Starting phenix.real_space_refine on Mon Jul 6 11:09:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d73_30600/07_2026/7d73_30600.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d73_30600/07_2026/7d73_30600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7d73_30600/07_2026/7d73_30600.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d73_30600/07_2026/7d73_30600.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7d73_30600/07_2026/7d73_30600.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d73_30600/07_2026/7d73_30600.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d73_30600/07_2026/7d73_30600.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d73_30600/07_2026/7d73_30600.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 219 5.16 5 C 22368 2.51 5 N 6189 2.21 5 O 6482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 354 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35292 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3172 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 31, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "E" Number of atoms: 2785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2785 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 6 Chain: "C" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 3167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3167 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 31, 'TRANS': 374} Chain breaks: 1 Chain: "F" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2714 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 22, 'TRANS': 327} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "G" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "I" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "J" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "K" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2783 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2783 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2789 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 22, 'TRANS': 337} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'GDD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.67, per 1000 atoms: 0.19 Number of scatterers: 35292 At special positions: 0 Unit cell: (132.552, 194.62, 184.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 219 16.00 P 34 15.00 O 6482 8.00 N 6189 7.00 C 22368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS J 289 " - pdb=" SG CYS J 306 " distance=2.03 Simple disulfide: pdb=" SG CYS L 289 " - pdb=" SG CYS L 306 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.3 seconds 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8256 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 79 sheets defined 26.8% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 25 through 28 Processing helix chain 'A' and resid 36 through 47 removed outlier: 4.343A pdb=" N HIS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 77 Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.854A pdb=" N GLY A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.845A pdb=" N LEU A 150 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 151 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 202 removed outlier: 3.974A pdb=" N LEU A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 250 through 269 removed outlier: 4.168A pdb=" N GLN A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ASP A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.275A pdb=" N HIS B 40 " --> pdb=" O MET B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 77 removed outlier: 3.518A pdb=" N ASN B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 98 removed outlier: 4.067A pdb=" N GLY B 94 " --> pdb=" O GLY B 90 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.660A pdb=" N LEU B 150 " --> pdb=" O THR B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 202 removed outlier: 3.925A pdb=" N LEU B 194 " --> pdb=" O ALA B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 252 through 269 removed outlier: 4.138A pdb=" N TYR B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLN B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ASP B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 32 through 41 Processing helix chain 'E' and resid 56 through 72 removed outlier: 3.847A pdb=" N LEU E 60 " --> pdb=" O MET E 56 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 93 removed outlier: 3.632A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 98 Processing helix chain 'E' and resid 116 through 128 removed outlier: 3.861A pdb=" N GLY E 128 " --> pdb=" O HIS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 removed outlier: 3.653A pdb=" N LEU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 204 removed outlier: 3.865A pdb=" N ILE E 200 " --> pdb=" O GLU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 240 removed outlier: 3.724A pdb=" N GLN E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 28 Processing helix chain 'C' and resid 37 through 46 Processing helix chain 'C' and resid 62 through 77 Processing helix chain 'C' and resid 89 through 98 removed outlier: 3.872A pdb=" N GLY C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N LEU C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 122 through 131 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 190 through 203 removed outlier: 3.938A pdb=" N LEU C 194 " --> pdb=" O ALA C 190 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 250 through 268 removed outlier: 4.018A pdb=" N GLN C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ASP C 267 " --> pdb=" O SER C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 18 removed outlier: 3.923A pdb=" N ARG D 16 " --> pdb=" O LYS D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 28 Processing helix chain 'D' and resid 36 through 45 removed outlier: 4.353A pdb=" N HIS D 40 " --> pdb=" O MET D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 Processing helix chain 'D' and resid 89 through 98 removed outlier: 3.955A pdb=" N GLY D 94 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 Processing helix chain 'D' and resid 122 through 134 removed outlier: 3.727A pdb=" N GLN D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.714A pdb=" N LEU D 150 " --> pdb=" O THR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 203 removed outlier: 3.784A pdb=" N LEU D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP D 196 " --> pdb=" O LYS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 226 through 231 Processing helix chain 'D' and resid 252 through 269 removed outlier: 3.994A pdb=" N TYR D 256 " --> pdb=" O GLY D 252 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 20 removed outlier: 3.638A pdb=" N LEU F 19 " --> pdb=" O PRO F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 26 removed outlier: 3.716A pdb=" N VAL F 26 " --> pdb=" O LYS F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 45 Processing helix chain 'F' and resid 56 through 72 removed outlier: 3.856A pdb=" N LEU F 60 " --> pdb=" O MET F 56 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLN F 69 " --> pdb=" O LYS F 65 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ARG F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 93 Processing helix chain 'F' and resid 93 through 98 Processing helix chain 'F' and resid 116 through 128 removed outlier: 3.577A pdb=" N GLN F 122 " --> pdb=" O GLN F 118 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS F 126 " --> pdb=" O GLN F 122 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HIS F 127 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY F 128 " --> pdb=" O HIS F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 205 removed outlier: 3.527A pdb=" N ILE F 200 " --> pdb=" O GLU F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 240 Processing helix chain 'G' and resid 14 through 19 removed outlier: 3.675A pdb=" N THR G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 26 removed outlier: 3.789A pdb=" N VAL G 26 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.607A pdb=" N GLN G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 72 removed outlier: 3.572A pdb=" N LEU G 60 " --> pdb=" O MET G 56 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLN G 69 " --> pdb=" O LYS G 65 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 93 removed outlier: 3.834A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 99 Processing helix chain 'G' and resid 116 through 128 removed outlier: 4.336A pdb=" N HIS G 126 " --> pdb=" O GLN G 122 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS G 127 " --> pdb=" O PHE G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 183 Processing helix chain 'G' and resid 196 through 205 removed outlier: 4.020A pdb=" N LYS G 203 " --> pdb=" O PRO G 199 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU G 204 " --> pdb=" O ILE G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 239 Processing helix chain 'I' and resid 32 through 44 removed outlier: 3.701A pdb=" N GLN I 37 " --> pdb=" O ILE I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 72 removed outlier: 3.768A pdb=" N GLU I 61 " --> pdb=" O SER I 57 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA I 66 " --> pdb=" O LYS I 62 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N GLN I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 93 removed outlier: 4.215A pdb=" N LEU I 90 " --> pdb=" O THR I 86 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 99 removed outlier: 3.522A pdb=" N LEU I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 128 Processing helix chain 'I' and resid 181 through 185 removed outlier: 3.573A pdb=" N GLN I 184 " --> pdb=" O ALA I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 203 Processing helix chain 'I' and resid 221 through 240 removed outlier: 3.600A pdb=" N LEU I 226 " --> pdb=" O PRO I 222 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 26 Processing helix chain 'J' and resid 32 through 45 removed outlier: 3.651A pdb=" N HIS J 36 " --> pdb=" O PRO J 32 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN J 37 " --> pdb=" O ILE J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 72 removed outlier: 3.864A pdb=" N LEU J 60 " --> pdb=" O MET J 56 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS J 62 " --> pdb=" O GLN J 58 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN J 69 " --> pdb=" O LYS J 65 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY J 72 " --> pdb=" O GLU J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 93 removed outlier: 3.634A pdb=" N ALA J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA J 93 " --> pdb=" O PRO J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 98 Processing helix chain 'J' and resid 116 through 128 Processing helix chain 'J' and resid 140 through 144 Processing helix chain 'J' and resid 192 through 197 Processing helix chain 'J' and resid 197 through 205 Processing helix chain 'J' and resid 221 through 240 Processing helix chain 'K' and resid 16 through 21 removed outlier: 4.138A pdb=" N SER K 20 " --> pdb=" O PRO K 16 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR K 21 " --> pdb=" O LEU K 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 16 through 21' Processing helix chain 'K' and resid 22 through 26 removed outlier: 3.564A pdb=" N VAL K 26 " --> pdb=" O LYS K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 45 Processing helix chain 'K' and resid 56 through 71 removed outlier: 3.865A pdb=" N LEU K 60 " --> pdb=" O MET K 56 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN K 69 " --> pdb=" O LYS K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 93 Processing helix chain 'K' and resid 93 through 98 Processing helix chain 'K' and resid 116 through 128 removed outlier: 3.987A pdb=" N HIS K 126 " --> pdb=" O GLN K 122 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS K 127 " --> pdb=" O PHE K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 205 removed outlier: 4.377A pdb=" N ILE K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 240 Processing helix chain 'L' and resid 14 through 19 removed outlier: 3.587A pdb=" N THR L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 25 Processing helix chain 'L' and resid 33 through 45 Processing helix chain 'L' and resid 56 through 72 removed outlier: 3.832A pdb=" N GLU L 63 " --> pdb=" O VAL L 59 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA L 66 " --> pdb=" O LYS L 62 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N GLN L 69 " --> pdb=" O LYS L 65 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 93 Processing helix chain 'L' and resid 116 through 128 removed outlier: 4.087A pdb=" N ARG L 125 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS L 126 " --> pdb=" O GLN L 122 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS L 127 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY L 128 " --> pdb=" O HIS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 186 removed outlier: 3.881A pdb=" N ILE L 186 " --> pdb=" O LEU L 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 205 Processing helix chain 'L' and resid 221 through 239 removed outlier: 3.513A pdb=" N CYS L 230 " --> pdb=" O LEU L 226 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER L 235 " --> pdb=" O LEU L 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 20 removed outlier: 3.635A pdb=" N LEU H 19 " --> pdb=" O PRO H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 25 Processing helix chain 'H' and resid 33 through 45 removed outlier: 3.886A pdb=" N GLN H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 72 removed outlier: 3.843A pdb=" N GLU H 61 " --> pdb=" O SER H 57 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 93 removed outlier: 3.923A pdb=" N ALA H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 98 Processing helix chain 'H' and resid 116 through 128 Processing helix chain 'H' and resid 181 through 186 Processing helix chain 'H' and resid 196 through 204 removed outlier: 3.841A pdb=" N ILE H 200 " --> pdb=" O GLU H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 240 removed outlier: 3.651A pdb=" N LEU H 226 " --> pdb=" O PRO H 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.104A pdb=" N LEU A 2 " --> pdb=" O MET A 50 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 52 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N GLY A 182 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU A 140 " --> pdb=" O CYS A 181 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A 183 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU A 138 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE A 137 " --> pdb=" O TYR A 237 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N HIS A 239 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 139 " --> pdb=" O HIS A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.601A pdb=" N VAL A 34 " --> pdb=" O VAL A 31 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 119 Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 158 removed outlier: 6.710A pdb=" N CYS A 154 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR A 167 " --> pdb=" O CYS A 154 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL A 156 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 163 " --> pdb=" O ASN A 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 282 through 283 removed outlier: 6.597A pdb=" N TRP A 282 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL A 300 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG A 318 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 287 through 289 removed outlier: 6.520A pdb=" N SER A 306 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 386 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE A 403 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 294 through 295 removed outlier: 6.534A pdb=" N LYS A 294 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N THR A 312 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR A 329 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR A 346 " --> pdb=" O ILE A 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 80 through 84 removed outlier: 8.230A pdb=" N ARG B 81 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 53 " --> pdb=" O ARG B 81 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N LEU B 83 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 55 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU B 2 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B 53 " --> pdb=" O LEU B 2 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA B 4 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU B 55 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE B 6 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLY B 57 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS B 3 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LEU B 113 " --> pdb=" O LYS B 3 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 5 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLY B 182 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE B 178 " --> pdb=" O ILE B 155 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N CYS B 154 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR B 167 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 156 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU B 163 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ILE B 236 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 138 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 183 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU B 140 " --> pdb=" O CYS B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.710A pdb=" N VAL B 34 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AB2, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.394A pdb=" N SER B 306 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE B 323 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE B 340 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE B 386 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 403 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 294 through 295 removed outlier: 6.381A pdb=" N LYS B 294 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR B 312 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR B 329 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N THR B 346 " --> pdb=" O ILE B 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 318 through 320 removed outlier: 6.457A pdb=" N ARG B 352 " --> pdb=" O ILE B 399 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 74 through 79 removed outlier: 5.823A pdb=" N ALA E 3 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ALA E 52 " --> pdb=" O ALA E 3 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE E 5 " --> pdb=" O ALA E 52 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LYS E 2 " --> pdb=" O PHE E 105 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU E 107 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU E 4 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY E 174 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU E 134 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET E 175 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N SER E 132 " --> pdb=" O MET E 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 111 through 112 Processing sheet with id=AB7, first strand: chain 'E' and resid 254 through 256 removed outlier: 6.116A pdb=" N SER E 273 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N THR E 290 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 261 through 262 removed outlier: 6.849A pdb=" N ARG E 261 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL E 279 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG E 296 " --> pdb=" O VAL E 314 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG E 313 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE E 331 " --> pdb=" O ILE E 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'E' and resid 267 through 268 removed outlier: 6.804A pdb=" N SER E 267 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ARG E 319 " --> pdb=" O LEU E 338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 325 through 326 removed outlier: 6.774A pdb=" N VAL E 325 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N SER E 342 " --> pdb=" O ILE E 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 80 through 84 removed outlier: 8.624A pdb=" N ARG C 81 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE C 53 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU C 83 " --> pdb=" O ILE C 53 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU C 55 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU C 2 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N LEU C 54 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ALA C 4 " --> pdb=" O LEU C 54 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE C 56 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 6 " --> pdb=" O ILE C 56 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 3 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLY C 182 " --> pdb=" O ASN C 114 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU C 140 " --> pdb=" O CYS C 181 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE C 183 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU C 138 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.680A pdb=" N VAL C 34 " --> pdb=" O VAL C 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 117 through 119 Processing sheet with id=AC5, first strand: chain 'C' and resid 154 through 157 removed outlier: 6.657A pdb=" N CYS C 154 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR C 167 " --> pdb=" O CYS C 154 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL C 156 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 282 through 283 removed outlier: 6.565A pdb=" N TRP C 282 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 300 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ARG C 318 " --> pdb=" O VAL C 336 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS C 335 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG C 352 " --> pdb=" O ILE C 399 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 287 through 288 removed outlier: 6.651A pdb=" N TYR C 288 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER C 306 " --> pdb=" O VAL C 324 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 323 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE C 340 " --> pdb=" O LEU C 387 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 386 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE C 403 " --> pdb=" O ILE C 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 294 through 295 removed outlier: 6.437A pdb=" N LYS C 294 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR C 312 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR C 329 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR C 346 " --> pdb=" O ILE C 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'D' and resid 80 through 84 removed outlier: 8.406A pdb=" N ARG D 81 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE D 53 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU D 83 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU D 55 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU D 2 " --> pdb=" O GLU D 52 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N LEU D 54 " --> pdb=" O LEU D 2 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA D 4 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE D 56 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ILE D 6 " --> pdb=" O ILE D 56 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLY D 182 " --> pdb=" O ASN D 114 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N CYS D 181 " --> pdb=" O THR D 142 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR D 142 " --> pdb=" O CYS D 181 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ILE D 183 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.678A pdb=" N VAL D 34 " --> pdb=" O VAL D 31 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AD3, first strand: chain 'D' and resid 154 through 158 removed outlier: 6.711A pdb=" N CYS D 154 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR D 167 " --> pdb=" O CYS D 154 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL D 156 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU D 163 " --> pdb=" O ASN D 158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 282 through 283 removed outlier: 6.728A pdb=" N TRP D 282 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 300 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG D 318 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG D 352 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 287 through 289 Processing sheet with id=AD6, first strand: chain 'D' and resid 294 through 295 removed outlier: 6.889A pdb=" N LYS D 294 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR D 312 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR D 329 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N THR D 346 " --> pdb=" O ILE D 393 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 323 through 324 removed outlier: 6.740A pdb=" N ILE D 323 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE D 340 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 386 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE D 403 " --> pdb=" O ILE D 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'F' and resid 74 through 79 removed outlier: 6.629A pdb=" N VAL F 49 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N SER F 78 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU F 51 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA F 3 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA F 52 " --> pdb=" O ALA F 3 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE F 5 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LYS F 2 " --> pdb=" O PHE F 105 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N LEU F 107 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU F 4 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU F 134 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N MET F 175 " --> pdb=" O SER F 132 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N SER F 132 " --> pdb=" O MET F 175 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 111 through 113 Processing sheet with id=AE1, first strand: chain 'F' and resid 254 through 256 removed outlier: 6.239A pdb=" N SER F 273 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR F 290 " --> pdb=" O VAL F 308 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE F 307 " --> pdb=" O LEU F 326 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 261 through 262 removed outlier: 6.454A pdb=" N ARG F 261 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL F 279 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG F 296 " --> pdb=" O VAL F 314 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG F 313 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE F 331 " --> pdb=" O ILE F 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 267 through 268 removed outlier: 6.218A pdb=" N CYS F 285 " --> pdb=" O LEU F 303 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TRP F 302 " --> pdb=" O MET F 320 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG F 319 " --> pdb=" O LEU F 338 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 76 through 78 removed outlier: 6.129A pdb=" N VAL G 49 " --> pdb=" O SER G 76 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N SER G 78 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU G 51 " --> pdb=" O SER G 78 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA G 3 " --> pdb=" O ILE G 50 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ALA G 52 " --> pdb=" O ALA G 3 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ILE G 5 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 6 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLY G 174 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU G 134 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N MET G 175 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N SER G 132 " --> pdb=" O MET G 175 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 111 through 112 removed outlier: 3.570A pdb=" N MET G 217 " --> pdb=" O ILE G 112 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 146 through 149 removed outlier: 7.009A pdb=" N VAL G 146 " --> pdb=" O PHE G 159 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE G 159 " --> pdb=" O VAL G 146 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL G 148 " --> pdb=" O HIS G 157 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 254 through 256 removed outlier: 6.504A pdb=" N LEU G 255 " --> pdb=" O LEU G 274 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N SER G 273 " --> pdb=" O VAL G 291 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR G 290 " --> pdb=" O VAL G 308 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE G 307 " --> pdb=" O LEU G 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'G' and resid 261 through 262 removed outlier: 6.367A pdb=" N ARG G 261 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL G 279 " --> pdb=" O ILE G 297 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG G 296 " --> pdb=" O VAL G 314 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG G 313 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE G 331 " --> pdb=" O ILE G 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'G' and resid 267 through 268 removed outlier: 6.582A pdb=" N SER G 267 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ARG G 319 " --> pdb=" O LEU G 338 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 342 through 343 removed outlier: 6.786A pdb=" N SER G 342 " --> pdb=" O ILE G 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'I' and resid 74 through 75 removed outlier: 7.580A pdb=" N SER I 78 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU I 51 " --> pdb=" O SER I 78 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 74 through 75 removed outlier: 6.905A pdb=" N HIS I 48 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU I 4 " --> pdb=" O HIS I 48 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE I 50 " --> pdb=" O LEU I 4 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU I 6 " --> pdb=" O ILE I 50 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA I 52 " --> pdb=" O LEU I 6 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS I 2 " --> pdb=" O PHE I 105 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LEU I 107 " --> pdb=" O LYS I 2 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU I 4 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N GLY I 174 " --> pdb=" O ASN I 108 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU I 134 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET I 175 " --> pdb=" O SER I 132 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER I 132 " --> pdb=" O MET I 175 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 111 through 113 Processing sheet with id=AF5, first strand: chain 'I' and resid 146 through 147 Processing sheet with id=AF6, first strand: chain 'I' and resid 254 through 255 removed outlier: 6.363A pdb=" N SER I 273 " --> pdb=" O VAL I 291 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR I 290 " --> pdb=" O VAL I 308 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE I 307 " --> pdb=" O LEU I 326 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL I 325 " --> pdb=" O VAL I 343 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER I 342 " --> pdb=" O ILE I 359 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 261 through 262 removed outlier: 6.757A pdb=" N ARG I 261 " --> pdb=" O VAL I 280 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL I 279 " --> pdb=" O ILE I 297 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG I 296 " --> pdb=" O VAL I 314 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG I 313 " --> pdb=" O VAL I 332 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE I 331 " --> pdb=" O ILE I 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'I' and resid 285 through 287 removed outlier: 6.448A pdb=" N TRP I 302 " --> pdb=" O MET I 320 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG I 319 " --> pdb=" O LEU I 338 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 74 through 77 removed outlier: 6.198A pdb=" N VAL J 49 " --> pdb=" O SER J 76 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA J 3 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA J 52 " --> pdb=" O ALA J 3 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE J 5 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY J 174 " --> pdb=" O ASN J 108 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS J 170 " --> pdb=" O VAL J 147 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL J 146 " --> pdb=" O PHE J 159 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N PHE J 159 " --> pdb=" O VAL J 146 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL J 148 " --> pdb=" O HIS J 157 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 74 through 77 removed outlier: 6.198A pdb=" N VAL J 49 " --> pdb=" O SER J 76 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ALA J 3 " --> pdb=" O ILE J 50 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA J 52 " --> pdb=" O ALA J 3 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE J 5 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY J 174 " --> pdb=" O ASN J 108 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ALA J 173 " --> pdb=" O THR J 136 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR J 136 " --> pdb=" O ALA J 173 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N MET J 175 " --> pdb=" O LEU J 134 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 111 through 112 Processing sheet with id=AG3, first strand: chain 'J' and resid 254 through 256 removed outlier: 6.645A pdb=" N LEU J 255 " --> pdb=" O LEU J 274 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N SER J 273 " --> pdb=" O VAL J 291 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR J 290 " --> pdb=" O VAL J 308 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL J 325 " --> pdb=" O VAL J 343 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N SER J 342 " --> pdb=" O ILE J 359 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 261 through 262 removed outlier: 6.754A pdb=" N ARG J 261 " --> pdb=" O VAL J 280 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL J 279 " --> pdb=" O ILE J 297 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG J 296 " --> pdb=" O VAL J 314 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG J 313 " --> pdb=" O VAL J 332 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE J 331 " --> pdb=" O ILE J 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'J' and resid 285 through 287 removed outlier: 6.232A pdb=" N TRP J 302 " --> pdb=" O MET J 320 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ARG J 319 " --> pdb=" O LEU J 338 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 74 through 79 removed outlier: 6.358A pdb=" N VAL K 49 " --> pdb=" O SER K 76 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N SER K 78 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU K 51 " --> pdb=" O SER K 78 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE K 5 " --> pdb=" O ILE K 50 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE K 105 " --> pdb=" O LYS K 2 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU K 134 " --> pdb=" O ALA K 173 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET K 175 " --> pdb=" O SER K 132 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER K 132 " --> pdb=" O MET K 175 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N GLY K 131 " --> pdb=" O TYR K 208 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N MET K 210 " --> pdb=" O GLY K 131 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE K 133 " --> pdb=" O MET K 210 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 111 through 113 Processing sheet with id=AG8, first strand: chain 'K' and resid 147 through 149 removed outlier: 3.569A pdb=" N ARG K 158 " --> pdb=" O VAL K 148 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 261 through 262 removed outlier: 6.452A pdb=" N ARG K 261 " --> pdb=" O VAL K 280 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL K 279 " --> pdb=" O ILE K 297 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ARG K 296 " --> pdb=" O VAL K 314 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ARG K 313 " --> pdb=" O VAL K 332 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE K 331 " --> pdb=" O ILE K 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'K' and resid 267 through 268 removed outlier: 6.769A pdb=" N SER K 267 " --> pdb=" O ILE K 286 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N CYS K 285 " --> pdb=" O LEU K 303 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG K 319 " --> pdb=" O LEU K 338 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 273 through 274 removed outlier: 6.437A pdb=" N SER K 273 " --> pdb=" O VAL K 291 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR K 290 " --> pdb=" O VAL K 308 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE K 307 " --> pdb=" O LEU K 326 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL K 325 " --> pdb=" O VAL K 343 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 74 through 79 removed outlier: 5.846A pdb=" N VAL L 49 " --> pdb=" O SER L 76 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER L 78 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU L 51 " --> pdb=" O SER L 78 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA L 3 " --> pdb=" O ILE L 50 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA L 52 " --> pdb=" O ALA L 3 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE L 5 " --> pdb=" O ALA L 52 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ALA L 173 " --> pdb=" O THR L 136 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR L 136 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET L 175 " --> pdb=" O LEU L 134 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET L 210 " --> pdb=" O ILE L 133 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL L 135 " --> pdb=" O MET L 210 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 27 through 28 Processing sheet with id=AH5, first strand: chain 'L' and resid 111 through 113 Processing sheet with id=AH6, first strand: chain 'L' and resid 254 through 256 removed outlier: 6.359A pdb=" N SER L 273 " --> pdb=" O VAL L 291 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS L 285 " --> pdb=" O LEU L 303 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N SER L 305 " --> pdb=" O CYS L 285 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N ARG L 287 " --> pdb=" O SER L 305 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE L 307 " --> pdb=" O ARG L 287 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N CYS L 289 " --> pdb=" O ILE L 307 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TRP L 302 " --> pdb=" O MET L 320 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG L 319 " --> pdb=" O LEU L 338 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 267 through 268 removed outlier: 6.620A pdb=" N SER L 267 " --> pdb=" O ILE L 286 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG L 288 " --> pdb=" O SER L 267 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N CYS L 285 " --> pdb=" O LEU L 303 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N SER L 305 " --> pdb=" O CYS L 285 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N ARG L 287 " --> pdb=" O SER L 305 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE L 307 " --> pdb=" O ARG L 287 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N CYS L 289 " --> pdb=" O ILE L 307 " (cutoff:3.500A) removed outlier: 9.775A pdb=" N THR L 324 " --> pdb=" O LEU L 303 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N SER L 305 " --> pdb=" O THR L 324 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LEU L 326 " --> pdb=" O SER L 305 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE L 307 " --> pdb=" O LEU L 326 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL L 325 " --> pdb=" O VAL L 343 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N SER L 342 " --> pdb=" O ILE L 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'L' and resid 261 through 262 removed outlier: 6.601A pdb=" N ARG L 261 " --> pdb=" O VAL L 280 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL L 279 " --> pdb=" O ILE L 297 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG L 296 " --> pdb=" O VAL L 314 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG L 313 " --> pdb=" O VAL L 332 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'H' and resid 74 through 79 removed outlier: 3.518A pdb=" N SER H 76 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU H 51 " --> pdb=" O SER H 76 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL H 53 " --> pdb=" O SER H 78 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY H 174 " --> pdb=" O ASN H 108 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU H 134 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N MET H 175 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER H 132 " --> pdb=" O MET H 175 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY H 131 " --> pdb=" O TYR H 208 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N MET H 210 " --> pdb=" O GLY H 131 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE H 133 " --> pdb=" O MET H 210 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'H' and resid 27 through 28 removed outlier: 3.758A pdb=" N LYS H 31 " --> pdb=" O PHE H 28 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 111 through 113 Processing sheet with id=AI3, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.671A pdb=" N ARG H 158 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 254 through 256 removed outlier: 6.133A pdb=" N SER H 273 " --> pdb=" O VAL H 291 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR H 290 " --> pdb=" O VAL H 308 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 261 through 262 removed outlier: 6.420A pdb=" N ARG H 261 " --> pdb=" O VAL H 280 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL H 279 " --> pdb=" O ILE H 297 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG H 296 " --> pdb=" O VAL H 314 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG H 313 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE H 331 " --> pdb=" O ILE H 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'H' and resid 267 through 268 removed outlier: 6.429A pdb=" N CYS H 285 " --> pdb=" O LEU H 303 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP H 302 " --> pdb=" O MET H 320 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG H 319 " --> pdb=" O LEU H 338 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 325 through 326 removed outlier: 6.756A pdb=" N VAL H 325 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER H 342 " --> pdb=" O ILE H 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 947 hydrogen bonds defined for protein. 2688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.32 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8433 1.33 - 1.45: 7263 1.45 - 1.57: 19957 1.57 - 1.70: 92 1.70 - 1.82: 335 Bond restraints: 36080 Sorted by residual: bond pdb=" O2A GDD A 501 " pdb=" PA GDD A 501 " ideal model delta sigma weight residual 1.496 1.606 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" O2B GDD C 501 " pdb=" PB GDD C 501 " ideal model delta sigma weight residual 1.496 1.605 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" O2A GDD C 501 " pdb=" PA GDD C 501 " ideal model delta sigma weight residual 1.496 1.604 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O2G GTP B 501 " pdb=" PG GTP B 501 " ideal model delta sigma weight residual 1.510 1.616 -0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" O2A GTP H 401 " pdb=" PA GTP H 401 " ideal model delta sigma weight residual 1.510 1.616 -0.106 2.00e-02 2.50e+03 2.81e+01 ... (remaining 36075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 48239 3.89 - 7.78: 686 7.78 - 11.67: 122 11.67 - 15.56: 14 15.56 - 19.45: 2 Bond angle restraints: 49063 Sorted by residual: angle pdb=" N VAL E 160 " pdb=" CA VAL E 160 " pdb=" C VAL E 160 " ideal model delta sigma weight residual 108.84 124.50 -15.66 1.32e+00 5.74e-01 1.41e+02 angle pdb=" C LYS L 31 " pdb=" N PRO L 32 " pdb=" CA PRO L 32 " ideal model delta sigma weight residual 119.78 108.27 11.51 1.03e+00 9.43e-01 1.25e+02 angle pdb=" N ARG C 16 " pdb=" CA ARG C 16 " pdb=" C ARG C 16 " ideal model delta sigma weight residual 111.36 123.45 -12.09 1.09e+00 8.42e-01 1.23e+02 angle pdb=" N GLN K 164 " pdb=" CA GLN K 164 " pdb=" C GLN K 164 " ideal model delta sigma weight residual 110.80 91.35 19.45 2.13e+00 2.20e-01 8.34e+01 angle pdb=" N ARG B 18 " pdb=" CA ARG B 18 " pdb=" C ARG B 18 " ideal model delta sigma weight residual 113.16 125.74 -12.58 1.42e+00 4.96e-01 7.85e+01 ... (remaining 49058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 20650 35.89 - 71.77: 995 71.77 - 107.66: 82 107.66 - 143.54: 9 143.54 - 179.43: 7 Dihedral angle restraints: 21743 sinusoidal: 8917 harmonic: 12826 Sorted by residual: dihedral pdb=" C8 GTP D 501 " pdb=" C1' GTP D 501 " pdb=" N9 GTP D 501 " pdb=" O4' GTP D 501 " ideal model delta sinusoidal sigma weight residual 104.59 -74.83 179.43 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C4' GTP H 401 " pdb=" C5' GTP H 401 " pdb=" O5' GTP H 401 " pdb=" PA GTP H 401 " ideal model delta sinusoidal sigma weight residual 260.87 88.81 172.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP B 501 " pdb=" C1' GTP B 501 " pdb=" N9 GTP B 501 " pdb=" O4' GTP B 501 " ideal model delta sinusoidal sigma weight residual 104.59 -54.13 158.73 1 2.00e+01 2.50e-03 4.64e+01 ... (remaining 21740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4791 0.106 - 0.211: 685 0.211 - 0.317: 56 0.317 - 0.422: 12 0.422 - 0.528: 5 Chirality restraints: 5549 Sorted by residual: chirality pdb=" CA ASN D 361 " pdb=" N ASN D 361 " pdb=" C ASN D 361 " pdb=" CB ASN D 361 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.97e+00 chirality pdb=" CA ARG B 18 " pdb=" N ARG B 18 " pdb=" C ARG B 18 " pdb=" CB ARG B 18 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.59e+00 chirality pdb=" CA ARG C 16 " pdb=" N ARG C 16 " pdb=" C ARG C 16 " pdb=" CB ARG C 16 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.00e+00 ... (remaining 5546 not shown) Planarity restraints: 6308 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP D 282 " -0.022 2.00e-02 2.50e+03 4.67e-02 2.18e+01 pdb=" C TRP D 282 " 0.081 2.00e-02 2.50e+03 pdb=" O TRP D 282 " -0.032 2.00e-02 2.50e+03 pdb=" N ILE D 283 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 165 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C VAL I 165 " -0.069 2.00e-02 2.50e+03 pdb=" O VAL I 165 " 0.026 2.00e-02 2.50e+03 pdb=" N PHE I 166 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY K 88 " 0.061 5.00e-02 4.00e+02 9.10e-02 1.33e+01 pdb=" N PRO K 89 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO K 89 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO K 89 " 0.050 5.00e-02 4.00e+02 ... (remaining 6305 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 5 2.02 - 2.74: 3338 2.74 - 3.46: 47775 3.46 - 4.18: 90071 4.18 - 4.90: 157220 Nonbonded interactions: 298409 Sorted by model distance: nonbonded pdb=" O VAL H 146 " pdb=" CG1 VAL H 160 " model vdw 1.302 3.460 nonbonded pdb=" O PRO C 406 " pdb=" NH2 ARG D 18 " model vdw 1.659 3.120 nonbonded pdb=" CG1 VAL I 146 " pdb=" O SER I 168 " model vdw 1.880 3.460 nonbonded pdb=" OE2 GLU I 80 " pdb=" CB PRO I 89 " model vdw 1.945 3.440 nonbonded pdb=" NH2 ARG B 16 " pdb=" O ASP B 370 " model vdw 1.971 3.120 ... (remaining 298404 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 203 or resid 218 through 420)) selection = (chain 'B' and resid 1 through 420) selection = (chain 'C' and resid 1 through 420) selection = (chain 'D' and resid 1 through 420) } ncs_group { reference = (chain 'E' and (resid 1 through 147 or resid 158 through 160 or (resid 161 throu \ gh 162 and (name N or name CA or name C or name O or name CB )) or resid 163 thr \ ough 166 or (resid 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 through 401)) selection = (chain 'F' and (resid 1 through 160 or (resid 161 through 162 and (name N or nam \ e CA or name C or name O or name CB )) or resid 163 through 166 or (resid 167 an \ d (name N or name CA or name C or name O or name CB )) or resid 168 through 401) \ ) selection = (chain 'G' and (resid 1 through 147 or resid 158 through 160 or (resid 161 throu \ gh 162 and (name N or name CA or name C or name O or name CB )) or resid 163 thr \ ough 166 or (resid 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 through 401)) selection = (chain 'H' and (resid 1 through 147 or resid 158 through 160 or (resid 161 throu \ gh 162 and (name N or name CA or name C or name O or name CB )) or resid 163 thr \ ough 166 or (resid 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 through 401)) selection = (chain 'I' and (resid 1 through 147 or resid 158 through 160 or (resid 161 throu \ gh 162 and (name N or name CA or name C or name O or name CB )) or resid 163 thr \ ough 166 or (resid 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 through 401)) selection = (chain 'J' and (resid 1 through 147 or resid 158 through 160 or (resid 161 throu \ gh 162 and (name N or name CA or name C or name O or name CB )) or resid 163 thr \ ough 166 or (resid 167 and (name N or name CA or name C or name O or name CB )) \ or resid 168 through 401)) selection = (chain 'K' and (resid 1 through 147 or resid 158 through 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 through 401)) selection = (chain 'L' and (resid 1 through 147 or resid 158 through 161 or (resid 162 and ( \ name N or name CA or name C or name O or name CB )) or resid 163 through 401)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.630 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 0.011 0.326 36092 Z= 0.492 Angle : 1.232 19.454 49067 Z= 0.661 Chirality : 0.074 0.528 5549 Planarity : 0.009 0.091 6308 Dihedral : 19.917 179.427 13481 Min Nonbonded Distance : 1.302 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.30 % Favored : 93.43 % Rotamer: Outliers : 10.36 % Allowed : 22.30 % Favored : 67.34 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.11), residues: 4461 helix: -2.87 (0.12), residues: 970 sheet: -1.43 (0.19), residues: 609 loop : -1.87 (0.10), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 349 TYR 0.023 0.003 TYR G 55 PHE 0.036 0.004 PHE K 225 TRP 0.044 0.004 TRP D 282 HIS 0.015 0.002 HIS J 48 Details of bonding type rmsd/Z covalent geometry : bond 0.01050 / 0.45 (36080) covalent geometry : angle 1.23218 / 0.66 (49063) SS BOND : bond 0.00166 / 0.08 ( 2) SS BOND : angle 1.07521 / 0.55 ( 4) hydrogen bonds : bond 0.16855 / 11.50 ( 937) hydrogen bonds : angle 8.40564 / 5.91 ( 2688) Misc. bond : bond 0.12000 / 6.05 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 405 poor density : 556 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping REVERT: A 276 HIS cc_start: 0.6483 (OUTLIER) cc_final: 0.6014 (m-70) REVERT: A 304 ASN cc_start: 0.7099 (m110) cc_final: 0.6453 (t0) REVERT: A 363 ASN cc_start: 0.7690 (m110) cc_final: 0.7465 (m110) REVERT: A 390 ARG cc_start: 0.7360 (mtt-85) cc_final: 0.7067 (mtp85) REVERT: B 18 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7276 (tpt170) REVERT: B 51 GLN cc_start: 0.6907 (OUTLIER) cc_final: 0.6111 (tt0) REVERT: B 219 THR cc_start: 0.7666 (OUTLIER) cc_final: 0.7260 (m) REVERT: E 31 LYS cc_start: 0.5277 (ttpt) cc_final: 0.4821 (ttmm) REVERT: E 140 GLU cc_start: 0.2735 (OUTLIER) cc_final: 0.1518 (mp0) REVERT: C 12 GLN cc_start: 0.6030 (tp40) cc_final: 0.5724 (tp40) REVERT: C 81 ARG cc_start: 0.7250 (mmm160) cc_final: 0.7002 (mmm160) REVERT: C 99 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8379 (ptt-90) REVERT: C 225 ASP cc_start: 0.7566 (m-30) cc_final: 0.7338 (m-30) REVERT: C 294 LYS cc_start: 0.7546 (tttt) cc_final: 0.7177 (tmtt) REVERT: C 304 ASN cc_start: 0.7315 (m110) cc_final: 0.6738 (t0) REVERT: C 392 ARG cc_start: 0.7689 (mtt90) cc_final: 0.7413 (mtp180) REVERT: C 408 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8055 (mmmt) REVERT: D 63 GLU cc_start: 0.7101 (tt0) cc_final: 0.6372 (pt0) REVERT: D 70 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7036 (mt-10) REVERT: D 258 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8687 (t) REVERT: D 269 HIS cc_start: 0.7103 (m90) cc_final: 0.6902 (m-70) REVERT: D 283 ILE cc_start: 0.7834 (OUTLIER) cc_final: 0.7348 (mp) REVERT: D 312 THR cc_start: 0.7552 (OUTLIER) cc_final: 0.7339 (p) REVERT: D 390 ARG cc_start: 0.7275 (mtp85) cc_final: 0.6796 (mtp180) REVERT: F 1 MET cc_start: 0.1570 (ttm) cc_final: 0.1347 (ptp) REVERT: F 4 LEU cc_start: 0.5603 (OUTLIER) cc_final: 0.5183 (tm) REVERT: F 184 GLN cc_start: 0.4678 (OUTLIER) cc_final: 0.3828 (pm20) REVERT: F 207 LEU cc_start: 0.4816 (pt) cc_final: 0.4609 (pp) REVERT: F 322 ASN cc_start: 0.7606 (t0) cc_final: 0.7393 (t0) REVERT: G 1 MET cc_start: 0.4754 (mmm) cc_final: 0.4416 (mmm) REVERT: G 102 ASP cc_start: 0.3815 (OUTLIER) cc_final: 0.3117 (p0) REVERT: G 122 GLN cc_start: 0.4312 (tt0) cc_final: 0.3501 (tp-100) REVERT: G 125 ARG cc_start: 0.4411 (mtm-85) cc_final: 0.4047 (mtp85) REVERT: G 175 MET cc_start: 0.5331 (mtt) cc_final: 0.5067 (mtp) REVERT: G 183 LEU cc_start: 0.4890 (mt) cc_final: 0.4572 (mt) REVERT: G 210 MET cc_start: 0.6516 (ttt) cc_final: 0.6298 (ttt) REVERT: G 320 MET cc_start: 0.7263 (mtp) cc_final: 0.7030 (mtm) REVERT: I 20 SER cc_start: 0.6681 (OUTLIER) cc_final: 0.6297 (m) REVERT: I 65 LYS cc_start: 0.4256 (OUTLIER) cc_final: 0.3661 (ptpt) REVERT: I 169 ASN cc_start: 0.3362 (OUTLIER) cc_final: 0.2908 (t0) REVERT: I 201 MET cc_start: 0.2142 (ttp) cc_final: 0.1759 (ttm) REVERT: I 210 MET cc_start: 0.4896 (ttt) cc_final: 0.4512 (ttt) REVERT: I 223 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6103 (mppt) REVERT: I 229 MET cc_start: 0.7535 (tmm) cc_final: 0.6961 (ttt) REVERT: I 233 LEU cc_start: 0.7278 (OUTLIER) cc_final: 0.6989 (mp) REVERT: I 242 GLU cc_start: 0.4661 (pp20) cc_final: 0.4260 (pm20) REVERT: I 243 ARG cc_start: 0.3626 (ttm170) cc_final: 0.3411 (mpt-90) REVERT: I 257 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7133 (t0) REVERT: I 319 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7976 (ttm-80) REVERT: I 320 MET cc_start: 0.8432 (mtp) cc_final: 0.8204 (mtm) REVERT: J 6 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5492 (mt) REVERT: J 63 GLU cc_start: 0.5090 (tp30) cc_final: 0.4609 (mm-30) REVERT: J 146 VAL cc_start: 0.7599 (m) cc_final: 0.7327 (t) REVERT: J 176 TYR cc_start: 0.6220 (m-80) cc_final: 0.5958 (m-80) REVERT: J 208 TYR cc_start: 0.6064 (m-80) cc_final: 0.5827 (m-80) REVERT: J 211 GLU cc_start: 0.6513 (pm20) cc_final: 0.6161 (pm20) REVERT: J 229 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7428 (ttp) REVERT: J 333 ASN cc_start: 0.6908 (m-40) cc_final: 0.6515 (m-40) REVERT: K 5 ILE cc_start: 0.5204 (OUTLIER) cc_final: 0.4883 (pp) REVERT: K 35 LEU cc_start: 0.6599 (tp) cc_final: 0.6340 (tp) REVERT: K 58 GLN cc_start: 0.5563 (mm-40) cc_final: 0.5324 (mp10) REVERT: K 92 LEU cc_start: 0.3139 (OUTLIER) cc_final: 0.2527 (pt) REVERT: K 95 ASP cc_start: 0.5506 (OUTLIER) cc_final: 0.4027 (t0) REVERT: K 122 GLN cc_start: 0.4416 (tp-100) cc_final: 0.4039 (tp-100) REVERT: K 158 ARG cc_start: 0.4177 (OUTLIER) cc_final: 0.3912 (ppt170) REVERT: K 194 GLU cc_start: 0.4521 (OUTLIER) cc_final: 0.3650 (mm-30) REVERT: K 195 LYS cc_start: 0.4744 (tttm) cc_final: 0.3866 (pttp) REVERT: K 210 MET cc_start: 0.5582 (tpp) cc_final: 0.5106 (tpp) REVERT: K 229 MET cc_start: 0.7698 (tmm) cc_final: 0.7421 (ttp) REVERT: K 333 ASN cc_start: 0.7959 (m-40) cc_final: 0.7694 (m110) REVERT: L 77 MET cc_start: 0.5240 (ptp) cc_final: 0.4302 (pp-130) REVERT: L 80 GLU cc_start: 0.3933 (mt-10) cc_final: 0.3517 (mm-30) REVERT: L 120 MET cc_start: 0.2882 (OUTLIER) cc_final: 0.2671 (tpt) REVERT: L 139 GLU cc_start: 0.4735 (OUTLIER) cc_final: 0.4480 (tm-30) REVERT: L 210 MET cc_start: 0.4372 (OUTLIER) cc_final: 0.3982 (ttp) REVERT: L 225 PHE cc_start: 0.7885 (t80) cc_final: 0.7650 (t80) REVERT: H 195 LYS cc_start: 0.4892 (mmtt) cc_final: 0.3649 (ttmt) REVERT: H 282 ASP cc_start: 0.6952 (m-30) cc_final: 0.6734 (m-30) REVERT: H 299 SER cc_start: 0.8744 (OUTLIER) cc_final: 0.8516 (t) outliers start: 405 outliers final: 187 residues processed: 900 average time/residue: 0.5932 time to fit residues: 648.0721 Evaluate side-chains 638 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 420 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 108 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 389 CYS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 149 CYS Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 149 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 361 ASN Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 258 SER Chi-restraints excluded: chain D residue 276 HIS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 78 SER Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 113 CYS Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 348 SER Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 20 SER Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 192 SER Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 169 ASN Chi-restraints excluded: chain I residue 179 SER Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 223 LYS Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 235 SER Chi-restraints excluded: chain I residue 251 VAL Chi-restraints excluded: chain I residue 253 ASN Chi-restraints excluded: chain I residue 257 ASP Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 319 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 161 GLU Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 229 MET Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 279 VAL Chi-restraints excluded: chain J residue 286 ILE Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 95 ASP Chi-restraints excluded: chain K residue 113 CYS Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 158 ARG Chi-restraints excluded: chain K residue 159 PHE Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 194 GLU Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 273 SER Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 301 SER Chi-restraints excluded: chain K residue 342 SER Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 31 LYS Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 78 SER Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain L residue 120 MET Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 152 ASP Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 210 MET Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain L residue 266 CYS Chi-restraints excluded: chain L residue 282 ASP Chi-restraints excluded: chain L residue 299 SER Chi-restraints excluded: chain L residue 324 THR Chi-restraints excluded: chain L residue 352 SER Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 278 VAL Chi-restraints excluded: chain H residue 299 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A 40 HIS A 60 GLN A 73 GLN A 135 HIS A 145 ASN A 158 ASN A 286 ASN A 331 GLN A 338 HIS A 363 ASN A 401 ASN A 417 GLN B 12 GLN B 40 HIS B 51 GLN B 74 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN B 276 HIS B 286 ASN B 401 ASN E 67 GLN E 79 HIS E 169 ASN E 339 ASN C 40 HIS C 67 GLN C 266 GLN C 304 ASN C 363 ASN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 GLN D 40 HIS D 51 GLN D 73 GLN D 135 HIS D 145 ASN D 201 ASN D 202 GLN ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 ASN D 338 HIS D 401 ASN F 69 GLN F 316 GLN G 67 GLN G 264 GLN G 316 GLN I 36 HIS I 221 GLN J 169 ASN ** K 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 67 GLN K 118 GLN K 122 GLN L 48 HIS L 157 HIS L 346 HIS H 30 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 GLN H 253 ASN H 265 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.198284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.177577 restraints weight = 41382.442| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 0.96 r_work: 0.3566 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 36092 Z= 0.158 Angle : 0.698 10.964 49067 Z= 0.349 Chirality : 0.051 0.169 5549 Planarity : 0.007 0.269 6308 Dihedral : 13.583 176.263 5330 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.45 % Favored : 94.44 % Rotamer: Outliers : 7.49 % Allowed : 25.68 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.27 (0.11), residues: 4461 helix: -1.55 (0.15), residues: 982 sheet: -1.56 (0.16), residues: 886 loop : -1.45 (0.11), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 158 TYR 0.013 0.001 TYR K 55 PHE 0.020 0.002 PHE A 110 TRP 0.036 0.002 TRP D 282 HIS 0.009 0.001 HIS G 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (36080) covalent geometry : angle 0.69745 / 0.35 (49063) SS BOND : bond 0.00197 / 0.10 ( 2) SS BOND : angle 1.20330 / 0.58 ( 4) hydrogen bonds : bond 0.04332 / 2.77 ( 937) hydrogen bonds : angle 6.34478 / 4.43 ( 2688) Misc. bond : bond 0.00209 / 0.09 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 295 poor density : 458 time to evaluate : 0.975 Fit side-chains revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: L residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping REVERT: A 77 ASN cc_start: 0.6188 (m-40) cc_final: 0.5471 (t0) REVERT: A 276 HIS cc_start: 0.6584 (OUTLIER) cc_final: 0.6211 (m-70) REVERT: A 304 ASN cc_start: 0.7284 (m110) cc_final: 0.6611 (t0) REVERT: B 113 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8605 (mt) REVERT: B 133 GLN cc_start: 0.5857 (OUTLIER) cc_final: 0.5583 (tp-100) REVERT: B 165 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8255 (mt) REVERT: B 200 ARG cc_start: 0.7392 (mpp-170) cc_final: 0.7006 (mtt180) REVERT: B 219 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7326 (m) REVERT: E 48 HIS cc_start: 0.3093 (OUTLIER) cc_final: 0.2183 (t70) REVERT: E 51 LEU cc_start: 0.5151 (OUTLIER) cc_final: 0.4648 (pp) REVERT: E 114 ASP cc_start: 0.3515 (OUTLIER) cc_final: 0.2951 (t70) REVERT: E 140 GLU cc_start: 0.2902 (OUTLIER) cc_final: 0.1793 (mt-10) REVERT: E 176 TYR cc_start: 0.5409 (OUTLIER) cc_final: 0.5155 (m-80) REVERT: E 195 LYS cc_start: 0.3245 (ttpp) cc_final: 0.2593 (mttm) REVERT: E 279 VAL cc_start: 0.6966 (OUTLIER) cc_final: 0.6634 (t) REVERT: C 12 GLN cc_start: 0.6052 (tp40) cc_final: 0.5419 (mm110) REVERT: C 20 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6596 (mp) REVERT: C 225 ASP cc_start: 0.8034 (m-30) cc_final: 0.7779 (m-30) REVERT: C 294 LYS cc_start: 0.7820 (tttt) cc_final: 0.7411 (tmtt) REVERT: C 321 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7676 (mt-10) REVERT: C 389 CYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8006 (p) REVERT: D 70 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7448 (mt-10) REVERT: D 283 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7581 (mp) REVERT: D 312 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7953 (p) REVERT: D 390 ARG cc_start: 0.7983 (mtp85) cc_final: 0.7575 (mtp180) REVERT: F 1 MET cc_start: 0.1764 (ttm) cc_final: 0.1541 (ptp) REVERT: F 10 TYR cc_start: 0.6509 (OUTLIER) cc_final: 0.5996 (m-80) REVERT: F 33 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.7108 (tt) REVERT: F 108 ASN cc_start: 0.6176 (t0) cc_final: 0.5958 (t0) REVERT: F 184 GLN cc_start: 0.4533 (OUTLIER) cc_final: 0.3705 (pm20) REVERT: F 219 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7451 (pt) REVERT: F 257 ASP cc_start: 0.7136 (OUTLIER) cc_final: 0.6433 (t70) REVERT: G 1 MET cc_start: 0.4424 (mmm) cc_final: 0.4166 (mmm) REVERT: G 118 GLN cc_start: 0.5601 (pm20) cc_final: 0.5040 (mm-40) REVERT: G 122 GLN cc_start: 0.5068 (tt0) cc_final: 0.4292 (tp-100) REVERT: G 125 ARG cc_start: 0.4498 (mtm-85) cc_final: 0.4132 (mtp85) REVERT: G 133 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.5973 (pt) REVERT: G 176 TYR cc_start: 0.5975 (m-80) cc_final: 0.5208 (m-80) REVERT: G 310 TRP cc_start: 0.7995 (m-90) cc_final: 0.7627 (m-90) REVERT: G 320 MET cc_start: 0.8087 (mtp) cc_final: 0.7877 (mtm) REVERT: I 20 SER cc_start: 0.6521 (OUTLIER) cc_final: 0.6279 (m) REVERT: I 25 LEU cc_start: 0.6538 (mm) cc_final: 0.5988 (mp) REVERT: I 56 MET cc_start: 0.4329 (mmt) cc_final: 0.4094 (mmp) REVERT: I 63 GLU cc_start: 0.5029 (OUTLIER) cc_final: 0.4782 (mm-30) REVERT: I 65 LYS cc_start: 0.3919 (OUTLIER) cc_final: 0.3427 (ptpt) REVERT: I 99 GLU cc_start: 0.4540 (OUTLIER) cc_final: 0.4174 (mm-30) REVERT: I 196 GLU cc_start: 0.4307 (tt0) cc_final: 0.3959 (pm20) REVERT: I 223 LYS cc_start: 0.7205 (mtmm) cc_final: 0.6322 (mppt) REVERT: I 233 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6789 (mp) REVERT: I 239 LYS cc_start: 0.6561 (mtmt) cc_final: 0.6037 (mmpt) REVERT: I 242 GLU cc_start: 0.4519 (pp20) cc_final: 0.4154 (pm20) REVERT: I 243 ARG cc_start: 0.3551 (ttm170) cc_final: 0.3222 (mpt-90) REVERT: J 81 GLU cc_start: 0.5128 (OUTLIER) cc_final: 0.4254 (mm-30) REVERT: J 135 VAL cc_start: 0.6412 (m) cc_final: 0.6125 (t) REVERT: J 146 VAL cc_start: 0.7648 (m) cc_final: 0.7386 (t) REVERT: J 175 MET cc_start: 0.6689 (ptm) cc_final: 0.6387 (ptp) REVERT: J 176 TYR cc_start: 0.6498 (OUTLIER) cc_final: 0.6088 (m-80) REVERT: J 208 TYR cc_start: 0.5666 (m-80) cc_final: 0.5454 (m-80) REVERT: J 211 GLU cc_start: 0.6927 (pm20) cc_final: 0.6718 (pm20) REVERT: J 237 ARG cc_start: 0.6563 (OUTLIER) cc_final: 0.6204 (tpt170) REVERT: J 333 ASN cc_start: 0.6911 (m-40) cc_final: 0.6581 (m-40) REVERT: K 5 ILE cc_start: 0.5587 (OUTLIER) cc_final: 0.5154 (pp) REVERT: K 58 GLN cc_start: 0.5747 (mm-40) cc_final: 0.5516 (mp10) REVERT: K 133 ILE cc_start: 0.3501 (OUTLIER) cc_final: 0.3222 (pt) REVERT: K 157 HIS cc_start: 0.3778 (m-70) cc_final: 0.3387 (m170) REVERT: K 162 LYS cc_start: 0.3521 (OUTLIER) cc_final: 0.2671 (pmtt) REVERT: K 172 ASN cc_start: 0.6542 (p0) cc_final: 0.6143 (p0) REVERT: K 229 MET cc_start: 0.8090 (tmm) cc_final: 0.7848 (ttt) REVERT: K 236 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6787 (mp) REVERT: K 333 ASN cc_start: 0.8087 (m-40) cc_final: 0.7845 (m110) REVERT: K 351 GLU cc_start: 0.7742 (tt0) cc_final: 0.7147 (pm20) REVERT: L 35 LEU cc_start: 0.6938 (mt) cc_final: 0.6648 (tt) REVERT: L 37 GLN cc_start: 0.6136 (mm110) cc_final: 0.5763 (mm-40) REVERT: L 77 MET cc_start: 0.5788 (ptp) cc_final: 0.4199 (pp-130) REVERT: L 80 GLU cc_start: 0.4166 (OUTLIER) cc_final: 0.3623 (mm-30) REVERT: L 82 GLU cc_start: 0.4256 (OUTLIER) cc_final: 0.3483 (tt0) REVERT: L 127 HIS cc_start: 0.4111 (p90) cc_final: 0.2906 (m170) REVERT: L 178 LEU cc_start: 0.4666 (OUTLIER) cc_final: 0.4184 (tt) REVERT: L 184 GLN cc_start: 0.5857 (tm-30) cc_final: 0.5619 (pt0) REVERT: L 306 CYS cc_start: 0.6066 (p) cc_final: 0.5855 (p) REVERT: L 313 ARG cc_start: 0.6710 (tpp80) cc_final: 0.6333 (ttm170) REVERT: L 347 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7356 (ttmm) REVERT: H 27 ASP cc_start: 0.6449 (m-30) cc_final: 0.6249 (m-30) REVERT: H 130 GLU cc_start: 0.4511 (mm-30) cc_final: 0.4002 (mm-30) REVERT: H 195 LYS cc_start: 0.4936 (mmtt) cc_final: 0.3503 (ttmt) REVERT: H 265 ASN cc_start: 0.7327 (OUTLIER) cc_final: 0.7107 (t0) outliers start: 295 outliers final: 124 residues processed: 702 average time/residue: 0.5648 time to fit residues: 486.8847 Evaluate side-chains 566 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 403 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 276 HIS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 257 ASP Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 20 SER Chi-restraints excluded: chain I residue 63 GLU Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 360 MET Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 100 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 176 TYR Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 237 ARG Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 323 VAL Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 347 LYS Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 265 ASN Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 187 optimal weight: 0.1980 chunk 319 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 210 optimal weight: 30.0000 chunk 342 optimal weight: 8.9990 chunk 383 optimal weight: 0.0060 chunk 443 optimal weight: 10.0000 chunk 375 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 overall best weight: 2.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 GLN A 158 ASN A 201 ASN A 338 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 GLN D 130 HIS ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 HIS ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN K 118 GLN H 30 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.196537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.174431 restraints weight = 41541.364| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.05 r_work: 0.3566 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 36092 Z= 0.149 Angle : 0.659 8.659 49067 Z= 0.327 Chirality : 0.050 0.157 5549 Planarity : 0.006 0.077 6308 Dihedral : 12.282 175.196 5140 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.54 % Favored : 94.40 % Rotamer: Outliers : 7.44 % Allowed : 26.44 % Favored : 66.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.79 (0.12), residues: 4461 helix: -0.81 (0.16), residues: 973 sheet: -1.40 (0.16), residues: 894 loop : -1.22 (0.11), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 155 TYR 0.012 0.001 TYR K 55 PHE 0.023 0.002 PHE L 225 TRP 0.030 0.002 TRP D 282 HIS 0.008 0.001 HIS I 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (36080) covalent geometry : angle 0.65949 / 0.33 (49063) SS BOND : bond 0.00117 / 0.06 ( 2) SS BOND : angle 0.68307 / 0.30 ( 4) hydrogen bonds : bond 0.03962 / 2.53 ( 937) hydrogen bonds : angle 5.95257 / 4.14 ( 2688) Misc. bond : bond 0.00220 / 0.10 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 294 poor density : 422 time to evaluate : 1.333 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: H residue: PRO 199 >>> skipping REVERT: A 50 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7486 (tpp) REVERT: A 276 HIS cc_start: 0.6543 (OUTLIER) cc_final: 0.6197 (m-70) REVERT: A 294 LYS cc_start: 0.7416 (OUTLIER) cc_final: 0.7072 (mmtm) REVERT: A 304 ASN cc_start: 0.7175 (m110) cc_final: 0.6584 (t0) REVERT: A 376 LYS cc_start: 0.6787 (OUTLIER) cc_final: 0.6479 (ttpt) REVERT: B 51 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6970 (tm130) REVERT: B 113 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8603 (mt) REVERT: B 165 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8348 (mt) REVERT: B 332 GLU cc_start: 0.7522 (mp0) cc_final: 0.7240 (mp0) REVERT: B 349 ARG cc_start: 0.7806 (ptp-110) cc_final: 0.7366 (ptp-110) REVERT: E 25 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6715 (tp) REVERT: E 48 HIS cc_start: 0.2960 (OUTLIER) cc_final: 0.2197 (t70) REVERT: E 51 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.5081 (pp) REVERT: E 71 LEU cc_start: 0.4770 (OUTLIER) cc_final: 0.4365 (tm) REVERT: E 94 ARG cc_start: 0.4884 (OUTLIER) cc_final: 0.4552 (ttm170) REVERT: E 114 ASP cc_start: 0.3543 (OUTLIER) cc_final: 0.3072 (t70) REVERT: E 140 GLU cc_start: 0.2528 (OUTLIER) cc_final: 0.1669 (pm20) REVERT: E 176 TYR cc_start: 0.5258 (OUTLIER) cc_final: 0.5056 (m-80) REVERT: E 184 GLN cc_start: 0.2428 (OUTLIER) cc_final: 0.1739 (pp30) REVERT: E 195 LYS cc_start: 0.3171 (ttpp) cc_final: 0.2619 (mttt) REVERT: E 279 VAL cc_start: 0.6864 (OUTLIER) cc_final: 0.6552 (t) REVERT: C 12 GLN cc_start: 0.6248 (tp40) cc_final: 0.5646 (mm110) REVERT: C 225 ASP cc_start: 0.8091 (m-30) cc_final: 0.7756 (m-30) REVERT: C 294 LYS cc_start: 0.8078 (tttt) cc_final: 0.7519 (tmtt) REVERT: C 321 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7882 (mt-10) REVERT: C 389 CYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8073 (p) REVERT: D 18 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.6924 (tpt90) REVERT: D 70 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7519 (mt-10) REVERT: D 202 GLN cc_start: 0.6242 (OUTLIER) cc_final: 0.5929 (tt0) REVERT: D 221 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7536 (ptt-90) REVERT: D 283 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7559 (mp) REVERT: D 390 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7702 (mtp180) REVERT: F 1 MET cc_start: 0.1729 (ttm) cc_final: 0.1485 (ptp) REVERT: F 108 ASN cc_start: 0.5989 (m-40) cc_final: 0.5772 (t0) REVERT: F 130 GLU cc_start: 0.3460 (OUTLIER) cc_final: 0.3112 (tt0) REVERT: F 219 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7352 (pt) REVERT: F 261 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6959 (ptt-90) REVERT: G 125 ARG cc_start: 0.4508 (mtm-85) cc_final: 0.4137 (mtt90) REVERT: G 176 TYR cc_start: 0.5998 (OUTLIER) cc_final: 0.5306 (m-80) REVERT: G 177 ILE cc_start: 0.6660 (mm) cc_final: 0.5927 (tt) REVERT: G 310 TRP cc_start: 0.7998 (m-90) cc_final: 0.7640 (m-90) REVERT: G 320 MET cc_start: 0.8159 (mtp) cc_final: 0.7955 (mtm) REVERT: I 56 MET cc_start: 0.4667 (mmt) cc_final: 0.3417 (ptt) REVERT: I 65 LYS cc_start: 0.4432 (OUTLIER) cc_final: 0.3560 (ptpt) REVERT: I 99 GLU cc_start: 0.4508 (OUTLIER) cc_final: 0.4264 (mm-30) REVERT: I 201 MET cc_start: 0.2632 (OUTLIER) cc_final: 0.1981 (ttm) REVERT: I 223 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6399 (mppt) REVERT: I 229 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7476 (ttp) REVERT: I 233 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6769 (mp) REVERT: I 239 LYS cc_start: 0.6421 (mtmt) cc_final: 0.6057 (mmpt) REVERT: I 242 GLU cc_start: 0.4634 (pp20) cc_final: 0.4232 (pm20) REVERT: I 243 ARG cc_start: 0.3603 (ttm170) cc_final: 0.3261 (mpt-90) REVERT: J 62 LYS cc_start: 0.5485 (OUTLIER) cc_final: 0.4898 (tttm) REVERT: J 81 GLU cc_start: 0.5217 (OUTLIER) cc_final: 0.4253 (mm-30) REVERT: J 135 VAL cc_start: 0.6483 (m) cc_final: 0.6243 (t) REVERT: J 158 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5705 (ptm-80) REVERT: J 175 MET cc_start: 0.6550 (ptm) cc_final: 0.6317 (ptp) REVERT: J 176 TYR cc_start: 0.6620 (OUTLIER) cc_final: 0.6239 (m-80) REVERT: J 211 GLU cc_start: 0.7213 (pm20) cc_final: 0.6990 (pm20) REVERT: J 304 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: J 333 ASN cc_start: 0.6978 (m-40) cc_final: 0.6686 (m-40) REVERT: K 5 ILE cc_start: 0.5500 (OUTLIER) cc_final: 0.5062 (pp) REVERT: K 122 GLN cc_start: 0.4472 (tp40) cc_final: 0.4257 (tp-100) REVERT: K 157 HIS cc_start: 0.3687 (m-70) cc_final: 0.3333 (m170) REVERT: K 162 LYS cc_start: 0.3564 (OUTLIER) cc_final: 0.2871 (pmtt) REVERT: K 172 ASN cc_start: 0.6470 (p0) cc_final: 0.6161 (p0) REVERT: K 229 MET cc_start: 0.8294 (tmm) cc_final: 0.8087 (ttp) REVERT: K 333 ASN cc_start: 0.8118 (m-40) cc_final: 0.7838 (m110) REVERT: K 351 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7164 (pm20) REVERT: L 35 LEU cc_start: 0.6976 (mt) cc_final: 0.6657 (tt) REVERT: L 37 GLN cc_start: 0.6225 (mm110) cc_final: 0.5963 (mm110) REVERT: L 51 LEU cc_start: 0.5109 (OUTLIER) cc_final: 0.4882 (mt) REVERT: L 77 MET cc_start: 0.6048 (OUTLIER) cc_final: 0.4330 (pp-130) REVERT: L 80 GLU cc_start: 0.4179 (mt-10) cc_final: 0.3272 (tp30) REVERT: L 82 GLU cc_start: 0.4272 (OUTLIER) cc_final: 0.3563 (tt0) REVERT: L 127 HIS cc_start: 0.4034 (p90) cc_final: 0.3170 (m170) REVERT: L 178 LEU cc_start: 0.4227 (OUTLIER) cc_final: 0.3846 (tt) REVERT: L 212 LEU cc_start: 0.4486 (OUTLIER) cc_final: 0.4037 (mt) REVERT: L 334 ASP cc_start: 0.6325 (m-30) cc_final: 0.5343 (p0) REVERT: L 351 GLU cc_start: 0.7129 (mt-10) cc_final: 0.6690 (mt-10) REVERT: H 27 ASP cc_start: 0.6565 (m-30) cc_final: 0.6352 (m-30) REVERT: H 98 SER cc_start: 0.4195 (OUTLIER) cc_final: 0.3877 (m) REVERT: H 126 HIS cc_start: 0.5481 (OUTLIER) cc_final: 0.4495 (m-70) REVERT: H 130 GLU cc_start: 0.4819 (mm-30) cc_final: 0.4310 (mm-30) REVERT: H 195 LYS cc_start: 0.5096 (mmtt) cc_final: 0.3792 (ttpt) REVERT: H 210 MET cc_start: 0.6021 (ttt) cc_final: 0.5652 (ttt) REVERT: H 265 ASN cc_start: 0.7390 (t0) cc_final: 0.7122 (t0) REVERT: H 334 ASP cc_start: 0.7855 (m-30) cc_final: 0.7652 (m-30) outliers start: 294 outliers final: 130 residues processed: 653 average time/residue: 0.5672 time to fit residues: 454.7553 Evaluate side-chains 571 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 393 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 276 HIS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 223 LYS Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 360 MET Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 56 MET Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 158 ARG Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 176 TYR Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 251 VAL Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 351 GLU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 77 MET Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 353 optimal weight: 4.9990 chunk 330 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 319 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN A 158 ASN A 338 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS E 108 ASN E 164 GLN C 203 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN D 73 GLN ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 HIS ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 108 ASN K 108 ASN K 118 GLN H 30 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.195809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.173723 restraints weight = 41352.968| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.05 r_work: 0.3535 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36092 Z= 0.183 Angle : 0.681 9.265 49067 Z= 0.337 Chirality : 0.051 0.170 5549 Planarity : 0.006 0.078 6308 Dihedral : 12.012 174.316 5114 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.01 % Rotamer: Outliers : 7.42 % Allowed : 26.96 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.63 (0.12), residues: 4461 helix: -0.48 (0.16), residues: 973 sheet: -1.35 (0.16), residues: 912 loop : -1.19 (0.12), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 155 TYR 0.013 0.002 TYR F 10 PHE 0.031 0.002 PHE E 117 TRP 0.031 0.002 TRP D 282 HIS 0.008 0.001 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (36080) covalent geometry : angle 0.68100 / 0.34 (49063) SS BOND : bond 0.00244 / 0.12 ( 2) SS BOND : angle 1.96901 / 0.69 ( 4) hydrogen bonds : bond 0.04014 / 2.57 ( 937) hydrogen bonds : angle 5.89639 / 4.11 ( 2688) Misc. bond : bond 0.00123 / 0.07 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 293 poor density : 413 time to evaluate : 1.344 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping REVERT: A 50 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7437 (tpp) REVERT: A 51 GLN cc_start: 0.8006 (tt0) cc_final: 0.7797 (tt0) REVERT: A 169 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6324 (tm-30) REVERT: A 242 ASP cc_start: 0.6464 (t0) cc_final: 0.6058 (m-30) REVERT: A 276 HIS cc_start: 0.6601 (OUTLIER) cc_final: 0.6240 (m-70) REVERT: A 294 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.6952 (mmtm) REVERT: A 304 ASN cc_start: 0.7261 (m110) cc_final: 0.6590 (t0) REVERT: B 113 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8594 (mt) REVERT: B 165 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8233 (mt) REVERT: E 48 HIS cc_start: 0.2995 (OUTLIER) cc_final: 0.2241 (t70) REVERT: E 51 LEU cc_start: 0.5541 (OUTLIER) cc_final: 0.4964 (pp) REVERT: E 94 ARG cc_start: 0.4693 (OUTLIER) cc_final: 0.4437 (ttm170) REVERT: E 114 ASP cc_start: 0.3094 (OUTLIER) cc_final: 0.2675 (t70) REVERT: E 140 GLU cc_start: 0.2802 (OUTLIER) cc_final: 0.1436 (pm20) REVERT: E 176 TYR cc_start: 0.5300 (OUTLIER) cc_final: 0.4938 (m-80) REVERT: E 184 GLN cc_start: 0.2468 (OUTLIER) cc_final: 0.2186 (pp30) REVERT: E 198 PHE cc_start: 0.4534 (m-80) cc_final: 0.3116 (t80) REVERT: C 12 GLN cc_start: 0.6330 (tp40) cc_final: 0.5732 (mm110) REVERT: C 75 GLU cc_start: 0.7516 (tm-30) cc_final: 0.7273 (tp30) REVERT: C 225 ASP cc_start: 0.8064 (m-30) cc_final: 0.7707 (m-30) REVERT: C 294 LYS cc_start: 0.8014 (tttt) cc_final: 0.7438 (tmtt) REVERT: C 321 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7872 (mt-10) REVERT: D 18 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6982 (tpt90) REVERT: D 70 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7628 (mt-10) REVERT: D 202 GLN cc_start: 0.6216 (OUTLIER) cc_final: 0.5874 (tt0) REVERT: D 221 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7518 (ptt-90) REVERT: D 283 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7711 (mp) REVERT: D 390 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7814 (mtp180) REVERT: F 108 ASN cc_start: 0.6024 (m-40) cc_final: 0.5799 (t0) REVERT: F 261 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6976 (ptt-90) REVERT: G 125 ARG cc_start: 0.4552 (mtm-85) cc_final: 0.4149 (mtt90) REVERT: G 133 ILE cc_start: 0.6402 (OUTLIER) cc_final: 0.5947 (pt) REVERT: G 176 TYR cc_start: 0.6049 (m-80) cc_final: 0.5324 (m-80) REVERT: G 177 ILE cc_start: 0.6708 (mm) cc_final: 0.6022 (tt) REVERT: G 310 TRP cc_start: 0.7997 (m-90) cc_final: 0.7633 (m-90) REVERT: I 56 MET cc_start: 0.5033 (mmt) cc_final: 0.3762 (ptt) REVERT: I 65 LYS cc_start: 0.4530 (OUTLIER) cc_final: 0.3579 (ptpt) REVERT: I 99 GLU cc_start: 0.4516 (OUTLIER) cc_final: 0.4218 (mm-30) REVERT: I 201 MET cc_start: 0.2682 (OUTLIER) cc_final: 0.1910 (ttm) REVERT: I 223 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6362 (mppt) REVERT: I 229 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7400 (ttp) REVERT: I 233 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6696 (mp) REVERT: I 239 LYS cc_start: 0.6440 (mtmt) cc_final: 0.6049 (mmpt) REVERT: I 242 GLU cc_start: 0.4699 (pp20) cc_final: 0.4268 (pm20) REVERT: I 243 ARG cc_start: 0.3661 (ttm170) cc_final: 0.3170 (mpt-90) REVERT: J 6 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5671 (mt) REVERT: J 81 GLU cc_start: 0.5261 (OUTLIER) cc_final: 0.4290 (mm-30) REVERT: J 135 VAL cc_start: 0.6489 (m) cc_final: 0.6177 (t) REVERT: J 158 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5654 (ptm-80) REVERT: J 175 MET cc_start: 0.6617 (ptm) cc_final: 0.6380 (ptp) REVERT: J 176 TYR cc_start: 0.6561 (m-80) cc_final: 0.6139 (m-80) REVERT: J 211 GLU cc_start: 0.7106 (pm20) cc_final: 0.6877 (pm20) REVERT: J 236 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6622 (tp) REVERT: J 333 ASN cc_start: 0.6972 (m-40) cc_final: 0.6636 (m-40) REVERT: K 157 HIS cc_start: 0.3890 (m-70) cc_final: 0.3487 (m170) REVERT: K 162 LYS cc_start: 0.3696 (OUTLIER) cc_final: 0.3035 (pmtt) REVERT: K 172 ASN cc_start: 0.6526 (p0) cc_final: 0.6196 (p0) REVERT: K 236 LEU cc_start: 0.7169 (OUTLIER) cc_final: 0.6905 (mp) REVERT: K 333 ASN cc_start: 0.8121 (m-40) cc_final: 0.7817 (m110) REVERT: K 351 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: L 35 LEU cc_start: 0.6921 (mt) cc_final: 0.6511 (tt) REVERT: L 37 GLN cc_start: 0.6205 (mm110) cc_final: 0.5966 (mm110) REVERT: L 51 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4770 (mt) REVERT: L 77 MET cc_start: 0.6092 (OUTLIER) cc_final: 0.4373 (pp-130) REVERT: L 80 GLU cc_start: 0.4196 (OUTLIER) cc_final: 0.3775 (mm-30) REVERT: L 127 HIS cc_start: 0.3969 (p90) cc_final: 0.3104 (m170) REVERT: L 178 LEU cc_start: 0.4135 (OUTLIER) cc_final: 0.3641 (tt) REVERT: L 186 ILE cc_start: 0.4241 (OUTLIER) cc_final: 0.3762 (mp) REVERT: L 212 LEU cc_start: 0.4388 (OUTLIER) cc_final: 0.4096 (mt) REVERT: L 223 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.6648 (tptp) REVERT: L 334 ASP cc_start: 0.6277 (m-30) cc_final: 0.5294 (p0) REVERT: L 351 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6610 (mt-10) REVERT: H 27 ASP cc_start: 0.6501 (m-30) cc_final: 0.6281 (m-30) REVERT: H 130 GLU cc_start: 0.4958 (mm-30) cc_final: 0.4419 (mm-30) REVERT: H 195 LYS cc_start: 0.4885 (mmtt) cc_final: 0.3260 (ttmt) REVERT: H 210 MET cc_start: 0.5992 (ttt) cc_final: 0.5602 (ttt) REVERT: H 265 ASN cc_start: 0.7445 (t0) cc_final: 0.7203 (t0) REVERT: H 334 ASP cc_start: 0.7935 (m-30) cc_final: 0.7683 (m-30) outliers start: 293 outliers final: 157 residues processed: 650 average time/residue: 0.5707 time to fit residues: 454.6182 Evaluate side-chains 591 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 394 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 376 LYS Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 94 ARG Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 309 LYS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 276 HIS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain I residue 223 LYS Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 360 MET Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 56 MET Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 158 ARG Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 71 LEU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 175 MET Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 351 GLU Chi-restraints excluded: chain L residue 14 LEU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 77 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 98 SER Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 223 LYS Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 369 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 349 optimal weight: 20.0000 chunk 361 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 439 optimal weight: 8.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 338 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 GLN J 108 ASN K 118 GLN K 122 GLN H 30 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.197078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.175036 restraints weight = 41286.046| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.01 r_work: 0.3548 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36092 Z= 0.132 Angle : 0.630 8.430 49067 Z= 0.309 Chirality : 0.049 0.171 5549 Planarity : 0.005 0.075 6308 Dihedral : 11.554 166.959 5110 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.40 % Favored : 94.51 % Rotamer: Outliers : 6.64 % Allowed : 27.82 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.12), residues: 4461 helix: -0.09 (0.16), residues: 973 sheet: -1.14 (0.17), residues: 896 loop : -1.07 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 412 TYR 0.011 0.001 TYR K 55 PHE 0.035 0.002 PHE E 117 TRP 0.025 0.002 TRP D 282 HIS 0.007 0.001 HIS I 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (36080) covalent geometry : angle 0.62954 / 0.31 (49063) SS BOND : bond 0.00125 / 0.06 ( 2) SS BOND : angle 1.33679 / 0.47 ( 4) hydrogen bonds : bond 0.03583 / 2.29 ( 937) hydrogen bonds : angle 5.64920 / 3.93 ( 2688) Misc. bond : bond 0.00124 / 0.07 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 446 time to evaluate : 0.924 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: L residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping REVERT: A 50 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7507 (tpp) REVERT: A 169 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6236 (tm-30) REVERT: A 276 HIS cc_start: 0.6495 (OUTLIER) cc_final: 0.6055 (m-70) REVERT: A 370 ASP cc_start: 0.5226 (p0) cc_final: 0.4876 (p0) REVERT: A 381 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7429 (mp) REVERT: B 62 ASP cc_start: 0.7203 (m-30) cc_final: 0.6869 (p0) REVERT: B 113 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8577 (mt) REVERT: B 165 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8163 (mt) REVERT: E 71 LEU cc_start: 0.4578 (OUTLIER) cc_final: 0.3799 (tm) REVERT: E 140 GLU cc_start: 0.2837 (OUTLIER) cc_final: 0.1459 (pm20) REVERT: E 176 TYR cc_start: 0.5410 (OUTLIER) cc_final: 0.5158 (m-80) REVERT: E 184 GLN cc_start: 0.2389 (OUTLIER) cc_final: 0.2124 (pp30) REVERT: E 193 ILE cc_start: 0.5733 (tt) cc_final: 0.5124 (tt) REVERT: E 198 PHE cc_start: 0.4369 (m-80) cc_final: 0.3689 (m-80) REVERT: C 12 GLN cc_start: 0.6393 (tp40) cc_final: 0.5774 (mm110) REVERT: C 20 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6659 (mp) REVERT: C 225 ASP cc_start: 0.8009 (m-30) cc_final: 0.7692 (m-30) REVERT: C 294 LYS cc_start: 0.7999 (tttt) cc_final: 0.7414 (tmtt) REVERT: C 389 CYS cc_start: 0.8556 (OUTLIER) cc_final: 0.7926 (p) REVERT: D 202 GLN cc_start: 0.6216 (OUTLIER) cc_final: 0.5829 (tt0) REVERT: D 221 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7536 (ptt-90) REVERT: D 294 LYS cc_start: 0.7704 (mmpt) cc_final: 0.7329 (mtmm) REVERT: D 390 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7772 (mtp180) REVERT: F 4 LEU cc_start: 0.4813 (OUTLIER) cc_final: 0.4403 (tm) REVERT: F 15 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7478 (tpt-90) REVERT: F 61 GLU cc_start: 0.5808 (mp0) cc_final: 0.5528 (mp0) REVERT: F 77 MET cc_start: 0.4076 (mtt) cc_final: 0.3449 (ptt) REVERT: F 130 GLU cc_start: 0.4030 (OUTLIER) cc_final: 0.3631 (tt0) REVERT: F 184 GLN cc_start: 0.4127 (OUTLIER) cc_final: 0.3777 (pm20) REVERT: F 261 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6924 (ptt-90) REVERT: F 294 ASP cc_start: 0.7367 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: G 82 GLU cc_start: 0.3920 (OUTLIER) cc_final: 0.3639 (pp20) REVERT: G 96 LEU cc_start: 0.4922 (OUTLIER) cc_final: 0.4606 (tm) REVERT: G 102 ASP cc_start: 0.3653 (OUTLIER) cc_final: 0.2884 (p0) REVERT: G 125 ARG cc_start: 0.4532 (mtm-85) cc_final: 0.4153 (mtp85) REVERT: G 133 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.5925 (pt) REVERT: G 155 ARG cc_start: 0.4439 (mtm180) cc_final: 0.3873 (mtm-85) REVERT: G 176 TYR cc_start: 0.6008 (OUTLIER) cc_final: 0.5198 (m-80) REVERT: G 177 ILE cc_start: 0.6687 (mm) cc_final: 0.5893 (tt) REVERT: G 310 TRP cc_start: 0.7983 (m-90) cc_final: 0.7700 (m-90) REVERT: I 56 MET cc_start: 0.4659 (mmt) cc_final: 0.3579 (ptt) REVERT: I 99 GLU cc_start: 0.4590 (OUTLIER) cc_final: 0.4387 (mm-30) REVERT: I 223 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6280 (mppt) REVERT: I 229 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.7278 (ttp) REVERT: I 233 LEU cc_start: 0.6850 (OUTLIER) cc_final: 0.6535 (mp) REVERT: I 239 LYS cc_start: 0.6306 (mtmt) cc_final: 0.5911 (mmpt) REVERT: I 242 GLU cc_start: 0.4755 (pp20) cc_final: 0.4182 (pm20) REVERT: I 243 ARG cc_start: 0.3581 (ttm170) cc_final: 0.3125 (mpt-90) REVERT: J 51 LEU cc_start: 0.5854 (OUTLIER) cc_final: 0.5594 (tp) REVERT: J 81 GLU cc_start: 0.5271 (OUTLIER) cc_final: 0.4039 (mm-30) REVERT: J 107 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.5960 (tt) REVERT: J 135 VAL cc_start: 0.6312 (m) cc_final: 0.6050 (t) REVERT: J 158 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5842 (mtp-110) REVERT: J 175 MET cc_start: 0.6539 (ptm) cc_final: 0.6302 (ptp) REVERT: J 176 TYR cc_start: 0.6367 (OUTLIER) cc_final: 0.5934 (m-80) REVERT: J 211 GLU cc_start: 0.7083 (pm20) cc_final: 0.6843 (pm20) REVERT: J 236 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6592 (tp) REVERT: J 242 GLU cc_start: 0.6586 (mm-30) cc_final: 0.5742 (pm20) REVERT: J 304 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: J 333 ASN cc_start: 0.6916 (m-40) cc_final: 0.6612 (m-40) REVERT: K 5 ILE cc_start: 0.5453 (OUTLIER) cc_final: 0.4869 (pt) REVERT: K 80 GLU cc_start: 0.5252 (OUTLIER) cc_final: 0.4629 (mp0) REVERT: K 112 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.7062 (mm) REVERT: K 157 HIS cc_start: 0.3872 (m-70) cc_final: 0.3529 (m170) REVERT: K 162 LYS cc_start: 0.3598 (OUTLIER) cc_final: 0.2933 (pmtt) REVERT: K 172 ASN cc_start: 0.6490 (p0) cc_final: 0.6181 (p0) REVERT: K 333 ASN cc_start: 0.8095 (m-40) cc_final: 0.7795 (m110) REVERT: K 351 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7148 (pm20) REVERT: L 37 GLN cc_start: 0.6008 (mm110) cc_final: 0.5791 (mm110) REVERT: L 56 MET cc_start: 0.6189 (ttm) cc_final: 0.5826 (ttt) REVERT: L 77 MET cc_start: 0.6037 (ptp) cc_final: 0.4321 (pp-130) REVERT: L 80 GLU cc_start: 0.4098 (OUTLIER) cc_final: 0.3331 (tp30) REVERT: L 124 HIS cc_start: 0.3380 (t70) cc_final: 0.3013 (t70) REVERT: L 127 HIS cc_start: 0.4208 (p90) cc_final: 0.3230 (m170) REVERT: L 178 LEU cc_start: 0.4467 (OUTLIER) cc_final: 0.4001 (tt) REVERT: L 219 ILE cc_start: 0.6842 (mm) cc_final: 0.6625 (mm) REVERT: L 334 ASP cc_start: 0.6300 (m-30) cc_final: 0.5315 (p0) REVERT: L 351 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6683 (mt-10) REVERT: H 126 HIS cc_start: 0.5425 (OUTLIER) cc_final: 0.4458 (m-70) REVERT: H 130 GLU cc_start: 0.4792 (mm-30) cc_final: 0.4372 (mm-30) REVERT: H 195 LYS cc_start: 0.4968 (mmtt) cc_final: 0.3362 (ttmt) REVERT: H 265 ASN cc_start: 0.7373 (t0) cc_final: 0.7153 (t0) REVERT: H 266 CYS cc_start: 0.7695 (p) cc_final: 0.7408 (p) REVERT: H 282 ASP cc_start: 0.7879 (m-30) cc_final: 0.7390 (m-30) outliers start: 262 outliers final: 134 residues processed: 655 average time/residue: 0.5671 time to fit residues: 452.7159 Evaluate side-chains 576 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 398 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 276 HIS Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 15 ARG Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 GLN Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain I residue 223 LYS Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 158 ARG Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 176 TYR Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 279 VAL Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 187 GLN Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 351 GLU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 149 CYS Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 288 ARG Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 137 optimal weight: 7.9990 chunk 360 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 chunk 426 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 308 optimal weight: 9.9990 chunk 197 optimal weight: 0.7980 chunk 288 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 338 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 118 GLN E 240 GLN C 73 GLN C 235 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 HIS ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 108 ASN K 118 GLN H 30 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.196284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.174253 restraints weight = 41267.334| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.04 r_work: 0.3555 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3350 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3350 r_free = 0.3350 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3350 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36092 Z= 0.160 Angle : 0.657 8.559 49067 Z= 0.323 Chirality : 0.051 0.260 5549 Planarity : 0.005 0.075 6308 Dihedral : 11.379 166.526 5083 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 6.87 % Allowed : 28.02 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.25 (0.12), residues: 4461 helix: 0.03 (0.16), residues: 972 sheet: -1.10 (0.17), residues: 887 loop : -1.04 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 13 TYR 0.013 0.001 TYR C 256 PHE 0.035 0.002 PHE E 117 TRP 0.027 0.002 TRP D 282 HIS 0.007 0.001 HIS C 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (36080) covalent geometry : angle 0.65726 / 0.32 (49063) SS BOND : bond 0.00161 / 0.08 ( 2) SS BOND : angle 1.09223 / 0.40 ( 4) hydrogen bonds : bond 0.03759 / 2.40 ( 937) hydrogen bonds : angle 5.69545 / 3.96 ( 2688) Misc. bond : bond 0.00110 / 0.06 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 415 time to evaluate : 1.317 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping REVERT: A 50 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7565 (tpp) REVERT: A 169 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6243 (tm-30) REVERT: A 276 HIS cc_start: 0.6538 (OUTLIER) cc_final: 0.6151 (m-70) REVERT: A 294 LYS cc_start: 0.7414 (OUTLIER) cc_final: 0.7019 (mmtm) REVERT: A 304 ASN cc_start: 0.7242 (m110) cc_final: 0.6564 (t0) REVERT: A 381 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7501 (mp) REVERT: B 42 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7294 (mt-10) REVERT: B 51 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: B 62 ASP cc_start: 0.7244 (m-30) cc_final: 0.6923 (p0) REVERT: B 113 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8587 (mt) REVERT: B 165 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8150 (mt) REVERT: B 369 MET cc_start: 0.7179 (mtm) cc_final: 0.6732 (mtp) REVERT: E 51 LEU cc_start: 0.5624 (OUTLIER) cc_final: 0.5248 (pp) REVERT: E 70 ARG cc_start: 0.2890 (OUTLIER) cc_final: 0.2331 (mmm160) REVERT: E 71 LEU cc_start: 0.4980 (OUTLIER) cc_final: 0.4285 (tm) REVERT: E 134 LEU cc_start: 0.4861 (OUTLIER) cc_final: 0.4580 (tp) REVERT: E 140 GLU cc_start: 0.2784 (OUTLIER) cc_final: 0.1433 (pm20) REVERT: E 176 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.5101 (m-80) REVERT: E 184 GLN cc_start: 0.2445 (OUTLIER) cc_final: 0.2171 (pp30) REVERT: E 198 PHE cc_start: 0.4364 (m-80) cc_final: 0.2837 (t80) REVERT: C 12 GLN cc_start: 0.6376 (tp40) cc_final: 0.5797 (mm110) REVERT: C 20 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6764 (mp) REVERT: C 225 ASP cc_start: 0.8002 (m-30) cc_final: 0.7703 (m-30) REVERT: C 294 LYS cc_start: 0.8032 (tttt) cc_final: 0.7421 (tmtt) REVERT: C 321 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: D 202 GLN cc_start: 0.6291 (OUTLIER) cc_final: 0.5934 (tt0) REVERT: D 221 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7479 (ptt-90) REVERT: D 366 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7058 (mmm160) REVERT: D 390 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7773 (mtp180) REVERT: F 4 LEU cc_start: 0.4834 (OUTLIER) cc_final: 0.4093 (tm) REVERT: F 61 GLU cc_start: 0.5899 (mp0) cc_final: 0.5421 (mp0) REVERT: F 77 MET cc_start: 0.4032 (mtt) cc_final: 0.3444 (ptt) REVERT: F 96 LEU cc_start: 0.4821 (OUTLIER) cc_final: 0.4326 (tt) REVERT: F 184 GLN cc_start: 0.4235 (OUTLIER) cc_final: 0.3780 (pm20) REVERT: F 219 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7053 (pt) REVERT: F 261 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6921 (ptt-90) REVERT: F 360 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6025 (mmt) REVERT: G 82 GLU cc_start: 0.4011 (OUTLIER) cc_final: 0.3597 (pp20) REVERT: G 96 LEU cc_start: 0.4963 (OUTLIER) cc_final: 0.4668 (tm) REVERT: G 102 ASP cc_start: 0.3569 (OUTLIER) cc_final: 0.2734 (p0) REVERT: G 125 ARG cc_start: 0.4736 (mtm-85) cc_final: 0.4374 (mtp85) REVERT: G 133 ILE cc_start: 0.6346 (OUTLIER) cc_final: 0.5910 (pt) REVERT: G 155 ARG cc_start: 0.4254 (mtm180) cc_final: 0.3683 (mtm-85) REVERT: G 176 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.5267 (m-80) REVERT: G 177 ILE cc_start: 0.6828 (mm) cc_final: 0.6100 (tt) REVERT: G 261 ARG cc_start: 0.5487 (mtp-110) cc_final: 0.4992 (ptp-110) REVERT: G 310 TRP cc_start: 0.8045 (m-90) cc_final: 0.7738 (m-90) REVERT: I 56 MET cc_start: 0.4763 (mmt) cc_final: 0.3587 (ptt) REVERT: I 64 MET cc_start: 0.5010 (OUTLIER) cc_final: 0.4400 (mmt) REVERT: I 99 GLU cc_start: 0.4474 (OUTLIER) cc_final: 0.4205 (mm-30) REVERT: I 223 LYS cc_start: 0.7201 (OUTLIER) cc_final: 0.6295 (mppt) REVERT: I 229 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7251 (ttp) REVERT: I 233 LEU cc_start: 0.6800 (OUTLIER) cc_final: 0.6550 (mp) REVERT: I 239 LYS cc_start: 0.6348 (mtmt) cc_final: 0.5973 (mmpt) REVERT: I 242 GLU cc_start: 0.4913 (pp20) cc_final: 0.4268 (pm20) REVERT: I 243 ARG cc_start: 0.3561 (ttm170) cc_final: 0.3055 (mpt-90) REVERT: I 294 ASP cc_start: 0.6291 (OUTLIER) cc_final: 0.5952 (m-30) REVERT: J 33 ILE cc_start: 0.7000 (tp) cc_final: 0.6541 (mt) REVERT: J 51 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5549 (tp) REVERT: J 81 GLU cc_start: 0.5109 (OUTLIER) cc_final: 0.4148 (mm-30) REVERT: J 107 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.5991 (tt) REVERT: J 135 VAL cc_start: 0.6369 (m) cc_final: 0.6096 (t) REVERT: J 158 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5822 (mtp-110) REVERT: J 175 MET cc_start: 0.6546 (ptm) cc_final: 0.6340 (ptp) REVERT: J 176 TYR cc_start: 0.6400 (OUTLIER) cc_final: 0.6060 (m-80) REVERT: J 211 GLU cc_start: 0.7091 (pm20) cc_final: 0.6808 (pm20) REVERT: J 236 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6641 (tp) REVERT: J 242 GLU cc_start: 0.6174 (mm-30) cc_final: 0.5810 (pm20) REVERT: J 304 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: J 333 ASN cc_start: 0.6908 (m-40) cc_final: 0.6574 (m-40) REVERT: K 118 GLN cc_start: 0.3854 (OUTLIER) cc_final: 0.3190 (mp10) REVERT: K 133 ILE cc_start: 0.3770 (OUTLIER) cc_final: 0.3359 (pt) REVERT: K 157 HIS cc_start: 0.3788 (m-70) cc_final: 0.3485 (m170) REVERT: K 162 LYS cc_start: 0.3680 (OUTLIER) cc_final: 0.3059 (pmtt) REVERT: K 172 ASN cc_start: 0.6461 (p0) cc_final: 0.6162 (p0) REVERT: K 351 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7198 (pm20) REVERT: L 27 ASP cc_start: 0.6826 (t0) cc_final: 0.6299 (t70) REVERT: L 37 GLN cc_start: 0.6023 (mm110) cc_final: 0.5816 (mm110) REVERT: L 56 MET cc_start: 0.6225 (ttm) cc_final: 0.5909 (ttt) REVERT: L 77 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.4314 (pp-130) REVERT: L 80 GLU cc_start: 0.4079 (OUTLIER) cc_final: 0.3267 (tt0) REVERT: L 124 HIS cc_start: 0.3082 (t70) cc_final: 0.2797 (t70) REVERT: L 127 HIS cc_start: 0.4040 (p90) cc_final: 0.3170 (m170) REVERT: L 178 LEU cc_start: 0.4229 (OUTLIER) cc_final: 0.3674 (tt) REVERT: L 184 GLN cc_start: 0.5907 (pt0) cc_final: 0.5529 (tt0) REVERT: L 186 ILE cc_start: 0.3987 (OUTLIER) cc_final: 0.3574 (mp) REVERT: L 219 ILE cc_start: 0.6884 (mm) cc_final: 0.6628 (mm) REVERT: L 334 ASP cc_start: 0.6262 (m-30) cc_final: 0.5282 (p0) REVERT: L 351 GLU cc_start: 0.7164 (mt-10) cc_final: 0.6659 (mt-10) REVERT: H 13 ARG cc_start: 0.5796 (mpp-170) cc_final: 0.5591 (mpp-170) REVERT: H 69 GLN cc_start: 0.5615 (OUTLIER) cc_final: 0.5396 (mp10) REVERT: H 126 HIS cc_start: 0.5412 (OUTLIER) cc_final: 0.4414 (m-70) REVERT: H 130 GLU cc_start: 0.4942 (mm-30) cc_final: 0.4574 (mm-30) REVERT: H 195 LYS cc_start: 0.5046 (mmtt) cc_final: 0.3411 (ttmt) REVERT: H 210 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.5541 (ttt) REVERT: H 265 ASN cc_start: 0.7552 (t0) cc_final: 0.7346 (t0) REVERT: H 266 CYS cc_start: 0.7641 (p) cc_final: 0.7377 (p) outliers start: 272 outliers final: 161 residues processed: 633 average time/residue: 0.5884 time to fit residues: 455.2616 Evaluate side-chains 606 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 391 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain E residue 359 ILE Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 276 HIS Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 261 ARG Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 99 GLU Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 GLN Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain I residue 223 LYS Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 294 ASP Chi-restraints excluded: chain I residue 360 MET Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 158 ARG Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 176 TYR Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 236 LEU Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 279 VAL Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 148 VAL Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 187 GLN Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 351 GLU Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 77 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 246 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 288 ARG Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 295 optimal weight: 4.9990 chunk 399 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 363 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 chunk 417 optimal weight: 3.9990 chunk 433 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 305 optimal weight: 20.0000 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 338 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** E 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN C 133 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN H 30 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.196633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.174491 restraints weight = 41358.956| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.03 r_work: 0.3578 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36092 Z= 0.156 Angle : 0.658 10.965 49067 Z= 0.322 Chirality : 0.051 0.217 5549 Planarity : 0.005 0.075 6308 Dihedral : 11.289 166.359 5082 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 6.61 % Allowed : 28.44 % Favored : 64.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.17 (0.12), residues: 4461 helix: 0.09 (0.17), residues: 971 sheet: -1.06 (0.18), residues: 789 loop : -1.00 (0.11), residues: 2701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 74 TYR 0.013 0.001 TYR K 55 PHE 0.037 0.002 PHE E 117 TRP 0.027 0.002 TRP D 282 HIS 0.007 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (36080) covalent geometry : angle 0.65828 / 0.32 (49063) SS BOND : bond 0.00180 / 0.09 ( 2) SS BOND : angle 0.91584 / 0.35 ( 4) hydrogen bonds : bond 0.03684 / 2.35 ( 937) hydrogen bonds : angle 5.65840 / 3.94 ( 2688) Misc. bond : bond 0.00110 / 0.06 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 415 time to evaluate : 0.948 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping REVERT: A 169 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6245 (tm-30) REVERT: A 276 HIS cc_start: 0.6571 (OUTLIER) cc_final: 0.6148 (m-70) REVERT: A 294 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7051 (mmtm) REVERT: A 304 ASN cc_start: 0.7145 (m110) cc_final: 0.6532 (t0) REVERT: A 381 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7480 (mp) REVERT: B 42 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7440 (mt-10) REVERT: B 62 ASP cc_start: 0.7204 (m-30) cc_final: 0.6938 (p0) REVERT: B 113 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8577 (mt) REVERT: B 242 ASP cc_start: 0.6548 (OUTLIER) cc_final: 0.6256 (t0) REVERT: B 369 MET cc_start: 0.7235 (mtm) cc_final: 0.6760 (mtp) REVERT: E 51 LEU cc_start: 0.5774 (OUTLIER) cc_final: 0.5363 (pp) REVERT: E 70 ARG cc_start: 0.2963 (OUTLIER) cc_final: 0.2208 (mmm-85) REVERT: E 71 LEU cc_start: 0.5179 (OUTLIER) cc_final: 0.4458 (tm) REVERT: E 140 GLU cc_start: 0.2813 (OUTLIER) cc_final: 0.1342 (pm20) REVERT: E 176 TYR cc_start: 0.5398 (OUTLIER) cc_final: 0.5122 (m-80) REVERT: E 198 PHE cc_start: 0.4397 (m-80) cc_final: 0.2867 (t80) REVERT: C 12 GLN cc_start: 0.6340 (tp40) cc_final: 0.5803 (mm110) REVERT: C 20 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6812 (mp) REVERT: C 225 ASP cc_start: 0.8073 (m-30) cc_final: 0.7750 (m-30) REVERT: C 294 LYS cc_start: 0.8005 (tttt) cc_final: 0.7452 (tmtt) REVERT: C 321 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7736 (mt-10) REVERT: D 202 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.6024 (tt0) REVERT: D 221 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7501 (ptt-90) REVERT: D 294 LYS cc_start: 0.7665 (mmpt) cc_final: 0.7359 (mtmm) REVERT: D 366 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7118 (mmm160) REVERT: D 390 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7745 (mtp180) REVERT: F 4 LEU cc_start: 0.4831 (OUTLIER) cc_final: 0.4114 (tm) REVERT: F 61 GLU cc_start: 0.5867 (mp0) cc_final: 0.5384 (mp0) REVERT: F 77 MET cc_start: 0.4252 (mtt) cc_final: 0.3630 (ptt) REVERT: F 96 LEU cc_start: 0.4950 (OUTLIER) cc_final: 0.4451 (tt) REVERT: F 112 ILE cc_start: 0.6876 (mm) cc_final: 0.6510 (mm) REVERT: F 184 GLN cc_start: 0.4377 (OUTLIER) cc_final: 0.3866 (pm20) REVERT: F 219 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7147 (pt) REVERT: F 294 ASP cc_start: 0.7364 (OUTLIER) cc_final: 0.7089 (m-30) REVERT: G 82 GLU cc_start: 0.3974 (OUTLIER) cc_final: 0.3648 (pp20) REVERT: G 96 LEU cc_start: 0.4989 (OUTLIER) cc_final: 0.4697 (tm) REVERT: G 102 ASP cc_start: 0.3687 (OUTLIER) cc_final: 0.2819 (p0) REVERT: G 125 ARG cc_start: 0.4574 (mtm-85) cc_final: 0.4229 (mtp85) REVERT: G 133 ILE cc_start: 0.6431 (OUTLIER) cc_final: 0.5996 (pt) REVERT: G 155 ARG cc_start: 0.4403 (mtm180) cc_final: 0.3834 (mtm-85) REVERT: G 176 TYR cc_start: 0.6081 (OUTLIER) cc_final: 0.5352 (m-80) REVERT: G 177 ILE cc_start: 0.6837 (mm) cc_final: 0.6160 (tt) REVERT: G 261 ARG cc_start: 0.5509 (mtp-110) cc_final: 0.5024 (ptp-110) REVERT: G 310 TRP cc_start: 0.8054 (m-90) cc_final: 0.7708 (m-90) REVERT: G 328 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: I 56 MET cc_start: 0.4921 (mmt) cc_final: 0.3541 (ptt) REVERT: I 64 MET cc_start: 0.5076 (OUTLIER) cc_final: 0.4457 (mmt) REVERT: I 65 LYS cc_start: 0.4457 (OUTLIER) cc_final: 0.3646 (ptpt) REVERT: I 223 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6484 (mppt) REVERT: I 229 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7428 (ttp) REVERT: I 239 LYS cc_start: 0.6443 (mtmt) cc_final: 0.6080 (mmpt) REVERT: I 242 GLU cc_start: 0.4874 (pp20) cc_final: 0.4469 (pm20) REVERT: I 243 ARG cc_start: 0.3643 (ttm170) cc_final: 0.3063 (mtp85) REVERT: I 294 ASP cc_start: 0.6329 (OUTLIER) cc_final: 0.5996 (m-30) REVERT: J 51 LEU cc_start: 0.5813 (OUTLIER) cc_final: 0.5574 (tp) REVERT: J 81 GLU cc_start: 0.5147 (OUTLIER) cc_final: 0.4177 (mm-30) REVERT: J 107 LEU cc_start: 0.6536 (OUTLIER) cc_final: 0.6099 (tt) REVERT: J 135 VAL cc_start: 0.6465 (m) cc_final: 0.6182 (t) REVERT: J 158 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.5897 (mtp-110) REVERT: J 176 TYR cc_start: 0.6493 (OUTLIER) cc_final: 0.6146 (m-80) REVERT: J 211 GLU cc_start: 0.7140 (pm20) cc_final: 0.6864 (pm20) REVERT: J 242 GLU cc_start: 0.6111 (mm-30) cc_final: 0.5813 (pm20) REVERT: J 333 ASN cc_start: 0.7010 (m-40) cc_final: 0.6697 (m-40) REVERT: K 80 GLU cc_start: 0.5281 (OUTLIER) cc_final: 0.4794 (mp0) REVERT: K 112 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7242 (mm) REVERT: K 118 GLN cc_start: 0.4061 (OUTLIER) cc_final: 0.3426 (mp10) REVERT: K 133 ILE cc_start: 0.3760 (OUTLIER) cc_final: 0.3336 (pt) REVERT: K 157 HIS cc_start: 0.3875 (m-70) cc_final: 0.3596 (m-70) REVERT: K 162 LYS cc_start: 0.3525 (OUTLIER) cc_final: 0.3042 (pmtt) REVERT: K 172 ASN cc_start: 0.6476 (p0) cc_final: 0.6188 (p0) REVERT: K 333 ASN cc_start: 0.8227 (m-40) cc_final: 0.7922 (m110) REVERT: K 351 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: L 27 ASP cc_start: 0.6936 (t0) cc_final: 0.6422 (t70) REVERT: L 56 MET cc_start: 0.6301 (ttm) cc_final: 0.6027 (ttt) REVERT: L 77 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.4408 (pp-130) REVERT: L 80 GLU cc_start: 0.4167 (OUTLIER) cc_final: 0.3298 (tt0) REVERT: L 82 GLU cc_start: 0.4071 (OUTLIER) cc_final: 0.3367 (tt0) REVERT: L 124 HIS cc_start: 0.2942 (t70) cc_final: 0.2739 (t70) REVERT: L 127 HIS cc_start: 0.4177 (p90) cc_final: 0.3282 (m170) REVERT: L 178 LEU cc_start: 0.4185 (OUTLIER) cc_final: 0.3693 (tt) REVERT: L 184 GLN cc_start: 0.5732 (pt0) cc_final: 0.5282 (tt0) REVERT: L 186 ILE cc_start: 0.4050 (OUTLIER) cc_final: 0.3603 (mp) REVERT: L 219 ILE cc_start: 0.6884 (mm) cc_final: 0.6622 (mm) REVERT: L 334 ASP cc_start: 0.6338 (m-30) cc_final: 0.5370 (p0) REVERT: L 351 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6604 (mt-10) REVERT: H 13 ARG cc_start: 0.5862 (mpp-170) cc_final: 0.5301 (mmt180) REVERT: H 69 GLN cc_start: 0.5661 (OUTLIER) cc_final: 0.5443 (mp10) REVERT: H 98 SER cc_start: 0.4046 (OUTLIER) cc_final: 0.3715 (m) REVERT: H 126 HIS cc_start: 0.5467 (OUTLIER) cc_final: 0.4479 (m-70) REVERT: H 130 GLU cc_start: 0.4954 (mm-30) cc_final: 0.4630 (mm-30) REVERT: H 193 ILE cc_start: 0.4030 (OUTLIER) cc_final: 0.3749 (mm) REVERT: H 195 LYS cc_start: 0.5002 (mmtt) cc_final: 0.3366 (ttmt) REVERT: H 210 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.5658 (ttt) REVERT: H 265 ASN cc_start: 0.7535 (t0) cc_final: 0.7006 (t0) REVERT: H 266 CYS cc_start: 0.7780 (p) cc_final: 0.7541 (p) outliers start: 262 outliers final: 158 residues processed: 626 average time/residue: 0.5801 time to fit residues: 443.4158 Evaluate side-chains 605 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 395 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 242 ASP Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 70 ARG Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 299 SER Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 276 HIS Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 218 ASP Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain I residue 10 TYR Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 GLN Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain I residue 223 LYS Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 294 ASP Chi-restraints excluded: chain I residue 360 MET Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 158 ARG Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 176 TYR Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 279 VAL Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 112 ILE Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 187 GLN Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 351 GLU Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 77 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 246 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 288 ARG Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 149 CYS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 68 optimal weight: 0.0010 chunk 101 optimal weight: 10.0000 chunk 222 optimal weight: 0.2980 chunk 330 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 213 optimal weight: 0.4980 chunk 408 optimal weight: 3.9990 overall best weight: 1.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 338 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN C 73 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 333 ASN H 30 ASN H 118 GLN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.197525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.175390 restraints weight = 41419.145| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.06 r_work: 0.3573 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36092 Z= 0.127 Angle : 0.634 12.491 49067 Z= 0.308 Chirality : 0.050 0.216 5549 Planarity : 0.005 0.074 6308 Dihedral : 10.981 165.861 5078 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.60 % Favored : 94.31 % Rotamer: Outliers : 5.98 % Allowed : 29.35 % Favored : 64.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.12), residues: 4461 helix: 0.25 (0.17), residues: 973 sheet: -0.97 (0.17), residues: 897 loop : -0.93 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 200 TYR 0.013 0.001 TYR K 55 PHE 0.035 0.002 PHE E 117 TRP 0.023 0.002 TRP D 282 HIS 0.007 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (36080) covalent geometry : angle 0.63379 / 0.31 (49063) SS BOND : bond 0.00174 / 0.09 ( 2) SS BOND : angle 0.75390 / 0.29 ( 4) hydrogen bonds : bond 0.03448 / 2.20 ( 937) hydrogen bonds : angle 5.51361 / 3.84 ( 2688) Misc. bond : bond 0.00103 / 0.06 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 238 poor density : 415 time to evaluate : 0.938 Fit side-chains revert: symmetry clash Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping REVERT: A 51 GLN cc_start: 0.8048 (tt0) cc_final: 0.7778 (pt0) REVERT: A 169 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6255 (tm-30) REVERT: A 294 LYS cc_start: 0.7474 (OUTLIER) cc_final: 0.7102 (mmtm) REVERT: B 42 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7307 (mt-10) REVERT: B 62 ASP cc_start: 0.7203 (m-30) cc_final: 0.6861 (p0) REVERT: B 113 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8571 (mt) REVERT: B 116 ASP cc_start: 0.8176 (p0) cc_final: 0.7778 (p0) REVERT: B 165 LEU cc_start: 0.8577 (mt) cc_final: 0.8118 (mt) REVERT: B 369 MET cc_start: 0.7279 (mtm) cc_final: 0.6815 (mtp) REVERT: E 51 LEU cc_start: 0.5613 (OUTLIER) cc_final: 0.5199 (pp) REVERT: E 140 GLU cc_start: 0.2704 (OUTLIER) cc_final: 0.1367 (pm20) REVERT: E 176 TYR cc_start: 0.5542 (OUTLIER) cc_final: 0.5221 (m-80) REVERT: E 198 PHE cc_start: 0.4189 (m-10) cc_final: 0.2566 (t80) REVERT: E 212 LEU cc_start: 0.5231 (OUTLIER) cc_final: 0.5013 (tm) REVERT: E 279 VAL cc_start: 0.6663 (OUTLIER) cc_final: 0.6280 (t) REVERT: C 12 GLN cc_start: 0.6343 (tp40) cc_final: 0.5773 (mm110) REVERT: C 20 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6785 (mp) REVERT: C 225 ASP cc_start: 0.8071 (m-30) cc_final: 0.7732 (m-30) REVERT: C 275 LYS cc_start: 0.6339 (OUTLIER) cc_final: 0.5655 (mttp) REVERT: C 294 LYS cc_start: 0.8050 (tttt) cc_final: 0.7419 (tmtt) REVERT: C 321 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7616 (mt-10) REVERT: C 389 CYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7911 (p) REVERT: D 202 GLN cc_start: 0.6457 (OUTLIER) cc_final: 0.6092 (tt0) REVERT: D 221 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7466 (ptt-90) REVERT: D 283 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7705 (mt) REVERT: D 294 LYS cc_start: 0.7664 (mmpt) cc_final: 0.7305 (mtmm) REVERT: D 366 ARG cc_start: 0.7800 (mtp180) cc_final: 0.7072 (mmm160) REVERT: D 390 ARG cc_start: 0.8155 (mtp85) cc_final: 0.7793 (mtp180) REVERT: F 4 LEU cc_start: 0.4659 (OUTLIER) cc_final: 0.4012 (tm) REVERT: F 61 GLU cc_start: 0.5921 (mp0) cc_final: 0.5373 (mp0) REVERT: F 77 MET cc_start: 0.4198 (mtt) cc_final: 0.3556 (ptt) REVERT: F 96 LEU cc_start: 0.4595 (OUTLIER) cc_final: 0.4133 (tt) REVERT: F 112 ILE cc_start: 0.6806 (mm) cc_final: 0.6439 (mm) REVERT: F 129 GLN cc_start: 0.4455 (mm110) cc_final: 0.3347 (mm-40) REVERT: F 137 LYS cc_start: 0.5017 (OUTLIER) cc_final: 0.4321 (ptpt) REVERT: F 184 GLN cc_start: 0.4340 (OUTLIER) cc_final: 0.3837 (pm20) REVERT: F 219 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7098 (pt) REVERT: F 271 ASN cc_start: 0.8048 (m-40) cc_final: 0.7663 (m110) REVERT: F 294 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.7031 (m-30) REVERT: G 1 MET cc_start: 0.3863 (mmm) cc_final: 0.3334 (mmp) REVERT: G 6 LEU cc_start: 0.5000 (OUTLIER) cc_final: 0.4770 (mt) REVERT: G 82 GLU cc_start: 0.3740 (OUTLIER) cc_final: 0.3412 (pp20) REVERT: G 96 LEU cc_start: 0.5044 (OUTLIER) cc_final: 0.4779 (tm) REVERT: G 102 ASP cc_start: 0.3464 (OUTLIER) cc_final: 0.2728 (p0) REVERT: G 125 ARG cc_start: 0.4590 (mtm-85) cc_final: 0.4165 (mtp85) REVERT: G 133 ILE cc_start: 0.6252 (OUTLIER) cc_final: 0.5840 (pt) REVERT: G 155 ARG cc_start: 0.4324 (mtm180) cc_final: 0.3695 (mtm-85) REVERT: G 176 TYR cc_start: 0.6053 (OUTLIER) cc_final: 0.5311 (m-80) REVERT: G 177 ILE cc_start: 0.6840 (mm) cc_final: 0.6115 (tt) REVERT: G 186 ILE cc_start: 0.5248 (OUTLIER) cc_final: 0.4597 (pp) REVERT: G 261 ARG cc_start: 0.5494 (mtp-110) cc_final: 0.5019 (ptp-110) REVERT: G 310 TRP cc_start: 0.8045 (m-90) cc_final: 0.7708 (m-90) REVERT: G 328 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: I 30 ASN cc_start: 0.6602 (m-40) cc_final: 0.6155 (m-40) REVERT: I 56 MET cc_start: 0.4964 (mmt) cc_final: 0.3564 (ptt) REVERT: I 64 MET cc_start: 0.5413 (OUTLIER) cc_final: 0.4669 (mmt) REVERT: I 223 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6345 (mppt) REVERT: I 229 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7284 (ttp) REVERT: I 239 LYS cc_start: 0.6341 (mtmt) cc_final: 0.5954 (mmpt) REVERT: I 242 GLU cc_start: 0.4802 (pp20) cc_final: 0.4463 (pm20) REVERT: J 51 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5543 (tp) REVERT: J 81 GLU cc_start: 0.5144 (OUTLIER) cc_final: 0.4194 (mm-30) REVERT: J 107 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6176 (tt) REVERT: J 135 VAL cc_start: 0.6364 (m) cc_final: 0.6099 (t) REVERT: J 158 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5927 (mtp-110) REVERT: J 211 GLU cc_start: 0.7162 (pm20) cc_final: 0.6898 (pm20) REVERT: J 242 GLU cc_start: 0.6084 (mm-30) cc_final: 0.5781 (pm20) REVERT: J 304 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: J 328 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6765 (tp30) REVERT: J 333 ASN cc_start: 0.6970 (m-40) cc_final: 0.6674 (m-40) REVERT: K 5 ILE cc_start: 0.5474 (OUTLIER) cc_final: 0.5017 (pp) REVERT: K 80 GLU cc_start: 0.5467 (OUTLIER) cc_final: 0.5058 (mp0) REVERT: K 118 GLN cc_start: 0.3922 (OUTLIER) cc_final: 0.3324 (mp10) REVERT: K 133 ILE cc_start: 0.3673 (OUTLIER) cc_final: 0.3265 (pt) REVERT: K 157 HIS cc_start: 0.3929 (m-70) cc_final: 0.3634 (m-70) REVERT: K 162 LYS cc_start: 0.3440 (OUTLIER) cc_final: 0.3058 (pmtt) REVERT: K 172 ASN cc_start: 0.6457 (p0) cc_final: 0.6189 (p0) REVERT: K 333 ASN cc_start: 0.8214 (m-40) cc_final: 0.7903 (m110) REVERT: K 351 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7178 (pm20) REVERT: L 27 ASP cc_start: 0.6947 (t0) cc_final: 0.6412 (t70) REVERT: L 77 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.4320 (pp-130) REVERT: L 80 GLU cc_start: 0.4034 (OUTLIER) cc_final: 0.3249 (tt0) REVERT: L 82 GLU cc_start: 0.4408 (OUTLIER) cc_final: 0.3682 (tt0) REVERT: L 124 HIS cc_start: 0.2899 (t70) cc_final: 0.2669 (t70) REVERT: L 127 HIS cc_start: 0.4265 (p90) cc_final: 0.3292 (m170) REVERT: L 178 LEU cc_start: 0.4293 (OUTLIER) cc_final: 0.3760 (tt) REVERT: L 186 ILE cc_start: 0.4005 (OUTLIER) cc_final: 0.3614 (mp) REVERT: L 334 ASP cc_start: 0.6272 (m-30) cc_final: 0.5295 (p0) REVERT: L 351 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6710 (mt-10) REVERT: H 13 ARG cc_start: 0.5850 (mpp-170) cc_final: 0.5215 (mmt180) REVERT: H 69 GLN cc_start: 0.5577 (OUTLIER) cc_final: 0.5360 (mp10) REVERT: H 98 SER cc_start: 0.4008 (OUTLIER) cc_final: 0.3714 (m) REVERT: H 126 HIS cc_start: 0.5308 (OUTLIER) cc_final: 0.4334 (m-70) REVERT: H 130 GLU cc_start: 0.4909 (mm-30) cc_final: 0.4629 (mm-30) REVERT: H 193 ILE cc_start: 0.4013 (OUTLIER) cc_final: 0.3713 (mm) REVERT: H 195 LYS cc_start: 0.4980 (mmtt) cc_final: 0.3353 (ttmt) REVERT: H 210 MET cc_start: 0.6024 (OUTLIER) cc_final: 0.5629 (ttt) REVERT: H 265 ASN cc_start: 0.7606 (t0) cc_final: 0.7355 (t0) REVERT: H 266 CYS cc_start: 0.7617 (p) cc_final: 0.7381 (p) outliers start: 238 outliers final: 140 residues processed: 601 average time/residue: 0.5926 time to fit residues: 434.2523 Evaluate side-chains 590 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 396 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 276 HIS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 137 LYS Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 328 GLU Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 GLN Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain I residue 223 LYS Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 360 MET Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 158 ARG Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 279 VAL Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 328 GLU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 187 GLN Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 351 GLU Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 77 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 246 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 288 ARG Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 321 optimal weight: 9.9990 chunk 342 optimal weight: 5.9990 chunk 246 optimal weight: 9.9990 chunk 441 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 415 optimal weight: 9.9990 chunk 304 optimal weight: 4.9990 chunk 340 optimal weight: 4.9990 chunk 426 optimal weight: 7.9990 chunk 435 optimal weight: 0.4980 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 338 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN L 333 ASN H 30 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.196304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.174516 restraints weight = 41249.124| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.01 r_work: 0.3580 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36092 Z= 0.165 Angle : 0.670 11.805 49067 Z= 0.327 Chirality : 0.051 0.206 5549 Planarity : 0.005 0.074 6308 Dihedral : 11.034 165.694 5075 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 6.06 % Allowed : 29.38 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.12 (0.12), residues: 4461 helix: 0.20 (0.17), residues: 973 sheet: -1.03 (0.17), residues: 906 loop : -0.98 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 200 TYR 0.014 0.001 TYR K 55 PHE 0.030 0.002 PHE E 117 TRP 0.027 0.002 TRP D 282 HIS 0.007 0.001 HIS B 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (36080) covalent geometry : angle 0.66962 / 0.33 (49063) SS BOND : bond 0.00177 / 0.09 ( 2) SS BOND : angle 0.81292 / 0.32 ( 4) hydrogen bonds : bond 0.03708 / 2.36 ( 937) hydrogen bonds : angle 5.61097 / 3.90 ( 2688) Misc. bond : bond 0.00107 / 0.06 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 399 time to evaluate : 1.195 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: J residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping REVERT: A 169 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6281 (tm-30) REVERT: A 294 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7005 (mmtm) REVERT: A 304 ASN cc_start: 0.7161 (m110) cc_final: 0.6548 (t0) REVERT: B 1 MET cc_start: 0.5660 (OUTLIER) cc_final: 0.5329 (tpt) REVERT: B 42 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7226 (mt-10) REVERT: B 62 ASP cc_start: 0.7122 (m-30) cc_final: 0.6888 (p0) REVERT: B 113 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8598 (mt) REVERT: B 133 GLN cc_start: 0.5466 (OUTLIER) cc_final: 0.4467 (pt0) REVERT: B 165 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8160 (mt) REVERT: B 369 MET cc_start: 0.7225 (mtm) cc_final: 0.6776 (mtp) REVERT: E 25 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6437 (mp) REVERT: E 51 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5249 (pp) REVERT: E 140 GLU cc_start: 0.2730 (OUTLIER) cc_final: 0.1406 (pm20) REVERT: E 176 TYR cc_start: 0.5495 (OUTLIER) cc_final: 0.5168 (m-80) REVERT: E 198 PHE cc_start: 0.4333 (m-10) cc_final: 0.2711 (t80) REVERT: E 212 LEU cc_start: 0.5232 (OUTLIER) cc_final: 0.5026 (tm) REVERT: E 279 VAL cc_start: 0.6649 (OUTLIER) cc_final: 0.6262 (t) REVERT: C 12 GLN cc_start: 0.6312 (tp40) cc_final: 0.5776 (mm110) REVERT: C 20 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.6808 (mp) REVERT: C 225 ASP cc_start: 0.8019 (m-30) cc_final: 0.7689 (m-30) REVERT: C 275 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.5835 (mttp) REVERT: C 294 LYS cc_start: 0.8025 (tttt) cc_final: 0.7422 (tmtt) REVERT: C 321 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7543 (mt-10) REVERT: C 389 CYS cc_start: 0.8500 (OUTLIER) cc_final: 0.7867 (p) REVERT: D 202 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.6073 (tt0) REVERT: D 221 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7481 (ptt-90) REVERT: D 294 LYS cc_start: 0.7677 (mmpt) cc_final: 0.7323 (mtmm) REVERT: D 366 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7081 (mmm160) REVERT: D 390 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7771 (mtp180) REVERT: F 4 LEU cc_start: 0.4613 (OUTLIER) cc_final: 0.3957 (tm) REVERT: F 61 GLU cc_start: 0.5880 (OUTLIER) cc_final: 0.5290 (mp0) REVERT: F 77 MET cc_start: 0.3955 (mtt) cc_final: 0.3453 (ptt) REVERT: F 96 LEU cc_start: 0.4567 (OUTLIER) cc_final: 0.4094 (tt) REVERT: F 112 ILE cc_start: 0.6725 (mm) cc_final: 0.6402 (mm) REVERT: F 129 GLN cc_start: 0.4678 (mm110) cc_final: 0.3527 (mm-40) REVERT: F 184 GLN cc_start: 0.4419 (OUTLIER) cc_final: 0.3888 (pm20) REVERT: F 213 GLN cc_start: 0.3335 (OUTLIER) cc_final: 0.2835 (mt0) REVERT: F 219 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7095 (pt) REVERT: F 294 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.7055 (m-30) REVERT: F 360 MET cc_start: 0.7143 (OUTLIER) cc_final: 0.5981 (mmt) REVERT: G 1 MET cc_start: 0.3919 (mmm) cc_final: 0.3345 (mmp) REVERT: G 6 LEU cc_start: 0.5110 (OUTLIER) cc_final: 0.4835 (mt) REVERT: G 82 GLU cc_start: 0.3768 (OUTLIER) cc_final: 0.3409 (pp20) REVERT: G 96 LEU cc_start: 0.5039 (OUTLIER) cc_final: 0.4746 (tm) REVERT: G 102 ASP cc_start: 0.3608 (OUTLIER) cc_final: 0.2777 (p0) REVERT: G 125 ARG cc_start: 0.4587 (mtm-85) cc_final: 0.4234 (mtp85) REVERT: G 133 ILE cc_start: 0.6255 (OUTLIER) cc_final: 0.5812 (pt) REVERT: G 155 ARG cc_start: 0.4339 (mtm180) cc_final: 0.3725 (mtm-85) REVERT: G 176 TYR cc_start: 0.6039 (OUTLIER) cc_final: 0.5263 (m-80) REVERT: G 177 ILE cc_start: 0.6838 (mm) cc_final: 0.6137 (tt) REVERT: G 186 ILE cc_start: 0.5256 (OUTLIER) cc_final: 0.4627 (pp) REVERT: G 261 ARG cc_start: 0.5483 (mtp-110) cc_final: 0.5000 (ptp-110) REVERT: I 56 MET cc_start: 0.4939 (mmt) cc_final: 0.3602 (ptt) REVERT: I 64 MET cc_start: 0.5403 (OUTLIER) cc_final: 0.4645 (mmt) REVERT: I 65 LYS cc_start: 0.4387 (OUTLIER) cc_final: 0.3600 (ptpt) REVERT: I 223 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6335 (mppt) REVERT: I 229 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7268 (ttp) REVERT: I 233 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6551 (mp) REVERT: I 239 LYS cc_start: 0.6356 (mtmt) cc_final: 0.5993 (mmpt) REVERT: I 242 GLU cc_start: 0.4964 (pp20) cc_final: 0.4616 (pm20) REVERT: I 294 ASP cc_start: 0.6339 (OUTLIER) cc_final: 0.5980 (m-30) REVERT: J 51 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.5195 (tp) REVERT: J 81 GLU cc_start: 0.5050 (OUTLIER) cc_final: 0.4178 (mm-30) REVERT: J 107 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6187 (tt) REVERT: J 135 VAL cc_start: 0.6409 (m) cc_final: 0.6131 (t) REVERT: J 158 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5863 (mtp-110) REVERT: J 211 GLU cc_start: 0.7155 (pm20) cc_final: 0.6873 (pm20) REVERT: J 328 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6749 (tp30) REVERT: J 333 ASN cc_start: 0.6876 (m-40) cc_final: 0.6575 (m-40) REVERT: K 5 ILE cc_start: 0.5484 (OUTLIER) cc_final: 0.5069 (pp) REVERT: K 64 MET cc_start: 0.5993 (mpp) cc_final: 0.5753 (mpp) REVERT: K 80 GLU cc_start: 0.5620 (OUTLIER) cc_final: 0.5122 (mp0) REVERT: K 118 GLN cc_start: 0.3860 (OUTLIER) cc_final: 0.3316 (mp10) REVERT: K 133 ILE cc_start: 0.3636 (OUTLIER) cc_final: 0.3256 (pt) REVERT: K 157 HIS cc_start: 0.3959 (m-70) cc_final: 0.3715 (m-70) REVERT: K 162 LYS cc_start: 0.3458 (OUTLIER) cc_final: 0.3056 (pmtt) REVERT: K 172 ASN cc_start: 0.6477 (p0) cc_final: 0.6208 (p0) REVERT: K 333 ASN cc_start: 0.8192 (m-40) cc_final: 0.7883 (m110) REVERT: K 351 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7231 (pm20) REVERT: L 27 ASP cc_start: 0.6863 (t0) cc_final: 0.6290 (t70) REVERT: L 77 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.4487 (pp-130) REVERT: L 80 GLU cc_start: 0.4049 (OUTLIER) cc_final: 0.3215 (tt0) REVERT: L 82 GLU cc_start: 0.4219 (OUTLIER) cc_final: 0.3532 (tt0) REVERT: L 124 HIS cc_start: 0.2918 (t70) cc_final: 0.2701 (t70) REVERT: L 127 HIS cc_start: 0.4163 (p90) cc_final: 0.3194 (m170) REVERT: L 178 LEU cc_start: 0.4280 (OUTLIER) cc_final: 0.3757 (tt) REVERT: L 184 GLN cc_start: 0.5749 (pt0) cc_final: 0.5303 (tt0) REVERT: L 186 ILE cc_start: 0.3975 (OUTLIER) cc_final: 0.3553 (mp) REVERT: L 351 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6657 (mt-10) REVERT: H 98 SER cc_start: 0.4048 (OUTLIER) cc_final: 0.3731 (m) REVERT: H 118 GLN cc_start: 0.5501 (mp10) cc_final: 0.5167 (pp30) REVERT: H 126 HIS cc_start: 0.5314 (OUTLIER) cc_final: 0.4370 (m-70) REVERT: H 130 GLU cc_start: 0.4915 (mm-30) cc_final: 0.4643 (mm-30) REVERT: H 195 LYS cc_start: 0.5062 (mmtt) cc_final: 0.3391 (ttmt) REVERT: H 210 MET cc_start: 0.5899 (OUTLIER) cc_final: 0.5526 (ttt) REVERT: H 265 ASN cc_start: 0.7553 (t0) cc_final: 0.7037 (t0) REVERT: H 266 CYS cc_start: 0.7702 (p) cc_final: 0.7443 (p) outliers start: 241 outliers final: 156 residues processed: 590 average time/residue: 0.5874 time to fit residues: 422.6734 Evaluate side-chains 602 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 388 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 275 LYS Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 276 HIS Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 148 VAL Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 GLN Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 192 SER Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain I residue 223 LYS Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 294 ASP Chi-restraints excluded: chain I residue 360 MET Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 51 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 158 ARG Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 199 PRO Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 279 VAL Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 328 GLU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 187 GLN Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 351 GLU Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 77 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 246 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 288 ARG Chi-restraints excluded: chain L residue 336 LEU Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 46 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 chunk 107 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 348 optimal weight: 0.9980 chunk 375 optimal weight: 20.0000 chunk 445 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 236 optimal weight: 20.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 338 HIS ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN E 240 GLN ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 HIS K 118 GLN L 333 ASN H 30 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.196680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.174783 restraints weight = 41446.797| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 1.02 r_work: 0.3565 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 36092 Z= 0.160 Angle : 0.673 11.225 49067 Z= 0.328 Chirality : 0.051 0.212 5549 Planarity : 0.005 0.074 6308 Dihedral : 11.010 165.659 5074 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.94 % Favored : 93.97 % Rotamer: Outliers : 5.88 % Allowed : 29.56 % Favored : 64.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.12 (0.12), residues: 4461 helix: 0.21 (0.17), residues: 973 sheet: -1.01 (0.17), residues: 905 loop : -0.98 (0.12), residues: 2583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 200 TYR 0.015 0.001 TYR K 55 PHE 0.029 0.002 PHE E 117 TRP 0.028 0.002 TRP B 282 HIS 0.007 0.001 HIS C 135 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (36080) covalent geometry : angle 0.67289 / 0.33 (49063) SS BOND : bond 0.00177 / 0.09 ( 2) SS BOND : angle 0.78181 / 0.31 ( 4) hydrogen bonds : bond 0.03697 / 2.35 ( 937) hydrogen bonds : angle 5.61765 / 3.91 ( 2688) Misc. bond : bond 0.00102 / 0.06 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8922 Ramachandran restraints generated. 4461 Oldfield, 0 Emsley, 4461 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 398 time to evaluate : 1.446 Fit side-chains Corrupt residue: chain: E residue: PRO 199 >>> skipping Corrupt residue: chain: F residue: PRO 199 >>> skipping Corrupt residue: chain: G residue: PRO 199 >>> skipping revert: symmetry clash Corrupt residue: chain: I residue: PRO 199 >>> skipping revert: symmetry clash revert: symmetry clash revert: symmetry clash Corrupt residue: chain: K residue: PRO 199 >>> skipping Corrupt residue: chain: L residue: PRO 199 >>> skipping Corrupt residue: chain: H residue: PRO 199 >>> skipping REVERT: A 169 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6322 (tm-30) REVERT: A 294 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7070 (mmtm) REVERT: A 304 ASN cc_start: 0.7268 (m110) cc_final: 0.6591 (t0) REVERT: B 1 MET cc_start: 0.5632 (OUTLIER) cc_final: 0.5341 (tpt) REVERT: B 42 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7305 (mt-10) REVERT: B 62 ASP cc_start: 0.7208 (m-30) cc_final: 0.6871 (p0) REVERT: B 113 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8601 (mt) REVERT: B 133 GLN cc_start: 0.5508 (OUTLIER) cc_final: 0.4478 (pt0) REVERT: B 165 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8131 (mt) REVERT: E 25 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6359 (mp) REVERT: E 51 LEU cc_start: 0.5683 (OUTLIER) cc_final: 0.5214 (pp) REVERT: E 140 GLU cc_start: 0.2769 (OUTLIER) cc_final: 0.1435 (pm20) REVERT: E 176 TYR cc_start: 0.5560 (OUTLIER) cc_final: 0.5340 (m-80) REVERT: E 198 PHE cc_start: 0.4174 (m-10) cc_final: 0.2511 (t80) REVERT: E 212 LEU cc_start: 0.5178 (OUTLIER) cc_final: 0.4964 (tm) REVERT: E 261 ARG cc_start: 0.4809 (pmm-80) cc_final: 0.4483 (pmm150) REVERT: E 279 VAL cc_start: 0.6688 (OUTLIER) cc_final: 0.6338 (t) REVERT: C 12 GLN cc_start: 0.6297 (tp40) cc_final: 0.5769 (mm110) REVERT: C 20 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.6913 (mp) REVERT: C 225 ASP cc_start: 0.8071 (m-30) cc_final: 0.7737 (m-30) REVERT: C 275 LYS cc_start: 0.6529 (OUTLIER) cc_final: 0.5838 (mttp) REVERT: C 294 LYS cc_start: 0.8054 (tttt) cc_final: 0.7425 (tmtt) REVERT: C 321 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: C 389 CYS cc_start: 0.8613 (OUTLIER) cc_final: 0.7962 (p) REVERT: D 202 GLN cc_start: 0.6432 (OUTLIER) cc_final: 0.6043 (tt0) REVERT: D 221 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7456 (ptt-90) REVERT: D 294 LYS cc_start: 0.7687 (mmpt) cc_final: 0.7269 (mtmm) REVERT: D 366 ARG cc_start: 0.7781 (mtp180) cc_final: 0.7051 (mmm160) REVERT: D 390 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7860 (mtp180) REVERT: F 4 LEU cc_start: 0.4626 (OUTLIER) cc_final: 0.3946 (tm) REVERT: F 61 GLU cc_start: 0.5829 (OUTLIER) cc_final: 0.5316 (mp0) REVERT: F 77 MET cc_start: 0.4086 (mtt) cc_final: 0.3532 (ptt) REVERT: F 96 LEU cc_start: 0.4538 (OUTLIER) cc_final: 0.4080 (tt) REVERT: F 112 ILE cc_start: 0.6790 (mm) cc_final: 0.6397 (mm) REVERT: F 129 GLN cc_start: 0.4634 (mm110) cc_final: 0.3476 (mm-40) REVERT: F 137 LYS cc_start: 0.5026 (OUTLIER) cc_final: 0.4315 (ptpt) REVERT: F 184 GLN cc_start: 0.4439 (OUTLIER) cc_final: 0.3875 (pm20) REVERT: F 219 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7161 (pt) REVERT: F 294 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7072 (m-30) REVERT: F 360 MET cc_start: 0.7137 (OUTLIER) cc_final: 0.5980 (mmt) REVERT: G 1 MET cc_start: 0.3877 (mmm) cc_final: 0.3297 (mmp) REVERT: G 6 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.5119 (mt) REVERT: G 82 GLU cc_start: 0.3725 (OUTLIER) cc_final: 0.3355 (pp20) REVERT: G 96 LEU cc_start: 0.5138 (OUTLIER) cc_final: 0.4861 (tm) REVERT: G 102 ASP cc_start: 0.3598 (OUTLIER) cc_final: 0.2773 (p0) REVERT: G 125 ARG cc_start: 0.4612 (mtm-85) cc_final: 0.4232 (mtp85) REVERT: G 133 ILE cc_start: 0.6265 (OUTLIER) cc_final: 0.5808 (pt) REVERT: G 155 ARG cc_start: 0.4248 (mtm180) cc_final: 0.3618 (mtm-85) REVERT: G 176 TYR cc_start: 0.6083 (OUTLIER) cc_final: 0.5359 (m-80) REVERT: G 177 ILE cc_start: 0.6764 (mm) cc_final: 0.6067 (tt) REVERT: G 186 ILE cc_start: 0.5465 (OUTLIER) cc_final: 0.4844 (pp) REVERT: G 261 ARG cc_start: 0.5482 (mtp-110) cc_final: 0.5059 (ptp-170) REVERT: I 56 MET cc_start: 0.5033 (mmt) cc_final: 0.3630 (ptm) REVERT: I 64 MET cc_start: 0.5472 (OUTLIER) cc_final: 0.4709 (mmt) REVERT: I 65 LYS cc_start: 0.4361 (OUTLIER) cc_final: 0.3569 (ptpt) REVERT: I 223 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6349 (mppt) REVERT: I 229 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7244 (ttp) REVERT: I 233 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6526 (mp) REVERT: I 239 LYS cc_start: 0.6391 (mtmt) cc_final: 0.6039 (mmpt) REVERT: I 242 GLU cc_start: 0.5048 (pp20) cc_final: 0.4681 (pm20) REVERT: I 294 ASP cc_start: 0.6315 (OUTLIER) cc_final: 0.5989 (m-30) REVERT: J 81 GLU cc_start: 0.5058 (OUTLIER) cc_final: 0.4175 (mm-30) REVERT: J 107 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6195 (tt) REVERT: J 135 VAL cc_start: 0.6413 (m) cc_final: 0.6139 (t) REVERT: J 158 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5897 (mtp-110) REVERT: J 211 GLU cc_start: 0.7139 (pm20) cc_final: 0.6837 (pm20) REVERT: J 328 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6714 (tp30) REVERT: K 5 ILE cc_start: 0.5454 (OUTLIER) cc_final: 0.5014 (pp) REVERT: K 80 GLU cc_start: 0.5624 (OUTLIER) cc_final: 0.5112 (mp0) REVERT: K 118 GLN cc_start: 0.3860 (OUTLIER) cc_final: 0.3333 (mp10) REVERT: K 133 ILE cc_start: 0.3818 (OUTLIER) cc_final: 0.3391 (pt) REVERT: K 157 HIS cc_start: 0.3982 (m-70) cc_final: 0.3751 (m-70) REVERT: K 162 LYS cc_start: 0.3482 (OUTLIER) cc_final: 0.3057 (pmtt) REVERT: K 172 ASN cc_start: 0.6493 (p0) cc_final: 0.6221 (p0) REVERT: K 333 ASN cc_start: 0.8179 (m-40) cc_final: 0.7868 (m110) REVERT: K 351 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: L 27 ASP cc_start: 0.6857 (t0) cc_final: 0.6271 (t70) REVERT: L 77 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.4559 (pp-130) REVERT: L 80 GLU cc_start: 0.4038 (OUTLIER) cc_final: 0.3194 (tt0) REVERT: L 82 GLU cc_start: 0.4156 (OUTLIER) cc_final: 0.3484 (tt0) REVERT: L 124 HIS cc_start: 0.3019 (t70) cc_final: 0.2765 (t70) REVERT: L 127 HIS cc_start: 0.4009 (p90) cc_final: 0.3139 (m170) REVERT: L 178 LEU cc_start: 0.4369 (OUTLIER) cc_final: 0.3820 (tt) REVERT: L 186 ILE cc_start: 0.4034 (OUTLIER) cc_final: 0.3591 (mp) REVERT: L 279 VAL cc_start: 0.7505 (t) cc_final: 0.7291 (t) REVERT: L 351 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6722 (mt-10) REVERT: H 13 ARG cc_start: 0.5891 (mpp-170) cc_final: 0.5258 (mmp80) REVERT: H 98 SER cc_start: 0.3809 (OUTLIER) cc_final: 0.3490 (m) REVERT: H 118 GLN cc_start: 0.5498 (mp10) cc_final: 0.5115 (pp30) REVERT: H 126 HIS cc_start: 0.5312 (OUTLIER) cc_final: 0.4354 (m-70) REVERT: H 130 GLU cc_start: 0.4938 (mm-30) cc_final: 0.4660 (mm-30) REVERT: H 162 LYS cc_start: 0.4941 (OUTLIER) cc_final: 0.3561 (tttt) REVERT: H 195 LYS cc_start: 0.5064 (mmtt) cc_final: 0.3444 (ttmt) REVERT: H 210 MET cc_start: 0.6037 (OUTLIER) cc_final: 0.5630 (ttt) REVERT: H 265 ASN cc_start: 0.7714 (t0) cc_final: 0.7217 (t0) REVERT: H 266 CYS cc_start: 0.7748 (p) cc_final: 0.7492 (p) outliers start: 233 outliers final: 152 residues processed: 581 average time/residue: 0.5875 time to fit residues: 416.5083 Evaluate side-chains 601 residues out of total 3856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 391 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 276 HIS Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 358 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 133 GLN Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 264 ARG Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 64 MET Chi-restraints excluded: chain E residue 75 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 176 TYR Chi-restraints excluded: chain E residue 199 PRO Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 235 SER Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain E residue 279 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 322 ASN Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 348 SER Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 16 ARG Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 142 THR Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 253 SER Chi-restraints excluded: chain C residue 264 ARG Chi-restraints excluded: chain C residue 275 LYS Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 329 THR Chi-restraints excluded: chain C residue 389 CYS Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 23 GLU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 118 CYS Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 276 HIS Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 411 SER Chi-restraints excluded: chain F residue 4 LEU Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 100 THR Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 137 LYS Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 186 ILE Chi-restraints excluded: chain F residue 199 PRO Chi-restraints excluded: chain F residue 219 ILE Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 294 ASP Chi-restraints excluded: chain F residue 306 CYS Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 360 MET Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 39 GLU Chi-restraints excluded: chain G residue 48 HIS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 102 ASP Chi-restraints excluded: chain G residue 133 ILE Chi-restraints excluded: chain G residue 152 ASP Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 TYR Chi-restraints excluded: chain G residue 179 SER Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 199 PRO Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 262 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain G residue 294 ASP Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain I residue 64 MET Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 122 GLN Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 177 ILE Chi-restraints excluded: chain I residue 199 PRO Chi-restraints excluded: chain I residue 201 MET Chi-restraints excluded: chain I residue 223 LYS Chi-restraints excluded: chain I residue 229 MET Chi-restraints excluded: chain I residue 233 LEU Chi-restraints excluded: chain I residue 266 CYS Chi-restraints excluded: chain I residue 279 VAL Chi-restraints excluded: chain I residue 294 ASP Chi-restraints excluded: chain I residue 360 MET Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 62 LYS Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 158 ARG Chi-restraints excluded: chain J residue 171 ILE Chi-restraints excluded: chain J residue 179 SER Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 272 VAL Chi-restraints excluded: chain J residue 290 THR Chi-restraints excluded: chain J residue 304 GLU Chi-restraints excluded: chain J residue 328 GLU Chi-restraints excluded: chain K residue 5 ILE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 80 GLU Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 138 VAL Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 162 LYS Chi-restraints excluded: chain K residue 170 LYS Chi-restraints excluded: chain K residue 177 ILE Chi-restraints excluded: chain K residue 187 GLN Chi-restraints excluded: chain K residue 199 PRO Chi-restraints excluded: chain K residue 229 MET Chi-restraints excluded: chain K residue 266 CYS Chi-restraints excluded: chain K residue 279 VAL Chi-restraints excluded: chain K residue 351 GLU Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 77 MET Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 121 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 153 THR Chi-restraints excluded: chain L residue 156 ILE Chi-restraints excluded: chain L residue 158 ARG Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 186 ILE Chi-restraints excluded: chain L residue 199 PRO Chi-restraints excluded: chain L residue 235 SER Chi-restraints excluded: chain L residue 246 SER Chi-restraints excluded: chain L residue 257 ASP Chi-restraints excluded: chain L residue 288 ARG Chi-restraints excluded: chain L residue 342 SER Chi-restraints excluded: chain H residue 19 LEU Chi-restraints excluded: chain H residue 35 LEU Chi-restraints excluded: chain H residue 69 GLN Chi-restraints excluded: chain H residue 98 SER Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 113 CYS Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 126 HIS Chi-restraints excluded: chain H residue 162 LYS Chi-restraints excluded: chain H residue 176 TYR Chi-restraints excluded: chain H residue 188 LEU Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 193 ILE Chi-restraints excluded: chain H residue 199 PRO Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 236 LEU Chi-restraints excluded: chain H residue 251 VAL Chi-restraints excluded: chain H residue 278 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 388 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 316 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 406 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 428 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 374 optimal weight: 3.9990 chunk 202 optimal weight: 6.9990 chunk 421 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN ** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 184 GLN E 240 GLN C 73 GLN C 401 ASN D 46 GLN D 417 GLN ** F 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 322 ASN K 118 GLN L 164 GLN L 333 ASN H 30 ASN ** H 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.194822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.173476 restraints weight = 41330.590| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 0.99 r_work: 0.3564 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 36092 Z= 0.238 Angle : 0.752 11.480 49067 Z= 0.369 Chirality : 0.054 0.208 5549 Planarity : 0.006 0.074 6308 Dihedral : 11.363 166.794 5073 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 5.88 % Allowed : 29.66 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.32 (0.12), residues: 4461 helix: -0.03 (0.16), residues: 971 sheet: -1.15 (0.17), residues: 793 loop : -1.10 (0.11), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 200 TYR 0.017 0.002 TYR K 55 PHE 0.033 0.003 PHE K 117 TRP 0.035 0.003 TRP B 282 HIS 0.011 0.002 HIS C 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.24 (36080) covalent geometry : angle 0.75203 / 0.37 (49063) SS BOND : bond 0.00188 / 0.09 ( 2) SS BOND : angle 1.00821 / 0.43 ( 4) hydrogen bonds : bond 0.04265 / 2.73 ( 937) hydrogen bonds : angle 5.89072 / 4.11 ( 2688) Misc. bond : bond 0.00115 / 0.07 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12323.35 seconds wall clock time: 210 minutes 16.97 seconds (12616.97 seconds total)