : 15.681 88.862 12227 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.80 % Allowed : 15.94 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.65 (0.13), residues: 4176 helix: 1.98 (0.15), residues: 1212 sheet: 0.14 (0.16), residues: 996 loop : -0.34 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 330 TYR 0.011 0.001 TYR I 200 PHE 0.007 0.001 PHE B 133 TRP 0.013 0.002 TRP C 288 HIS 0.007 0.001 HIS L 62 Details of bonding type rmsd covalent geometry : bond 0.00818 (32632) covalent geometry : angle 0.61437 (44011) hydrogen bonds : bond 0.12748 ( 1528) hydrogen bonds : angle 5.42609 ( 4116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 644 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LYS cc_start: 0.5385 (mttt) cc_final: 0.4957 (mtpp) REVERT: A 29 LYS cc_start: 0.5680 (tttt) cc_final: 0.5417 (ttpp) REVERT: A 96 LYS cc_start: 0.7024 (mttp) cc_final: 0.6466 (mtmm) REVERT: A 160 GLU cc_start: 0.6559 (mt-10) cc_final: 0.5233 (tp30) REVERT: A 232 THR cc_start: 0.7487 (p) cc_final: 0.7113 (t) REVERT: A 241 LYS cc_start: 0.4834 (mttt) cc_final: 0.4576 (tttp) REVERT: B 128 LYS cc_start: 0.4782 (mttp) cc_final: 0.4446 (mmtm) REVERT: C 29 LYS cc_start: 0.5132 (mttt) cc_final: 0.4891 (pttt) REVERT: C 96 LYS cc_start: 0.6618 (mttp) cc_final: 0.6009 (mtmm) REVERT: C 114 PRO cc_start: 0.2425 (Cg_endo) cc_final: 0.2218 (Cg_exo) REVERT: C 160 GLU cc_start: 0.5635 (tt0) cc_final: 0.4492 (tp30) REVERT: C 167 ASN cc_start: 0.5840 (m-40) cc_final: 0.5615 (m-40) REVERT: C 337 GLU cc_start: 0.5014 (mt-10) cc_final: 0.4795 (mt-10) REVERT: D 27 MET cc_start: 0.4690 (mmm) cc_final: 0.4438 (mmm) REVERT: D 40 ILE cc_start: 0.6014 (mt) cc_final: 0.5674 (mm) REVERT: D 49 LYS cc_start: 0.5349 (tttt) cc_final: 0.5070 (ttpp) REVERT: D 160 GLU cc_start: 0.6581 (mt-10) cc_final: 0.5059 (tp30) REVERT: D 211 LEU cc_start: 0.5669 (mt) cc_final: 0.5308 (mt) REVERT: D 241 LYS cc_start: 0.5034 (mttt) cc_final: 0.4719 (mttm) REVERT: D 263 ARG cc_start: 0.4879 (mtt180) cc_final: 0.4500 (mmt90) REVERT: D 270 LYS cc_start: 0.4763 (mtpp) cc_final: 0.4520 (mttt) REVERT: E 1 MET cc_start: 0.1010 (mtp) cc_final: 0.0359 (mmt) REVERT: E 8 LYS cc_start: 0.5144 (mtpp) cc_final: 0.4915 (mtmt) REVERT: E 29 LYS cc_start: 0.5003 (mttt) cc_final: 0.4801 (pttt) REVERT: E 49 LYS cc_start: 0.4605 (tttt) cc_final: 0.4265 (ttpp) REVERT: E 63 MET cc_start: 0.6150 (mtm) cc_final: 0.5919 (mtp) REVERT: E 160 GLU cc_start: 0.5907 (tt0) cc_final: 0.4647 (tp30) REVERT: E 187 MET cc_start: 0.4904 (mmm) cc_final: 0.4635 (mmm) REVERT: E 232 THR cc_start: 0.7098 (p) cc_final: 0.6852 (t) REVERT: E 263 ARG cc_start: 0.4298 (mtm-85) cc_final: 0.3872 (mmm-85) REVERT: E 280 GLU cc_start: 0.4056 (mt-10) cc_final: 0.3801 (mm-30) REVERT: E 337 GLU cc_start: 0.5061 (tt0) cc_final: 0.4858 (mt-10) REVERT: F 39 GLU cc_start: 0.5456 (OUTLIER) cc_final: 0.5106 (pp20) REVERT: F 42 ASN cc_start: 0.5250 (m-40) cc_final: 0.4640 (m-40) REVERT: F 49 LYS cc_start: 0.4522 (tttt) cc_final: 0.4039 (ttpp) REVERT: F 69 MET cc_start: 0.7593 (ttm) cc_final: 0.6977 (ttm) REVERT: F 76 ASN cc_start: 0.5483 (m110) cc_final: 0.4985 (m110) REVERT: F 128 LYS cc_start: 0.5592 (mttp) cc_final: 0.5112 (mmtp) REVERT: F 167 ASN cc_start: 0.5714 (m110) cc_final: 0.5162 (m-40) REVERT: F 330 ARG cc_start: 0.4985 (mtm-85) cc_final: 0.4600 (mtm-85) REVERT: G 1 MET cc_start: 0.0087 (mtm) cc_final: -0.0468 (mmt) REVERT: G 49 LYS cc_start: 0.4509 (tttt) cc_final: 0.4302 (ttpp) REVERT: G 131 ASP cc_start: 0.5493 (m-30) cc_final: 0.5272 (m-30) REVERT: G 147 MET cc_start: 0.5065 (ttm) cc_final: 0.4653 (ttm) REVERT: G 160 GLU cc_start: 0.6394 (mt-10) cc_final: 0.5074 (tp30) REVERT: G 167 ASN cc_start: 0.6038 (m110) cc_final: 0.5679 (m110) REVERT: G 241 LYS cc_start: 0.4802 (mttm) cc_final: 0.4283 (mtmt) REVERT: H 96 LYS cc_start: 0.6423 (mttp) cc_final: 0.5733 (mtmm) REVERT: H 304 THR cc_start: 0.5255 (OUTLIER) cc_final: 0.4851 (p) REVERT: I 29 LYS cc_start: 0.4826 (mttt) cc_final: 0.4519 (tptp) REVERT: I 69 MET cc_start: 0.7074 (ttm) cc_final: 0.6863 (ttm) REVERT: I 96 LYS cc_start: 0.6750 (mttp) cc_final: 0.5776 (mtmm) REVERT: I 160 GLU cc_start: 0.6169 (mt-10) cc_final: 0.4877 (tp30) REVERT: I 232 THR cc_start: 0.7304 (p) cc_final: 0.7089 (t) REVERT: I 263 ARG cc_start: 0.3928 (mmm-85) cc_final: 0.3700 (mmm-85) REVERT: I 330 ARG cc_start: 0.4600 (mtm180) cc_final: 0.4296 (mtm-85) REVERT: I 337 GLU cc_start: 0.5154 (mt-10) cc_final: 0.4876 (mt-10) REVERT: J 1 MET cc_start: 0.0566 (mtp) cc_final: 0.0182 (mmt) REVERT: J 58 MET cc_start: 0.5716 (ttm) cc_final: 0.5498 (ttm) REVERT: J 69 MET cc_start: 0.7178 (ttm) cc_final: 0.6399 (ttm) REVERT: J 96 LYS cc_start: 0.6605 (mttp) cc_final: 0.5978 (mtmm) REVERT: K 27 MET cc_start: 0.4747 (mmm) cc_final: 0.4300 (mmm) REVERT: K 285 ASP cc_start: 0.6307 (p0) cc_final: 0.5924 (m-30) REVERT: K 304 THR cc_start: 0.5496 (OUTLIER) cc_final: 0.4961 (p) REVERT: K 306 GLU cc_start: 0.5227 (mp0) cc_final: 0.4977 (mp0) REVERT: L 1 MET cc_start: 0.0449 (ttm) cc_final: 0.0089 (tpp) REVERT: L 89 ASP cc_start: 0.6641 (m-30) cc_final: 0.6434 (m-30) REVERT: L 96 LYS cc_start: 0.6227 (mttp) cc_final: 0.5518 (mtmm) outliers start: 62 outliers final: 26 residues processed: 698 average time/residue: 0.2378 time to fit residues: 250.7389 Evaluate side-chains 433 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 404 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 343 ILE Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 348 ASN Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 304 THR Chi-restraints excluded: chain H residue 312 VAL Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 304 THR Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain L residue 225 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 167 ASN B 321 HIS C 237 HIS ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 321 HIS F 321 HIS H 167 ASN I 167 ASN ** I 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 321 HIS ** K 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.118204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.101239 restraints weight = 42437.202| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.56 r_work: 0.3001 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32632 Z= 0.182 Angle : 0.588 7.954 44011 Z= 0.318 Chirality : 0.051 0.184 5065 Planarity : 0.004 0.059 5647 Dihedral : 4.761 39.972 4502 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.26 % Allowed : 17.36 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.13), residues: 4176 helix: 1.54 (0.15), residues: 1272 sheet: 0.17 (0.17), residues: 864 loop : -0.50 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 50 TYR 0.014 0.002 TYR I 340 PHE 0.010 0.002 PHE G 157 TRP 0.022 0.003 TRP C 154 HIS 0.007 0.002 HIS L 302 Details of bonding type rmsd covalent geometry : bond 0.00444 (32632) covalent geometry : angle 0.58777 (44011) hydrogen bonds : bond 0.04516 ( 1528) hydrogen bonds : angle 4.85154 ( 4116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 406 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1837 (mtm) cc_final: 0.1576 (mtp) REVERT: A 12 LYS cc_start: 0.7118 (mttt) cc_final: 0.6621 (mtpp) REVERT: A 29 LYS cc_start: 0.7172 (tttt) cc_final: 0.6969 (ttpp) REVERT: A 96 LYS cc_start: 0.7456 (mttp) cc_final: 0.7213 (mtmm) REVERT: A 160 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6676 (tp30) REVERT: A 241 LYS cc_start: 0.5950 (mttt) cc_final: 0.5475 (mmtt) REVERT: A 344 LYS cc_start: 0.6835 (mmmm) cc_final: 0.6593 (mmmt) REVERT: B 160 GLU cc_start: 0.7657 (mt-10) cc_final: 0.6669 (tp30) REVERT: C 12 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6817 (mmmt) REVERT: C 29 LYS cc_start: 0.6959 (mttt) cc_final: 0.6668 (tmmt) REVERT: C 114 PRO cc_start: 0.4272 (Cg_endo) cc_final: 0.3968 (Cg_exo) REVERT: C 160 GLU cc_start: 0.7104 (tt0) cc_final: 0.6110 (tp30) REVERT: C 189 ARG cc_start: 0.7038 (mtt180) cc_final: 0.6483 (mmm-85) REVERT: D 27 MET cc_start: 0.6596 (mmm) cc_final: 0.6377 (mmm) REVERT: D 160 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6562 (tp30) REVERT: D 241 LYS cc_start: 0.6687 (mttt) cc_final: 0.6197 (mttm) REVERT: D 270 LYS cc_start: 0.7440 (mtpp) cc_final: 0.6949 (mttt) REVERT: E 29 LYS cc_start: 0.7217 (mttt) cc_final: 0.6860 (tmmt) REVERT: E 49 LYS cc_start: 0.7264 (tttt) cc_final: 0.6970 (ttpp) REVERT: E 125 LYS cc_start: 0.5897 (tppp) cc_final: 0.5233 (mmmm) REVERT: E 187 MET cc_start: 0.7338 (mmm) cc_final: 0.7132 (mmm) REVERT: E 211 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7320 (mt) REVERT: E 242 LYS cc_start: 0.6934 (tttt) cc_final: 0.6442 (tptm) REVERT: E 280 GLU cc_start: 0.6620 (mt-10) cc_final: 0.5832 (mm-30) REVERT: E 344 LYS cc_start: 0.7063 (mmmm) cc_final: 0.6842 (mmmt) REVERT: F 160 GLU cc_start: 0.7615 (mt-10) cc_final: 0.6762 (tp30) REVERT: F 211 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6773 (mt) REVERT: G 125 LYS cc_start: 0.5786 (mmmm) cc_final: 0.5572 (mmmm) REVERT: G 160 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6979 (tp30) REVERT: H 49 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7157 (ttpt) REVERT: H 68 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8671 (mt) REVERT: H 233 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7794 (mm) REVERT: H 270 LYS cc_start: 0.7541 (mtpp) cc_final: 0.6955 (mttt) REVERT: H 273 ASP cc_start: 0.7091 (m-30) cc_final: 0.6851 (m-30) REVERT: I 29 LYS cc_start: 0.7074 (mttt) cc_final: 0.6743 (tmmt) REVERT: I 49 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7392 (tttp) REVERT: I 96 LYS cc_start: 0.7381 (mttp) cc_final: 0.6903 (mtmm) REVERT: I 160 GLU cc_start: 0.7573 (mt-10) cc_final: 0.6709 (tp30) REVERT: I 162 TYR cc_start: 0.8058 (m-80) cc_final: 0.7809 (m-80) REVERT: I 263 ARG cc_start: 0.6826 (mmm-85) cc_final: 0.6584 (mmm-85) REVERT: I 330 ARG cc_start: 0.6940 (mtm180) cc_final: 0.6449 (mtm-85) REVERT: J 1 MET cc_start: 0.1977 (mtp) cc_final: 0.1074 (mmt) REVERT: J 27 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6430 (mmm) REVERT: J 160 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7070 (tp30) REVERT: J 242 LYS cc_start: 0.6913 (tttt) cc_final: 0.6370 (tptm) REVERT: K 25 GLU cc_start: 0.6873 (pt0) cc_final: 0.6470 (mm-30) REVERT: K 125 LYS cc_start: 0.5848 (mmtt) cc_final: 0.5521 (mmmm) REVERT: K 211 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7299 (mt) REVERT: K 246 PRO cc_start: 0.7729 (Cg_endo) cc_final: 0.7495 (Cg_exo) REVERT: K 306 GLU cc_start: 0.7016 (mp0) cc_final: 0.6488 (mp0) REVERT: L 1 MET cc_start: 0.2163 (ttm) cc_final: 0.1328 (tpp) REVERT: L 29 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7000 (tptp) REVERT: L 89 ASP cc_start: 0.7762 (m-30) cc_final: 0.7470 (m-30) REVERT: L 162 TYR cc_start: 0.7895 (m-80) cc_final: 0.7689 (m-80) outliers start: 78 outliers final: 47 residues processed: 473 average time/residue: 0.2672 time to fit residues: 186.7521 Evaluate side-chains 428 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 372 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain J residue 263 ARG Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 225 VAL Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 263 ARG Chi-restraints excluded: chain K residue 270 LYS Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 197 CYS Chi-restraints excluded: chain L residue 211 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 346 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 247 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.118920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102861 restraints weight = 42719.603| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.42 r_work: 0.3043 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32632 Z= 0.127 Angle : 0.489 7.989 44011 Z= 0.264 Chirality : 0.048 0.159 5065 Planarity : 0.004 0.047 5647 Dihedral : 4.340 34.234 4470 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.61 % Allowed : 17.56 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.52 (0.13), residues: 4176 helix: 1.83 (0.15), residues: 1212 sheet: 0.06 (0.17), residues: 876 loop : -0.37 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 263 TYR 0.011 0.001 TYR H 340 PHE 0.014 0.001 PHE I 26 TRP 0.013 0.002 TRP C 154 HIS 0.006 0.001 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00305 (32632) covalent geometry : angle 0.48895 (44011) hydrogen bonds : bond 0.03847 ( 1528) hydrogen bonds : angle 4.61956 ( 4116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 383 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6731 (tp30) REVERT: A 211 LEU cc_start: 0.7923 (mt) cc_final: 0.7580 (mt) REVERT: A 241 LYS cc_start: 0.6081 (mttt) cc_final: 0.5549 (mmtt) REVERT: A 344 LYS cc_start: 0.6995 (mmmm) cc_final: 0.6666 (mmmt) REVERT: B 160 GLU cc_start: 0.7579 (mt-10) cc_final: 0.6655 (tp30) REVERT: B 270 LYS cc_start: 0.7447 (mtpp) cc_final: 0.6838 (mttt) REVERT: C 29 LYS cc_start: 0.6891 (mttt) cc_final: 0.6663 (tmmt) REVERT: C 160 GLU cc_start: 0.7040 (tt0) cc_final: 0.6193 (tp30) REVERT: C 189 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6512 (mmm-85) REVERT: C 211 LEU cc_start: 0.7527 (mt) cc_final: 0.7280 (mt) REVERT: D 65 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: D 160 GLU cc_start: 0.7619 (mt-10) cc_final: 0.6663 (tp30) REVERT: D 211 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7062 (mt) REVERT: D 241 LYS cc_start: 0.6879 (mttt) cc_final: 0.6564 (mmtt) REVERT: D 263 ARG cc_start: 0.6808 (mmt180) cc_final: 0.6563 (mmt90) REVERT: E 1 MET cc_start: 0.1983 (mtp) cc_final: 0.1368 (tpp) REVERT: E 29 LYS cc_start: 0.7148 (mttt) cc_final: 0.6842 (tmmt) REVERT: E 49 LYS cc_start: 0.7206 (tttt) cc_final: 0.6875 (ttpp) REVERT: E 187 MET cc_start: 0.7346 (mmm) cc_final: 0.7104 (mmm) REVERT: E 242 LYS cc_start: 0.6922 (tttt) cc_final: 0.6586 (tptm) REVERT: E 344 LYS cc_start: 0.7156 (mmmm) cc_final: 0.6853 (mmmt) REVERT: F 160 GLU cc_start: 0.7562 (mt-10) cc_final: 0.6712 (tp30) REVERT: G 65 GLU cc_start: 0.7400 (pt0) cc_final: 0.7180 (pt0) REVERT: G 160 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6798 (tp30) REVERT: H 49 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7093 (ttpt) REVERT: H 270 LYS cc_start: 0.7607 (mtpp) cc_final: 0.6985 (mttt) REVERT: H 330 ARG cc_start: 0.7452 (mtm-85) cc_final: 0.7136 (mtm-85) REVERT: I 29 LYS cc_start: 0.7160 (mttt) cc_final: 0.6868 (tmmt) REVERT: I 92 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7905 (pt) REVERT: I 160 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6720 (tp30) REVERT: I 162 TYR cc_start: 0.8046 (m-80) cc_final: 0.7817 (m-80) REVERT: I 263 ARG cc_start: 0.7042 (mmm-85) cc_final: 0.6780 (mmm-85) REVERT: I 330 ARG cc_start: 0.6982 (mtm180) cc_final: 0.6510 (mtm-85) REVERT: I 344 LYS cc_start: 0.7259 (mmmm) cc_final: 0.6912 (mmmt) REVERT: J 1 MET cc_start: 0.2060 (mtp) cc_final: 0.1095 (mmt) REVERT: J 160 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7082 (tp30) REVERT: J 241 LYS cc_start: 0.6401 (mtpp) cc_final: 0.5626 (mmtt) REVERT: J 242 LYS cc_start: 0.6985 (tttt) cc_final: 0.6466 (tptm) REVERT: K 25 GLU cc_start: 0.6966 (pt0) cc_final: 0.6641 (mm-30) REVERT: K 243 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6830 (pt0) REVERT: L 1 MET cc_start: 0.2097 (ttm) cc_final: 0.1686 (tpp) REVERT: L 29 LYS cc_start: 0.7586 (mtpp) cc_final: 0.7065 (tptp) REVERT: L 89 ASP cc_start: 0.7549 (m-30) cc_final: 0.7156 (m-30) REVERT: L 160 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6730 (tp30) outliers start: 90 outliers final: 49 residues processed: 458 average time/residue: 0.2738 time to fit residues: 186.2763 Evaluate side-chains 421 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 367 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 65 GLU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 197 CYS Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 58 MET Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 243 GLU Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 197 CYS Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 258 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 119 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 409 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 337 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.120128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.104177 restraints weight = 42146.054| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.43 r_work: 0.3032 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32632 Z= 0.163 Angle : 0.544 8.548 44011 Z= 0.293 Chirality : 0.050 0.166 5065 Planarity : 0.004 0.060 5647 Dihedral : 4.548 38.820 4468 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.85 % Allowed : 17.13 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 4176 helix: 1.61 (0.15), residues: 1212 sheet: 0.03 (0.17), residues: 876 loop : -0.52 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 330 TYR 0.010 0.001 TYR C 162 PHE 0.009 0.002 PHE C 157 TRP 0.013 0.002 TRP H 154 HIS 0.007 0.002 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00405 (32632) covalent geometry : angle 0.54368 (44011) hydrogen bonds : bond 0.04268 ( 1528) hydrogen bonds : angle 4.83196 ( 4116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 380 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.7527 (OUTLIER) cc_final: 0.6725 (tttt) REVERT: A 160 GLU cc_start: 0.7656 (mt-10) cc_final: 0.6794 (tp30) REVERT: A 211 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7539 (mt) REVERT: A 241 LYS cc_start: 0.6242 (mttt) cc_final: 0.5930 (mttm) REVERT: A 344 LYS cc_start: 0.7025 (mmmm) cc_final: 0.6705 (mmmt) REVERT: B 160 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6638 (tp30) REVERT: B 270 LYS cc_start: 0.7419 (mtpp) cc_final: 0.6807 (mttt) REVERT: C 1 MET cc_start: 0.1785 (mtm) cc_final: 0.1323 (mtp) REVERT: C 12 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7191 (mmmt) REVERT: C 29 LYS cc_start: 0.6911 (mttt) cc_final: 0.6677 (tmmt) REVERT: C 96 LYS cc_start: 0.7457 (mttp) cc_final: 0.7201 (mtmm) REVERT: C 160 GLU cc_start: 0.7055 (tt0) cc_final: 0.6192 (tp30) REVERT: C 189 ARG cc_start: 0.7067 (mtt180) cc_final: 0.6566 (mmm-85) REVERT: D 160 GLU cc_start: 0.7699 (mt-10) cc_final: 0.6678 (tp30) REVERT: D 211 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7100 (mt) REVERT: D 241 LYS cc_start: 0.6958 (mttt) cc_final: 0.6563 (mmtt) REVERT: E 29 LYS cc_start: 0.7118 (mttt) cc_final: 0.6777 (ttpp) REVERT: E 49 LYS cc_start: 0.7236 (tttt) cc_final: 0.6929 (ttpp) REVERT: E 160 GLU cc_start: 0.7822 (mt-10) cc_final: 0.6843 (tp30) REVERT: E 187 MET cc_start: 0.7357 (mmm) cc_final: 0.7089 (mmm) REVERT: E 242 LYS cc_start: 0.6927 (tttt) cc_final: 0.6642 (tptm) REVERT: E 279 SER cc_start: 0.7963 (OUTLIER) cc_final: 0.7291 (m) REVERT: E 344 LYS cc_start: 0.7205 (mmmm) cc_final: 0.6928 (mmmt) REVERT: F 147 MET cc_start: 0.7656 (mtt) cc_final: 0.7080 (ttm) REVERT: F 160 GLU cc_start: 0.7574 (mt-10) cc_final: 0.6696 (tp30) REVERT: F 211 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6865 (mt) REVERT: G 160 GLU cc_start: 0.7449 (mt-10) cc_final: 0.6782 (tp30) REVERT: G 330 ARG cc_start: 0.7568 (mtm-85) cc_final: 0.7208 (mtm-85) REVERT: H 49 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7021 (tttt) REVERT: H 160 GLU cc_start: 0.6893 (tp30) cc_final: 0.6375 (tp30) REVERT: H 270 LYS cc_start: 0.7577 (mtpp) cc_final: 0.6935 (mttt) REVERT: I 29 LYS cc_start: 0.7217 (mttt) cc_final: 0.6809 (tmmt) REVERT: I 49 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7345 (tttp) REVERT: I 160 GLU cc_start: 0.7672 (mt-10) cc_final: 0.6757 (tp30) REVERT: I 263 ARG cc_start: 0.7071 (mmm-85) cc_final: 0.6778 (mmm-85) REVERT: I 330 ARG cc_start: 0.7044 (mtm180) cc_final: 0.6636 (mtm-85) REVERT: J 160 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7085 (tp30) REVERT: J 241 LYS cc_start: 0.6381 (mtpp) cc_final: 0.5591 (mmtt) REVERT: J 263 ARG cc_start: 0.6900 (OUTLIER) cc_final: 0.6593 (mmt90) REVERT: K 243 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6793 (pt0) REVERT: L 1 MET cc_start: 0.2117 (ttm) cc_final: 0.1642 (tpp) REVERT: L 29 LYS cc_start: 0.7505 (mtpp) cc_final: 0.6977 (tmmt) REVERT: L 89 ASP cc_start: 0.7438 (m-30) cc_final: 0.7139 (m-30) REVERT: L 160 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6846 (tp30) outliers start: 133 outliers final: 83 residues processed: 494 average time/residue: 0.2390 time to fit residues: 176.4821 Evaluate side-chains 463 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 370 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 49 LYS Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain J residue 263 ARG Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 243 GLU Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 197 CYS Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 258 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 245 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 357 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 374 optimal weight: 6.9990 chunk 375 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.116999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.101142 restraints weight = 42787.774| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.42 r_work: 0.3049 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 32632 Z= 0.238 Angle : 0.650 9.108 44011 Z= 0.349 Chirality : 0.054 0.197 5065 Planarity : 0.005 0.056 5647 Dihedral : 4.992 44.540 4468 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.98 % Allowed : 17.56 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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 (0.13), residues: 4176 helix: 1.22 (0.15), residues: 1200 sheet: -0.01 (0.17), residues: 876 loop : -0.87 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 19 TYR 0.012 0.002 TYR B 162 PHE 0.013 0.002 PHE C 157 TRP 0.014 0.003 TRP H 154 HIS 0.009 0.002 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00599 (32632) covalent geometry : angle 0.64983 (44011) hydrogen bonds : bond 0.05114 ( 1528) hydrogen bonds : angle 5.25001 ( 4116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 380 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.6839 (ttpt) REVERT: A 160 GLU cc_start: 0.7695 (mt-10) cc_final: 0.6859 (tp30) REVERT: A 211 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7476 (mt) REVERT: A 330 ARG cc_start: 0.7524 (mtm-85) cc_final: 0.6995 (mtm-85) REVERT: A 344 LYS cc_start: 0.7100 (mmmm) cc_final: 0.6778 (mmmt) REVERT: B 160 GLU cc_start: 0.7589 (mt-10) cc_final: 0.6654 (tp30) REVERT: C 29 LYS cc_start: 0.6913 (mttt) cc_final: 0.6616 (tmmt) REVERT: C 96 LYS cc_start: 0.7479 (mttp) cc_final: 0.7219 (mtmm) REVERT: C 160 GLU cc_start: 0.7013 (tt0) cc_final: 0.6192 (tp30) REVERT: C 189 ARG cc_start: 0.7065 (mtt180) cc_final: 0.6558 (mmm-85) REVERT: D 160 GLU cc_start: 0.7840 (mt-10) cc_final: 0.6867 (tp30) REVERT: D 192 GLU cc_start: 0.5192 (mp0) cc_final: 0.4684 (pm20) REVERT: D 211 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7216 (mt) REVERT: D 241 LYS cc_start: 0.6996 (mttt) cc_final: 0.6701 (mmtt) REVERT: E 1 MET cc_start: 0.2258 (mtp) cc_final: 0.1175 (tpp) REVERT: E 29 LYS cc_start: 0.6841 (mttt) cc_final: 0.6498 (tptp) REVERT: E 49 LYS cc_start: 0.7294 (tttt) cc_final: 0.6918 (ttpp) REVERT: E 68 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8431 (mt) REVERT: E 130 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: E 160 GLU cc_start: 0.7809 (mt-10) cc_final: 0.6921 (tp30) REVERT: E 242 LYS cc_start: 0.7002 (tttt) cc_final: 0.6763 (tptm) REVERT: F 29 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.6988 (tttt) REVERT: F 160 GLU cc_start: 0.7709 (mt-10) cc_final: 0.6900 (tp30) REVERT: G 27 MET cc_start: 0.6935 (OUTLIER) cc_final: 0.6588 (mmm) REVERT: G 160 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6796 (tp30) REVERT: H 49 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7513 (ttmm) REVERT: H 68 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8677 (mt) REVERT: H 160 GLU cc_start: 0.6841 (tp30) cc_final: 0.6316 (tp30) REVERT: H 330 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7084 (mtm-85) REVERT: I 29 LYS cc_start: 0.7322 (mttt) cc_final: 0.6845 (tmmt) REVERT: I 126 ILE cc_start: 0.7584 (OUTLIER) cc_final: 0.7083 (tt) REVERT: I 160 GLU cc_start: 0.7696 (mt-10) cc_final: 0.6822 (tp30) REVERT: I 330 ARG cc_start: 0.7115 (mtm180) cc_final: 0.6829 (mtm-85) REVERT: I 344 LYS cc_start: 0.7362 (mmmm) cc_final: 0.6949 (mmmt) REVERT: J 68 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8543 (mt) REVERT: J 160 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7100 (tp30) REVERT: J 241 LYS cc_start: 0.6551 (mtpp) cc_final: 0.5713 (mmtt) REVERT: J 242 LYS cc_start: 0.7121 (tttt) cc_final: 0.6595 (tptm) REVERT: J 263 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6668 (mmt90) REVERT: K 125 LYS cc_start: 0.5971 (mmtt) cc_final: 0.5733 (tppp) REVERT: L 1 MET cc_start: 0.2106 (ttm) cc_final: 0.1531 (tpp) REVERT: L 29 LYS cc_start: 0.7678 (mtpp) cc_final: 0.7058 (tmmt) REVERT: L 160 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6883 (tp30) REVERT: L 194 ASP cc_start: 0.3816 (OUTLIER) cc_final: 0.3592 (m-30) REVERT: L 337 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6745 (mt-10) outliers start: 172 outliers final: 116 residues processed: 524 average time/residue: 0.2262 time to fit residues: 178.6251 Evaluate side-chains 496 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 367 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 197 CYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 248 ASP Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 42 ASN Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 126 ILE Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 249 LEU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 263 ARG Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 74 ASP Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 263 ARG Chi-restraints excluded: chain K residue 270 LYS Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 65 GLU Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 197 CYS Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 232 THR Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 258 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 148 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 267 optimal weight: 1.9990 chunk 264 optimal weight: 6.9990 chunk 314 optimal weight: 10.0000 chunk 398 optimal weight: 8.9990 chunk 396 optimal weight: 7.9990 chunk 376 optimal weight: 0.8980 chunk 410 optimal weight: 9.9990 chunk 303 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 ASN ** K 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102684 restraints weight = 42513.301| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.43 r_work: 0.3066 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32632 Z= 0.154 Angle : 0.540 9.063 44011 Z= 0.290 Chirality : 0.049 0.165 5065 Planarity : 0.004 0.064 5647 Dihedral : 4.668 39.035 4468 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.23 % Allowed : 19.12 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.01 (0.13), residues: 4176 helix: 1.37 (0.15), residues: 1212 sheet: -0.04 (0.17), residues: 852 loop : -0.75 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 330 TYR 0.012 0.001 TYR I 200 PHE 0.008 0.001 PHE C 157 TRP 0.013 0.002 TRP H 154 HIS 0.007 0.001 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00379 (32632) covalent geometry : angle 0.53963 (44011) hydrogen bonds : bond 0.04207 ( 1528) hydrogen bonds : angle 4.95320 ( 4116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 378 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6751 (ttpt) REVERT: A 160 GLU cc_start: 0.7642 (mt-10) cc_final: 0.6817 (tp30) REVERT: A 211 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7456 (mt) REVERT: A 330 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.6978 (mtm-85) REVERT: A 344 LYS cc_start: 0.7051 (mmmm) cc_final: 0.6724 (mmmt) REVERT: B 68 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8606 (mt) REVERT: B 160 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6692 (tp30) REVERT: B 251 LYS cc_start: 0.7448 (mmtm) cc_final: 0.7134 (mtpp) REVERT: C 1 MET cc_start: 0.1902 (mtm) cc_final: 0.1343 (mtp) REVERT: C 29 LYS cc_start: 0.6824 (mttt) cc_final: 0.6580 (tmmt) REVERT: C 96 LYS cc_start: 0.7484 (mttp) cc_final: 0.7234 (mtmm) REVERT: C 160 GLU cc_start: 0.6915 (tt0) cc_final: 0.6082 (tp30) REVERT: C 189 ARG cc_start: 0.7059 (mtt180) cc_final: 0.6571 (mmm-85) REVERT: D 160 GLU cc_start: 0.7763 (mt-10) cc_final: 0.6794 (tp30) REVERT: D 192 GLU cc_start: 0.5287 (mp0) cc_final: 0.4777 (pm20) REVERT: D 211 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7173 (mt) REVERT: D 241 LYS cc_start: 0.7066 (mttt) cc_final: 0.6602 (mmtm) REVERT: E 1 MET cc_start: 0.1854 (mtp) cc_final: 0.1178 (tpp) REVERT: E 29 LYS cc_start: 0.6856 (mttt) cc_final: 0.6483 (tptp) REVERT: E 49 LYS cc_start: 0.7281 (tttt) cc_final: 0.6947 (ttpp) REVERT: E 68 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8370 (mt) REVERT: E 160 GLU cc_start: 0.7788 (mt-10) cc_final: 0.6884 (tp30) REVERT: E 187 MET cc_start: 0.7348 (mmm) cc_final: 0.7081 (mmm) REVERT: E 192 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.5017 (pm20) REVERT: E 242 LYS cc_start: 0.7015 (tttt) cc_final: 0.6774 (tptm) REVERT: E 344 LYS cc_start: 0.7368 (mmmm) cc_final: 0.7050 (mmmt) REVERT: F 160 GLU cc_start: 0.7561 (mt-10) cc_final: 0.6832 (tp30) REVERT: F 330 ARG cc_start: 0.7075 (mtm-85) cc_final: 0.6844 (mtm-85) REVERT: G 27 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6611 (mmm) REVERT: G 160 GLU cc_start: 0.7487 (mt-10) cc_final: 0.6800 (tp30) REVERT: H 49 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.6980 (tttt) REVERT: H 160 GLU cc_start: 0.6815 (tp30) cc_final: 0.6341 (tp30) REVERT: H 270 LYS cc_start: 0.7605 (mtpp) cc_final: 0.6958 (mttt) REVERT: H 330 ARG cc_start: 0.7301 (mtm-85) cc_final: 0.6897 (mtm-85) REVERT: I 29 LYS cc_start: 0.7299 (mttt) cc_final: 0.6782 (tmmt) REVERT: I 160 GLU cc_start: 0.7690 (mt-10) cc_final: 0.6806 (tp30) REVERT: I 330 ARG cc_start: 0.7171 (mtm180) cc_final: 0.6813 (mtm-85) REVERT: I 344 LYS cc_start: 0.7294 (mmmm) cc_final: 0.6900 (mmmt) REVERT: J 27 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6373 (mmm) REVERT: J 68 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8498 (mt) REVERT: J 160 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7081 (tp30) REVERT: J 241 LYS cc_start: 0.6544 (mtpp) cc_final: 0.5721 (mmtt) REVERT: J 242 LYS cc_start: 0.7134 (tttt) cc_final: 0.6589 (tptm) REVERT: J 263 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.6460 (mmt90) REVERT: K 29 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6853 (tttt) REVERT: K 330 ARG cc_start: 0.7264 (mtm-85) cc_final: 0.7059 (mtm-85) REVERT: L 1 MET cc_start: 0.2039 (ttm) cc_final: 0.1637 (tpp) REVERT: L 29 LYS cc_start: 0.7525 (mtpp) cc_final: 0.6983 (tmmt) REVERT: L 68 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8549 (mt) REVERT: L 160 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6862 (tp30) REVERT: L 194 ASP cc_start: 0.3925 (OUTLIER) cc_final: 0.3705 (m-30) REVERT: L 337 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6845 (mt-10) outliers start: 146 outliers final: 105 residues processed: 502 average time/residue: 0.2308 time to fit residues: 174.0291 Evaluate side-chains 492 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 373 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 263 ARG Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 263 ARG Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 197 CYS Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 263 ARG Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 197 CYS Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 232 THR Chi-restraints excluded: chain L residue 258 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 321 optimal weight: 9.9990 chunk 302 optimal weight: 0.7980 chunk 392 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 356 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 228 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** I 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.105259 restraints weight = 42289.863| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.44 r_work: 0.3066 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32632 Z= 0.136 Angle : 0.513 8.678 44011 Z= 0.276 Chirality : 0.048 0.184 5065 Planarity : 0.004 0.061 5647 Dihedral : 4.517 36.059 4468 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.29 % Allowed : 19.47 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.11 (0.13), residues: 4176 helix: 1.52 (0.15), residues: 1212 sheet: -0.04 (0.17), residues: 852 loop : -0.71 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 330 TYR 0.011 0.001 TYR I 200 PHE 0.006 0.001 PHE C 157 TRP 0.012 0.002 TRP H 154 HIS 0.006 0.001 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00331 (32632) covalent geometry : angle 0.51350 (44011) hydrogen bonds : bond 0.03960 ( 1528) hydrogen bonds : angle 4.84476 ( 4116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 384 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6712 (ttpt) REVERT: A 160 GLU cc_start: 0.7637 (mt-10) cc_final: 0.6798 (tp30) REVERT: A 211 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7501 (mt) REVERT: A 344 LYS cc_start: 0.7053 (mmmm) cc_final: 0.6775 (mmmt) REVERT: B 68 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8590 (mt) REVERT: B 89 ASP cc_start: 0.7320 (m-30) cc_final: 0.6879 (m-30) REVERT: B 160 GLU cc_start: 0.7555 (mt-10) cc_final: 0.6673 (tp30) REVERT: B 249 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7734 (tp) REVERT: B 251 LYS cc_start: 0.7452 (mmtm) cc_final: 0.7042 (mtpp) REVERT: B 270 LYS cc_start: 0.7471 (mtpp) cc_final: 0.6937 (mttt) REVERT: C 1 MET cc_start: 0.1589 (mtm) cc_final: 0.1127 (mtp) REVERT: C 29 LYS cc_start: 0.6877 (mttt) cc_final: 0.6549 (tmmt) REVERT: C 96 LYS cc_start: 0.7484 (mttp) cc_final: 0.7228 (mtmm) REVERT: C 160 GLU cc_start: 0.6897 (tt0) cc_final: 0.6080 (tp30) REVERT: C 189 ARG cc_start: 0.7062 (mtt180) cc_final: 0.6576 (mmm-85) REVERT: D 160 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6758 (tp30) REVERT: D 192 GLU cc_start: 0.5118 (mp0) cc_final: 0.4548 (pm20) REVERT: D 211 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7142 (mt) REVERT: D 241 LYS cc_start: 0.7077 (mttt) cc_final: 0.6613 (mmtm) REVERT: E 1 MET cc_start: 0.1720 (mtp) cc_final: 0.1254 (tpp) REVERT: E 29 LYS cc_start: 0.6858 (mttt) cc_final: 0.6445 (tptp) REVERT: E 49 LYS cc_start: 0.7241 (tttt) cc_final: 0.6901 (ttpp) REVERT: E 68 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8387 (mt) REVERT: E 160 GLU cc_start: 0.7715 (mt-10) cc_final: 0.6890 (tp30) REVERT: E 187 MET cc_start: 0.7348 (mmm) cc_final: 0.7083 (mmm) REVERT: E 242 LYS cc_start: 0.7031 (tttt) cc_final: 0.6770 (tptm) REVERT: E 344 LYS cc_start: 0.7301 (mmmm) cc_final: 0.6984 (mmmt) REVERT: F 29 LYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6921 (tttt) REVERT: F 160 GLU cc_start: 0.7567 (mt-10) cc_final: 0.6842 (tp30) REVERT: G 27 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.6651 (mmm) REVERT: G 160 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6811 (tp30) REVERT: G 330 ARG cc_start: 0.7509 (mtm-85) cc_final: 0.7087 (mtm-85) REVERT: H 49 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.6942 (tttt) REVERT: H 68 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8378 (mt) REVERT: H 160 GLU cc_start: 0.6922 (tp30) cc_final: 0.6446 (tp30) REVERT: H 232 THR cc_start: 0.8604 (OUTLIER) cc_final: 0.8046 (t) REVERT: H 270 LYS cc_start: 0.7577 (mtpp) cc_final: 0.6917 (mttt) REVERT: H 279 SER cc_start: 0.7851 (OUTLIER) cc_final: 0.7314 (m) REVERT: H 330 ARG cc_start: 0.7341 (mtm-85) cc_final: 0.6943 (mtm-85) REVERT: I 29 LYS cc_start: 0.7232 (mttt) cc_final: 0.6698 (tmmt) REVERT: I 160 GLU cc_start: 0.7652 (mt-10) cc_final: 0.6762 (tp30) REVERT: I 330 ARG cc_start: 0.7166 (mtm180) cc_final: 0.6808 (mtm-85) REVERT: I 344 LYS cc_start: 0.7245 (mmmm) cc_final: 0.6859 (mmmt) REVERT: J 27 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.6407 (mmm) REVERT: J 68 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8486 (mt) REVERT: J 130 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6302 (mp0) REVERT: J 160 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7065 (tp30) REVERT: J 241 LYS cc_start: 0.6508 (mtpp) cc_final: 0.5680 (mmtt) REVERT: J 242 LYS cc_start: 0.7095 (tttt) cc_final: 0.6607 (tptp) REVERT: J 263 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6433 (mmt90) REVERT: K 29 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6741 (tttt) REVERT: L 1 MET cc_start: 0.2005 (ttm) cc_final: 0.1569 (tpp) REVERT: L 29 LYS cc_start: 0.7502 (mtpp) cc_final: 0.6978 (tmmt) REVERT: L 68 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8536 (mt) REVERT: L 160 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6835 (tp30) REVERT: L 194 ASP cc_start: 0.3934 (OUTLIER) cc_final: 0.3715 (m-30) outliers start: 148 outliers final: 105 residues processed: 508 average time/residue: 0.2539 time to fit residues: 194.2292 Evaluate side-chains 502 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 378 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain J residue 27 MET Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 263 ARG Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 263 ARG Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 232 THR Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 258 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 117 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 220 optimal weight: 0.0770 chunk 154 optimal weight: 10.0000 chunk 318 optimal weight: 6.9990 chunk 399 optimal weight: 1.9990 chunk 382 optimal weight: 3.9990 chunk 355 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 190 optimal weight: 0.0020 overall best weight: 2.0152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 GLN E 167 ASN F 237 HIS ** I 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.121568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105667 restraints weight = 42361.331| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.45 r_work: 0.3076 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32632 Z= 0.109 Angle : 0.474 8.400 44011 Z= 0.254 Chirality : 0.047 0.158 5065 Planarity : 0.003 0.061 5647 Dihedral : 4.296 32.539 4468 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.77 % Allowed : 20.14 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.27 (0.13), residues: 4176 helix: 1.72 (0.15), residues: 1212 sheet: -0.03 (0.17), residues: 852 loop : -0.62 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 263 TYR 0.013 0.001 TYR B 88 PHE 0.022 0.001 PHE I 26 TRP 0.012 0.002 TRP H 154 HIS 0.006 0.001 HIS F 62 Details of bonding type rmsd covalent geometry : bond 0.00257 (32632) covalent geometry : angle 0.47397 (44011) hydrogen bonds : bond 0.03537 ( 1528) hydrogen bonds : angle 4.66737 ( 4116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 381 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6650 (ttpt) REVERT: A 160 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6747 (tp30) REVERT: A 211 LEU cc_start: 0.7905 (mt) cc_final: 0.7416 (mt) REVERT: A 344 LYS cc_start: 0.7051 (mmmm) cc_final: 0.6789 (mmmt) REVERT: B 68 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8525 (mt) REVERT: B 89 ASP cc_start: 0.7348 (m-30) cc_final: 0.6910 (m-30) REVERT: B 160 GLU cc_start: 0.7532 (mt-10) cc_final: 0.6643 (tp30) REVERT: B 232 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8067 (t) REVERT: B 249 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7693 (tp) REVERT: B 251 LYS cc_start: 0.7610 (mmtm) cc_final: 0.7172 (mtpp) REVERT: B 270 LYS cc_start: 0.7543 (mtpp) cc_final: 0.6985 (mttt) REVERT: C 1 MET cc_start: 0.1604 (mtm) cc_final: 0.1134 (mtp) REVERT: C 29 LYS cc_start: 0.6830 (mttt) cc_final: 0.6539 (tmmt) REVERT: C 96 LYS cc_start: 0.7496 (mttp) cc_final: 0.7213 (mtmm) REVERT: C 160 GLU cc_start: 0.6892 (tt0) cc_final: 0.6071 (tp30) REVERT: C 189 ARG cc_start: 0.7030 (mtt180) cc_final: 0.6556 (mmm-85) REVERT: D 160 GLU cc_start: 0.7700 (mt-10) cc_final: 0.6713 (tp30) REVERT: D 211 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7098 (mt) REVERT: D 241 LYS cc_start: 0.7061 (mttt) cc_final: 0.6591 (mmtm) REVERT: D 270 LYS cc_start: 0.7484 (mtpp) cc_final: 0.7007 (mttt) REVERT: E 1 MET cc_start: 0.1762 (mtp) cc_final: 0.1365 (tpp) REVERT: E 29 LYS cc_start: 0.6956 (mttt) cc_final: 0.6580 (tptp) REVERT: E 49 LYS cc_start: 0.7207 (tttt) cc_final: 0.6859 (ttpp) REVERT: E 68 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8406 (mt) REVERT: E 160 GLU cc_start: 0.7712 (mt-10) cc_final: 0.6883 (tp30) REVERT: E 187 MET cc_start: 0.7283 (mmm) cc_final: 0.7023 (mmm) REVERT: E 193 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5692 (mp0) REVERT: E 242 LYS cc_start: 0.7023 (tttt) cc_final: 0.6745 (tptm) REVERT: E 279 SER cc_start: 0.7992 (OUTLIER) cc_final: 0.7245 (m) REVERT: E 344 LYS cc_start: 0.7195 (mmmm) cc_final: 0.6855 (mmmt) REVERT: F 29 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6968 (tttt) REVERT: F 160 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6813 (tp30) REVERT: G 27 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6668 (mmm) REVERT: G 160 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6798 (tp30) REVERT: H 68 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8396 (mt) REVERT: H 160 GLU cc_start: 0.6933 (tp30) cc_final: 0.6446 (tp30) REVERT: H 232 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8039 (t) REVERT: H 270 LYS cc_start: 0.7566 (mtpp) cc_final: 0.6904 (mttt) REVERT: H 279 SER cc_start: 0.7763 (OUTLIER) cc_final: 0.7265 (m) REVERT: H 330 ARG cc_start: 0.7310 (mtm-85) cc_final: 0.6940 (mtm-85) REVERT: I 29 LYS cc_start: 0.7229 (mttt) cc_final: 0.6736 (tmmt) REVERT: I 160 GLU cc_start: 0.7633 (mt-10) cc_final: 0.6723 (tp30) REVERT: I 330 ARG cc_start: 0.7177 (mtm180) cc_final: 0.6758 (mtm-85) REVERT: J 68 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8476 (mt) REVERT: J 130 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: J 160 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7039 (tp30) REVERT: J 241 LYS cc_start: 0.6498 (mtpp) cc_final: 0.5645 (mmtt) REVERT: J 242 LYS cc_start: 0.7058 (tttt) cc_final: 0.6538 (tptp) REVERT: J 263 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6438 (mmt90) REVERT: L 1 MET cc_start: 0.1915 (ttm) cc_final: 0.1432 (tpp) REVERT: L 29 LYS cc_start: 0.7487 (mtpp) cc_final: 0.6959 (tmmt) REVERT: L 68 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8551 (mt) REVERT: L 160 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6864 (tp30) REVERT: L 194 ASP cc_start: 0.3897 (OUTLIER) cc_final: 0.3694 (m-30) outliers start: 130 outliers final: 93 residues processed: 489 average time/residue: 0.2384 time to fit residues: 174.6872 Evaluate side-chains 488 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 377 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 263 ARG Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 263 ARG Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 232 THR Chi-restraints excluded: chain L residue 258 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 219 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 309 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 375 optimal weight: 2.9990 chunk 311 optimal weight: 7.9990 chunk 288 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 381 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.101452 restraints weight = 42821.354| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.42 r_work: 0.3055 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 32632 Z= 0.237 Angle : 0.642 9.063 44011 Z= 0.344 Chirality : 0.054 0.240 5065 Planarity : 0.005 0.064 5647 Dihedral : 4.943 44.805 4468 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.17 % Allowed : 19.91 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: -0.22 (0.13), residues: 4176 helix: 1.24 (0.15), residues: 1200 sheet: -0.13 (0.17), residues: 852 loop : -0.96 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 330 TYR 0.014 0.002 TYR H 340 PHE 0.013 0.003 PHE C 157 TRP 0.013 0.003 TRP H 154 HIS 0.009 0.002 HIS A 62 Details of bonding type rmsd covalent geometry : bond 0.00598 (32632) covalent geometry : angle 0.64168 (44011) hydrogen bonds : bond 0.05052 ( 1528) hydrogen bonds : angle 5.22351 ( 4116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 376 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.6834 (ttpt) REVERT: A 89 ASP cc_start: 0.7622 (m-30) cc_final: 0.7310 (m-30) REVERT: A 160 GLU cc_start: 0.7696 (mt-10) cc_final: 0.6848 (tp30) REVERT: A 211 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7470 (mt) REVERT: A 344 LYS cc_start: 0.7113 (mmmm) cc_final: 0.6870 (mmmt) REVERT: B 68 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8631 (mt) REVERT: B 89 ASP cc_start: 0.7293 (m-30) cc_final: 0.6823 (m-30) REVERT: B 160 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6710 (tp30) REVERT: C 29 LYS cc_start: 0.6841 (mttt) cc_final: 0.6423 (tmmt) REVERT: C 96 LYS cc_start: 0.7367 (mttp) cc_final: 0.7108 (mtmm) REVERT: C 160 GLU cc_start: 0.7012 (tt0) cc_final: 0.6224 (tp30) REVERT: C 189 ARG cc_start: 0.7105 (mtt180) cc_final: 0.6607 (mmm-85) REVERT: D 160 GLU cc_start: 0.7848 (mt-10) cc_final: 0.6877 (tp30) REVERT: D 192 GLU cc_start: 0.5247 (mp0) cc_final: 0.4704 (pm20) REVERT: D 211 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7172 (mt) REVERT: D 241 LYS cc_start: 0.7162 (mttt) cc_final: 0.6681 (mttm) REVERT: E 1 MET cc_start: 0.2264 (mtp) cc_final: 0.1299 (tpp) REVERT: E 29 LYS cc_start: 0.6950 (mttt) cc_final: 0.6515 (tptp) REVERT: E 49 LYS cc_start: 0.7285 (tttt) cc_final: 0.6878 (ttpp) REVERT: E 68 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8414 (mt) REVERT: E 242 LYS cc_start: 0.7090 (tttt) cc_final: 0.6830 (tptm) REVERT: E 344 LYS cc_start: 0.7336 (mmmm) cc_final: 0.7025 (mmmt) REVERT: F 29 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6942 (tttt) REVERT: F 160 GLU cc_start: 0.7691 (mt-10) cc_final: 0.6877 (tp30) REVERT: G 27 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6618 (mmm) REVERT: G 160 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6814 (tp30) REVERT: H 49 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7512 (ttmm) REVERT: H 160 GLU cc_start: 0.6918 (tp30) cc_final: 0.6436 (tp30) REVERT: H 232 THR cc_start: 0.8596 (OUTLIER) cc_final: 0.8063 (t) REVERT: I 29 LYS cc_start: 0.7167 (mttt) cc_final: 0.6712 (tmmt) REVERT: I 68 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8401 (mt) REVERT: I 160 GLU cc_start: 0.7721 (mt-10) cc_final: 0.6845 (tp30) REVERT: I 330 ARG cc_start: 0.7212 (mtm180) cc_final: 0.6916 (mtm-85) REVERT: J 68 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8541 (mt) REVERT: J 160 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7077 (tp30) REVERT: J 241 LYS cc_start: 0.6563 (mtpp) cc_final: 0.5743 (mmtt) REVERT: J 242 LYS cc_start: 0.7130 (tttt) cc_final: 0.6677 (tptp) REVERT: J 263 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6641 (mmt90) REVERT: L 1 MET cc_start: 0.2065 (ttm) cc_final: 0.1500 (tpp) REVERT: L 29 LYS cc_start: 0.7655 (mtpp) cc_final: 0.7054 (tmmt) REVERT: L 68 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8555 (mt) REVERT: L 194 ASP cc_start: 0.3860 (OUTLIER) cc_final: 0.3630 (m-30) REVERT: L 337 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6768 (mt-10) outliers start: 144 outliers final: 114 residues processed: 497 average time/residue: 0.2609 time to fit residues: 193.8809 Evaluate side-chains 500 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 372 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 197 CYS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 12 LYS Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 197 CYS Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 326 VAL Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 211 LEU Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 224 ASP Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 263 ARG Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 183 LEU Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 263 ARG Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 232 THR Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 258 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 409 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 327 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 387 optimal weight: 7.9990 chunk 356 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 373 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** I 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.120112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.104315 restraints weight = 42691.200| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.42 r_work: 0.3086 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32632 Z= 0.113 Angle : 0.491 8.401 44011 Z= 0.263 Chirality : 0.047 0.209 5065 Planarity : 0.004 0.059 5647 Dihedral : 4.454 34.801 4468 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.51 % Allowed : 20.60 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: 0.10 (0.13), residues: 4176 helix: 1.58 (0.15), residues: 1212 sheet: -0.08 (0.17), residues: 852 loop : -0.75 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 330 TYR 0.013 0.001 TYR H 340 PHE 0.011 0.001 PHE H 81 TRP 0.012 0.002 TRP E 154 HIS 0.006 0.001 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00263 (32632) covalent geometry : angle 0.49109 (44011) hydrogen bonds : bond 0.03712 ( 1528) hydrogen bonds : angle 4.78467 ( 4116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 381 time to evaluate : 1.212 Fit side-chains REVERT: A 49 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6704 (ttpt) REVERT: A 160 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6794 (tp30) REVERT: A 211 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7502 (mt) REVERT: A 344 LYS cc_start: 0.7094 (mmmm) cc_final: 0.6824 (mmmt) REVERT: B 89 ASP cc_start: 0.7219 (m-30) cc_final: 0.6759 (m-30) REVERT: B 160 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6686 (tp30) REVERT: B 251 LYS cc_start: 0.7623 (mmtm) cc_final: 0.7217 (mtpp) REVERT: B 270 LYS cc_start: 0.7553 (mtpp) cc_final: 0.7024 (mttt) REVERT: C 29 LYS cc_start: 0.6868 (mttt) cc_final: 0.6496 (tmmt) REVERT: C 96 LYS cc_start: 0.7447 (mttp) cc_final: 0.7190 (mtmm) REVERT: C 160 GLU cc_start: 0.6892 (tt0) cc_final: 0.6111 (tp30) REVERT: C 189 ARG cc_start: 0.7061 (mtt180) cc_final: 0.6586 (mmm-85) REVERT: D 160 GLU cc_start: 0.7726 (mt-10) cc_final: 0.6765 (tp30) REVERT: D 211 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7121 (mt) REVERT: D 241 LYS cc_start: 0.7172 (mttt) cc_final: 0.6693 (mttm) REVERT: E 1 MET cc_start: 0.1732 (mtp) cc_final: 0.1288 (tpp) REVERT: E 29 LYS cc_start: 0.6905 (mttt) cc_final: 0.6491 (tptp) REVERT: E 49 LYS cc_start: 0.7256 (tttt) cc_final: 0.6920 (ttpp) REVERT: E 68 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8398 (mt) REVERT: E 160 GLU cc_start: 0.7705 (mt-10) cc_final: 0.6919 (tp30) REVERT: E 187 MET cc_start: 0.7290 (mmm) cc_final: 0.7044 (mmm) REVERT: E 193 GLU cc_start: 0.6157 (OUTLIER) cc_final: 0.5824 (mp0) REVERT: E 242 LYS cc_start: 0.7022 (tttt) cc_final: 0.6769 (tptm) REVERT: E 344 LYS cc_start: 0.7225 (mmmm) cc_final: 0.6932 (mmmt) REVERT: F 29 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6920 (tttt) REVERT: F 160 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6825 (tp30) REVERT: F 167 ASN cc_start: 0.6793 (m110) cc_final: 0.6538 (m110) REVERT: G 160 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6831 (tp30) REVERT: H 49 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.6937 (tttt) REVERT: H 160 GLU cc_start: 0.7077 (tp30) cc_final: 0.6490 (tp30) REVERT: H 232 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8008 (t) REVERT: H 270 LYS cc_start: 0.7599 (mtpp) cc_final: 0.6939 (mttt) REVERT: H 279 SER cc_start: 0.7802 (OUTLIER) cc_final: 0.7295 (m) REVERT: I 29 LYS cc_start: 0.7137 (mttt) cc_final: 0.6755 (tmmt) REVERT: I 68 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8385 (mt) REVERT: I 160 GLU cc_start: 0.7664 (mt-10) cc_final: 0.6612 (tp30) REVERT: I 330 ARG cc_start: 0.7166 (mtm180) cc_final: 0.6794 (mtm-85) REVERT: I 344 LYS cc_start: 0.7270 (mmmm) cc_final: 0.6895 (mmmt) REVERT: J 68 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8499 (mt) REVERT: J 160 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7081 (tp30) REVERT: J 241 LYS cc_start: 0.6502 (mtpp) cc_final: 0.5697 (mmtt) REVERT: J 242 LYS cc_start: 0.7100 (tttt) cc_final: 0.6628 (tptp) REVERT: J 263 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.6484 (mmt90) REVERT: L 1 MET cc_start: 0.2017 (ttm) cc_final: 0.1612 (tpp) REVERT: L 29 LYS cc_start: 0.7512 (mtpp) cc_final: 0.6995 (tmmt) REVERT: L 68 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8556 (mt) REVERT: L 194 ASP cc_start: 0.3957 (OUTLIER) cc_final: 0.3732 (m-30) outliers start: 121 outliers final: 102 residues processed: 482 average time/residue: 0.2247 time to fit residues: 162.5987 Evaluate side-chains 489 residues out of total 3552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 373 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 49 LYS Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 325 GLU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain C residue 12 LYS Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 57 ILE Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 220 LYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 68 LEU Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 126 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 193 GLU Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain F residue 29 LYS Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain G residue 12 LYS Chi-restraints excluded: chain G residue 42 ASN Chi-restraints excluded: chain G residue 74 ASP Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 159 SER Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 347 ASN Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 49 LYS Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 74 ASP Chi-restraints excluded: chain H residue 156 SER Chi-restraints excluded: chain H residue 161 VAL Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 258 VAL Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 68 LEU Chi-restraints excluded: chain I residue 74 ASP Chi-restraints excluded: chain I residue 92 ILE Chi-restraints excluded: chain I residue 131 ASP Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 161 VAL Chi-restraints excluded: chain J residue 178 VAL Chi-restraints excluded: chain J residue 232 THR Chi-restraints excluded: chain J residue 243 GLU Chi-restraints excluded: chain J residue 258 VAL Chi-restraints excluded: chain J residue 263 ARG Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 325 GLU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 92 ILE Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 211 LEU Chi-restraints excluded: chain K residue 263 ARG Chi-restraints excluded: chain L residue 68 LEU Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain L residue 92 ILE Chi-restraints excluded: chain L residue 131 ASP Chi-restraints excluded: chain L residue 161 VAL Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 194 ASP Chi-restraints excluded: chain L residue 211 LEU Chi-restraints excluded: chain L residue 232 THR Chi-restraints excluded: chain L residue 249 LEU Chi-restraints excluded: chain L residue 258 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 134 optimal weight: 5.9990 chunk 387 optimal weight: 6.9990 chunk 345 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 320 optimal weight: 4.9990 chunk 392 optimal weight: 6.9990 chunk 158 optimal weight: 8.9990 chunk 267 optimal weight: 5.9990 chunk 361 optimal weight: 2.9990 chunk 370 optimal weight: 0.0970 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN ** C 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 ASN ** K 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.118455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102609 restraints weight = 42742.376| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.43 r_work: 0.3067 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32632 Z= 0.168 Angle : 0.555 8.751 44011 Z= 0.297 Chirality : 0.050 0.275 5065 Planarity : 0.004 0.060 5647 Dihedral : 4.649 39.015 4468 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.65 % Allowed : 20.60 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.30 % 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: -0.04 (0.13), residues: 4176 helix: 1.50 (0.15), residues: 1200 sheet: -0.11 (0.17), residues: 852 loop : -0.87 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 330 TYR 0.015 0.002 TYR E 340 PHE 0.023 0.002 PHE I 26 TRP 0.012 0.002 TRP H 154 HIS 0.007 0.002 HIS K 62 Details of bonding type rmsd covalent geometry : bond 0.00417 (32632) covalent geometry : angle 0.55526 (44011) hydrogen bonds : bond 0.04314 ( 1528) hydrogen bonds : angle 4.96037 ( 4116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7401.51 seconds wall clock time: 127 minutes 48.82 seconds (7668.82 seconds total)