Starting phenix.real_space_refine on Tue Aug 26 15:16:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vsv_43507/08_2025/8vsv_43507.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vsv_43507/08_2025/8vsv_43507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vsv_43507/08_2025/8vsv_43507.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vsv_43507/08_2025/8vsv_43507.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vsv_43507/08_2025/8vsv_43507.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vsv_43507/08_2025/8vsv_43507.map" } resolution = 3.8 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 216 5.16 5 C 23626 2.51 5 N 6914 2.21 5 O 7466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 185 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38222 Number of models: 1 Model: "" Number of chains: 28 Chain: "1" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 912 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 206} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 846 Unresolved non-hydrogen angles: 1245 Unresolved non-hydrogen dihedrals: 547 Unresolved non-hydrogen chiralities: 268 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 5, 'ARG:plan': 8, 'PHE:plan': 6, 'HIS:plan': 3, 'TYR:plan': 14, 'TRP:plan': 4, 'ASP:plan': 10, 'ASN:plan1': 8} Unresolved non-hydrogen planarities: 376 Chain: "2" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 856 Classifications: {'peptide': 214} Incomplete info: {'backbone_only': 201} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 815 Unresolved non-hydrogen angles: 1186 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 254 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 15, 'ARG:plan': 7, 'ASN:plan1': 7, 'TYR:plan': 8, 'TRP:plan': 2, 'PHE:plan': 9, 'GLU:plan': 10, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 360 Chain: "3" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 912 Classifications: {'peptide': 228} Incomplete info: {'backbone_only': 206} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 215} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 846 Unresolved non-hydrogen angles: 1245 Unresolved non-hydrogen dihedrals: 547 Unresolved non-hydrogen chiralities: 268 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 5, 'ARG:plan': 8, 'PHE:plan': 6, 'HIS:plan': 3, 'TYR:plan': 14, 'TRP:plan': 4, 'ASP:plan': 10, 'ASN:plan1': 8} Unresolved non-hydrogen planarities: 376 Chain: "4" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 856 Classifications: {'peptide': 214} Incomplete info: {'backbone_only': 201} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 815 Unresolved non-hydrogen angles: 1186 Unresolved non-hydrogen dihedrals: 518 Unresolved non-hydrogen chiralities: 254 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 15, 'ARG:plan': 7, 'ASN:plan1': 7, 'TYR:plan': 8, 'TRP:plan': 2, 'PHE:plan': 9, 'GLU:plan': 10, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 360 Chain: "A" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3064 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 370} Chain: "B" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3064 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 370} Chain: "C" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3064 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 370} Chain: "D" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3064 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 370} Chain: "E" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3064 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 370} Chain: "F" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3064 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 370} Chain: "a" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2664 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 312} Chain: "b" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2664 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 312} Chain: "c" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2664 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 312} Chain: "d" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2664 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 312} Chain: "e" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2664 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 312} Chain: "f" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2664 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 312} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "e" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.83, per 1000 atoms: 0.23 Number of scatterers: 38222 At special positions: 0 Unit cell: (298.32, 260.04, 224.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 216 16.00 O 7466 8.00 N 6914 7.00 C 23626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=84, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 114 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 94 " distance=2.04 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 68 " - pdb=" SG CYS A 78 " distance=2.01 Simple disulfide: pdb=" SG CYS A 260 " - pdb=" SG CYS A 272 " distance=2.03 Simple disulfide: pdb=" SG CYS A 302 " - pdb=" SG CYS A 377 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 381 " distance=2.04 Simple disulfide: pdb=" SG CYS A 329 " - pdb=" SG CYS A 371 " distance=2.03 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 94 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 68 " - pdb=" SG CYS B 78 " distance=2.03 Simple disulfide: pdb=" SG CYS B 260 " - pdb=" SG CYS B 272 " distance=2.03 Simple disulfide: pdb=" SG CYS B 302 " - pdb=" SG CYS B 377 " distance=2.03 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 329 " - pdb=" SG CYS B 371 " distance=2.03 Simple disulfide: pdb=" SG CYS C 49 " - pdb=" SG CYS C 114 " distance=2.01 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 94 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 68 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 260 " - pdb=" SG CYS C 272 " distance=2.03 Simple disulfide: pdb=" SG CYS C 302 " - pdb=" SG CYS C 377 " distance=2.03 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 329 " - pdb=" SG CYS C 371 " distance=2.03 Simple disulfide: pdb=" SG CYS D 49 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 94 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 68 " - pdb=" SG CYS D 78 " distance=2.03 Simple disulfide: pdb=" SG CYS D 260 " - pdb=" SG CYS D 272 " distance=2.01 Simple disulfide: pdb=" SG CYS D 302 " - pdb=" SG CYS D 377 " distance=2.02 Simple disulfide: pdb=" SG CYS D 307 " - pdb=" SG CYS D 381 " distance=2.01 Simple disulfide: pdb=" SG CYS D 329 " - pdb=" SG CYS D 371 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.04 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 68 " - pdb=" SG CYS E 78 " distance=2.03 Simple disulfide: pdb=" SG CYS E 260 " - pdb=" SG CYS E 272 " distance=2.03 Simple disulfide: pdb=" SG CYS E 302 " - pdb=" SG CYS E 377 " distance=2.03 Simple disulfide: pdb=" SG CYS E 307 " - pdb=" SG CYS E 381 " distance=2.06 Simple disulfide: pdb=" SG CYS E 329 " - pdb=" SG CYS E 371 " distance=2.01 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 78 " distance=2.03 Simple disulfide: pdb=" SG CYS F 260 " - pdb=" SG CYS F 272 " distance=2.03 Simple disulfide: pdb=" SG CYS F 302 " - pdb=" SG CYS F 377 " distance=2.03 Simple disulfide: pdb=" SG CYS F 307 " - pdb=" SG CYS F 381 " distance=2.03 Simple disulfide: pdb=" SG CYS F 329 " - pdb=" SG CYS F 371 " distance=2.02 Simple disulfide: pdb=" SG CYS a 19 " - pdb=" SG CYS a 122 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 27 " distance=2.03 Simple disulfide: pdb=" SG CYS a 89 " - pdb=" SG CYS a 103 " distance=2.03 Simple disulfide: pdb=" SG CYS a 150 " - pdb=" SG CYS a 263 " distance=2.03 Simple disulfide: pdb=" SG CYS a 199 " - pdb=" SG CYS a 223 " distance=2.02 Simple disulfide: pdb=" SG CYS a 201 " - pdb=" SG CYS a 217 " distance=2.04 Simple disulfide: pdb=" SG CYS b 19 " - pdb=" SG CYS b 122 " distance=2.03 Simple disulfide: pdb=" SG CYS b 22 " - pdb=" SG CYS b 27 " distance=2.03 Simple disulfide: pdb=" SG CYS b 89 " - pdb=" SG CYS b 103 " distance=2.03 Simple disulfide: pdb=" SG CYS b 150 " - pdb=" SG CYS b 263 " distance=2.03 Simple disulfide: pdb=" SG CYS b 199 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 201 " - pdb=" SG CYS b 217 " distance=2.03 Simple disulfide: pdb=" SG CYS c 19 " - pdb=" SG CYS c 122 " distance=2.02 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 27 " distance=2.03 Simple disulfide: pdb=" SG CYS c 89 " - pdb=" SG CYS c 103 " distance=2.04 Simple disulfide: pdb=" SG CYS c 150 " - pdb=" SG CYS c 263 " distance=2.05 Simple disulfide: pdb=" SG CYS c 199 " - pdb=" SG CYS c 223 " distance=2.03 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 217 " distance=2.02 Simple disulfide: pdb=" SG CYS d 19 " - pdb=" SG CYS d 122 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 27 " distance=2.03 Simple disulfide: pdb=" SG CYS d 89 " - pdb=" SG CYS d 103 " distance=2.03 Simple disulfide: pdb=" SG CYS d 150 " - pdb=" SG CYS d 263 " distance=2.03 Simple disulfide: pdb=" SG CYS d 199 " - pdb=" SG CYS d 223 " distance=2.03 Simple disulfide: pdb=" SG CYS d 201 " - pdb=" SG CYS d 217 " distance=2.04 Simple disulfide: pdb=" SG CYS e 19 " - pdb=" SG CYS e 122 " distance=2.03 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 27 " distance=2.03 Simple disulfide: pdb=" SG CYS e 89 " - pdb=" SG CYS e 103 " distance=2.02 Simple disulfide: pdb=" SG CYS e 150 " - pdb=" SG CYS e 263 " distance=2.03 Simple disulfide: pdb=" SG CYS e 199 " - pdb=" SG CYS e 223 " distance=2.04 Simple disulfide: pdb=" SG CYS e 201 " - pdb=" SG CYS e 217 " distance=2.04 Simple disulfide: pdb=" SG CYS f 19 " - pdb=" SG CYS f 122 " distance=2.00 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 27 " distance=2.02 Simple disulfide: pdb=" SG CYS f 89 " - pdb=" SG CYS f 103 " distance=2.03 Simple disulfide: pdb=" SG CYS f 150 " - pdb=" SG CYS f 263 " distance=2.03 Simple disulfide: pdb=" SG CYS f 199 " - pdb=" SG CYS f 223 " distance=2.04 Simple disulfide: pdb=" SG CYS f 201 " - pdb=" SG CYS f 217 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG G 1 " - " ASN A 134 " " NAG H 1 " - " ASN B 134 " " NAG I 1 " - " ASN C 134 " " NAG J 1 " - " ASN D 134 " " NAG K 1 " - " ASN E 134 " " NAG L 1 " - " ASN F 134 " " NAG a 401 " - " ASN a 315 " " NAG b 401 " - " ASN b 315 " " NAG c 401 " - " ASN c 315 " " NAG e 401 " - " ASN e 315 " " NAG f 401 " - " ASN f 315 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 1.2 microseconds 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8244 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 145 sheets defined 5.3% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain '1' and resid 28 through 32 Processing helix chain '1' and resid 74 through 76 No H-bonds generated for 'chain '1' and resid 74 through 76' Processing helix chain '1' and resid 87 through 91 Processing helix chain '1' and resid 139 through 141 No H-bonds generated for 'chain '1' and resid 139 through 141' Processing helix chain '1' and resid 168 through 170 No H-bonds generated for 'chain '1' and resid 168 through 170' Processing helix chain '1' and resid 199 through 201 No H-bonds generated for 'chain '1' and resid 199 through 201' Processing helix chain '1' and resid 213 through 216 Processing helix chain '2' and resid 79 through 83 removed outlier: 3.832A pdb=" N PHE 2 83 " --> pdb=" O PRO 2 80 " (cutoff:3.500A) Processing helix chain '2' and resid 121 through 127 removed outlier: 3.630A pdb=" N SER 2 127 " --> pdb=" O GLU 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 183 through 189 removed outlier: 3.675A pdb=" N HIS 2 189 " --> pdb=" O ASP 2 185 " (cutoff:3.500A) Processing helix chain '3' and resid 28 through 32 Processing helix chain '3' and resid 74 through 76 No H-bonds generated for 'chain '3' and resid 74 through 76' Processing helix chain '3' and resid 87 through 91 Processing helix chain '3' and resid 139 through 141 No H-bonds generated for 'chain '3' and resid 139 through 141' Processing helix chain '3' and resid 168 through 170 No H-bonds generated for 'chain '3' and resid 168 through 170' Processing helix chain '3' and resid 199 through 201 No H-bonds generated for 'chain '3' and resid 199 through 201' Processing helix chain '3' and resid 213 through 216 Processing helix chain '4' and resid 79 through 83 removed outlier: 3.719A pdb=" N PHE 4 83 " --> pdb=" O PRO 4 80 " (cutoff:3.500A) Processing helix chain '4' and resid 121 through 127 removed outlier: 3.627A pdb=" N SER 4 127 " --> pdb=" O GLU 4 123 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 189 removed outlier: 3.677A pdb=" N HIS 4 189 " --> pdb=" O ASP 4 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 4.086A pdb=" N GLY A 259 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A 260 " --> pdb=" O PRO A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 284 through 288 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 225 through 229 removed outlier: 4.526A pdb=" N GLY C 228 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 257 through 260 removed outlier: 3.922A pdb=" N CYS C 260 " --> pdb=" O PRO C 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 257 through 260' Processing helix chain 'C' and resid 284 through 288 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 256 through 260 removed outlier: 4.030A pdb=" N GLY D 259 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS D 260 " --> pdb=" O PRO D 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 256 through 260' Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'E' and resid 112 through 116 Processing helix chain 'E' and resid 251 through 255 Processing helix chain 'F' and resid 112 through 116 Processing helix chain 'F' and resid 251 through 255 Processing helix chain 'F' and resid 284 through 288 Processing helix chain 'a' and resid 5 through 12 removed outlier: 3.616A pdb=" N LEU a 11 " --> pdb=" O THR a 7 " (cutoff:3.500A) Processing helix chain 'a' and resid 175 through 178 Processing helix chain 'a' and resid 219 through 221 No H-bonds generated for 'chain 'a' and resid 219 through 221' Processing helix chain 'b' and resid 5 through 10 Processing helix chain 'b' and resid 219 through 223 removed outlier: 3.520A pdb=" N GLN b 222 " --> pdb=" O ASP b 219 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS b 223 " --> pdb=" O VAL b 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 219 through 223' Processing helix chain 'c' and resid 5 through 10 Processing helix chain 'c' and resid 219 through 221 No H-bonds generated for 'chain 'c' and resid 219 through 221' Processing helix chain 'd' and resid 5 through 10 Processing helix chain 'd' and resid 219 through 221 No H-bonds generated for 'chain 'd' and resid 219 through 221' Processing helix chain 'e' and resid 1 through 4 Processing helix chain 'e' and resid 5 through 12 removed outlier: 3.538A pdb=" N TYR e 9 " --> pdb=" O HIS e 5 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 178 Processing helix chain 'e' and resid 219 through 223 removed outlier: 3.900A pdb=" N CYS e 223 " --> pdb=" O VAL e 220 " (cutoff:3.500A) Processing helix chain 'f' and resid 1 through 4 Processing helix chain 'f' and resid 5 through 12 removed outlier: 3.830A pdb=" N TYR f 9 " --> pdb=" O HIS f 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU f 11 " --> pdb=" O THR f 7 " (cutoff:3.500A) Processing helix chain 'f' and resid 175 through 178 Processing helix chain 'f' and resid 219 through 223 removed outlier: 3.575A pdb=" N GLN f 222 " --> pdb=" O ASP f 219 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS f 223 " --> pdb=" O VAL f 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 219 through 223' Processing sheet with id=AA1, first strand: chain '1' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain '1' and resid 10 through 12 removed outlier: 6.920A pdb=" N MET 1 34 " --> pdb=" O VAL 1 50 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL 1 50 " --> pdb=" O MET 1 34 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TRP 1 36 " --> pdb=" O VAL 1 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 10 through 12 Processing sheet with id=AA4, first strand: chain '1' and resid 132 through 136 removed outlier: 5.144A pdb=" N ALA 1 149 " --> pdb=" O VAL 1 196 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL 1 196 " --> pdb=" O ALA 1 149 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLY 1 151 " --> pdb=" O VAL 1 194 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL 1 194 " --> pdb=" O GLY 1 151 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU 1 153 " --> pdb=" O SER 1 192 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER 1 192 " --> pdb=" O LEU 1 153 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS 1 155 " --> pdb=" O LEU 1 190 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU 1 190 " --> pdb=" O LYS 1 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 143 through 144 removed outlier: 5.144A pdb=" N ALA 1 149 " --> pdb=" O VAL 1 196 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL 1 196 " --> pdb=" O ALA 1 149 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N GLY 1 151 " --> pdb=" O VAL 1 194 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL 1 194 " --> pdb=" O GLY 1 151 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU 1 153 " --> pdb=" O SER 1 192 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SER 1 192 " --> pdb=" O LEU 1 153 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS 1 155 " --> pdb=" O LEU 1 190 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU 1 190 " --> pdb=" O LYS 1 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 163 through 166 removed outlier: 4.498A pdb=" N TYR 1 206 " --> pdb=" O VAL 1 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 4 through 7 removed outlier: 3.587A pdb=" N GLU 2 70 " --> pdb=" O SER 2 67 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 10 through 13 removed outlier: 6.518A pdb=" N MET 2 11 " --> pdb=" O GLU 2 105 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU 2 33 " --> pdb=" O TYR 2 49 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR 2 49 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP 2 35 " --> pdb=" O LEU 2 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 114 through 118 removed outlier: 5.697A pdb=" N TYR 2 173 " --> pdb=" O ASN 2 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '2' and resid 153 through 154 Processing sheet with id=AB2, first strand: chain '3' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain '3' and resid 10 through 12 removed outlier: 6.798A pdb=" N MET 3 34 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL 3 50 " --> pdb=" O MET 3 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP 3 36 " --> pdb=" O VAL 3 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '3' and resid 10 through 12 Processing sheet with id=AB5, first strand: chain '3' and resid 132 through 136 removed outlier: 5.144A pdb=" N ALA 3 149 " --> pdb=" O VAL 3 196 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL 3 196 " --> pdb=" O ALA 3 149 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLY 3 151 " --> pdb=" O VAL 3 194 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL 3 194 " --> pdb=" O GLY 3 151 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU 3 153 " --> pdb=" O SER 3 192 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER 3 192 " --> pdb=" O LEU 3 153 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS 3 155 " --> pdb=" O LEU 3 190 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU 3 190 " --> pdb=" O LYS 3 155 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '3' and resid 143 through 144 removed outlier: 5.144A pdb=" N ALA 3 149 " --> pdb=" O VAL 3 196 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL 3 196 " --> pdb=" O ALA 3 149 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLY 3 151 " --> pdb=" O VAL 3 194 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL 3 194 " --> pdb=" O GLY 3 151 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU 3 153 " --> pdb=" O SER 3 192 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER 3 192 " --> pdb=" O LEU 3 153 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS 3 155 " --> pdb=" O LEU 3 190 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU 3 190 " --> pdb=" O LYS 3 155 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '3' and resid 163 through 166 removed outlier: 4.483A pdb=" N TYR 3 206 " --> pdb=" O VAL 3 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '4' and resid 4 through 7 Processing sheet with id=AB9, first strand: chain '4' and resid 10 through 13 removed outlier: 6.492A pdb=" N MET 4 11 " --> pdb=" O GLU 4 105 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU 4 33 " --> pdb=" O TYR 4 49 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR 4 49 " --> pdb=" O LEU 4 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP 4 35 " --> pdb=" O LEU 4 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '4' and resid 114 through 118 removed outlier: 5.678A pdb=" N TYR 4 173 " --> pdb=" O ASN 4 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '4' and resid 153 through 154 Processing sheet with id=AC3, first strand: chain 'A' and resid 2 through 8 removed outlier: 3.829A pdb=" N LYS A 161 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AC5, first strand: chain 'A' and resid 31 through 37 removed outlier: 6.376A pdb=" N MET A 132 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR A 36 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLN A 130 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 145 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 184 through 186 removed outlier: 3.601A pdb=" N THR A 48 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N TYR A 46 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS A 123 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU A 44 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AC8, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AC9, first strand: chain 'A' and resid 221 through 222 Processing sheet with id=AD1, first strand: chain 'A' and resid 261 through 263 Processing sheet with id=AD2, first strand: chain 'A' and resid 301 through 304 removed outlier: 3.644A pdb=" N GLU A 301 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 319 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 353 " --> pdb=" O VAL A 319 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 307 through 308 removed outlier: 6.984A pdb=" N CYS A 307 " --> pdb=" O LYS A 382 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'A' and resid 344 through 347 removed outlier: 3.623A pdb=" N VAL A 345 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 2 through 8 removed outlier: 3.625A pdb=" N LYS B 161 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 18 through 19 removed outlier: 3.617A pdb=" N VAL B 27 " --> pdb=" O VAL B 19 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.336A pdb=" N MET B 132 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 42 through 48 removed outlier: 5.283A pdb=" N LEU B 44 " --> pdb=" O LYS B 123 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS B 123 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR B 46 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.958A pdb=" N TYR B 107 " --> pdb=" O LYS B 54 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.958A pdb=" N TYR B 107 " --> pdb=" O LYS B 54 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=AE3, first strand: chain 'B' and resid 204 through 206 Processing sheet with id=AE4, first strand: chain 'B' and resid 221 through 222 Processing sheet with id=AE5, first strand: chain 'B' and resid 338 through 340 removed outlier: 3.708A pdb=" N PHE B 353 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 319 " --> pdb=" O PHE B 353 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 316 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 301 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N LYS B 382 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS B 307 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 344 through 347 removed outlier: 3.692A pdb=" N GLY B 327 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE B 366 " --> pdb=" O CYS B 377 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 2 through 8 removed outlier: 3.761A pdb=" N LYS C 161 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 18 through 19 removed outlier: 6.337A pdb=" N MET C 132 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 184 through 186 removed outlier: 3.615A pdb=" N VAL C 178 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N TYR C 46 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS C 123 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N LEU C 44 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.579A pdb=" N TYR C 107 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 59 " --> pdb=" O MET C 103 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.579A pdb=" N TYR C 107 " --> pdb=" O LYS C 54 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 221 through 222 Processing sheet with id=AF4, first strand: chain 'C' and resid 338 through 340 removed outlier: 7.053A pdb=" N ILE C 316 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 301 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYS C 322 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP C 299 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N LYS C 382 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N CYS C 307 " --> pdb=" O LYS C 382 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 344 through 347 Processing sheet with id=AF6, first strand: chain 'C' and resid 366 through 367 removed outlier: 4.275A pdb=" N PHE C 366 " --> pdb=" O CYS C 377 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 2 through 8 Processing sheet with id=AF8, first strand: chain 'D' and resid 18 through 19 Processing sheet with id=AF9, first strand: chain 'D' and resid 24 through 25 removed outlier: 4.544A pdb=" N THR D 289 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 32 through 35 removed outlier: 6.333A pdb=" N MET D 132 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 145 " --> pdb=" O VAL D 133 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 42 through 48 removed outlier: 5.921A pdb=" N LEU D 44 " --> pdb=" O LYS D 123 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LYS D 123 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR D 46 " --> pdb=" O ALA D 121 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AG4, first strand: chain 'D' and resid 204 through 206 Processing sheet with id=AG5, first strand: chain 'D' and resid 221 through 222 Processing sheet with id=AG6, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AG7, first strand: chain 'D' and resid 301 through 307 removed outlier: 7.048A pdb=" N ILE D 316 " --> pdb=" O THR D 305 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 344 through 347 removed outlier: 3.555A pdb=" N VAL D 345 " --> pdb=" O CYS D 329 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE D 366 " --> pdb=" O CYS D 377 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 2 through 8 removed outlier: 3.501A pdb=" N ILE E 281 " --> pdb=" O HIS E 3 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 17 through 19 Processing sheet with id=AH2, first strand: chain 'E' and resid 31 through 33 Processing sheet with id=AH3, first strand: chain 'E' and resid 42 through 48 removed outlier: 6.854A pdb=" N ALA E 121 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ILE E 47 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA E 119 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.622A pdb=" N TYR E 107 " --> pdb=" O LYS E 54 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.622A pdb=" N TYR E 107 " --> pdb=" O LYS E 54 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 204 through 206 Processing sheet with id=AH7, first strand: chain 'E' and resid 221 through 222 Processing sheet with id=AH8, first strand: chain 'E' and resid 301 through 306 removed outlier: 7.014A pdb=" N ILE E 316 " --> pdb=" O THR E 305 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 344 through 347 Processing sheet with id=AI1, first strand: chain 'F' and resid 2 through 8 removed outlier: 3.676A pdb=" N ILE F 281 " --> pdb=" O HIS F 3 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS F 161 " --> pdb=" O ASP F 282 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AI3, first strand: chain 'F' and resid 31 through 33 removed outlier: 3.892A pdb=" N VAL F 133 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA F 145 " --> pdb=" O VAL F 133 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 42 through 48 removed outlier: 5.915A pdb=" N LEU F 44 " --> pdb=" O LYS F 123 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS F 123 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TYR F 46 " --> pdb=" O ALA F 121 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.902A pdb=" N TYR F 107 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 59 " --> pdb=" O MET F 103 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.902A pdb=" N TYR F 107 " --> pdb=" O LYS F 54 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 204 through 205 Processing sheet with id=AI8, first strand: chain 'F' and resid 221 through 222 Processing sheet with id=AI9, first strand: chain 'F' and resid 339 through 340 removed outlier: 6.869A pdb=" N ILE F 316 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU F 301 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N LYS F 382 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N CYS F 307 " --> pdb=" O LYS F 382 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 344 through 347 Processing sheet with id=AJ2, first strand: chain 'a' and resid 34 through 37 removed outlier: 4.849A pdb=" N GLU a 35 " --> pdb=" O GLN a 48 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN a 48 " --> pdb=" O GLU a 35 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG a 46 " --> pdb=" O ARG a 37 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR a 64 " --> pdb=" O GLY a 54 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'a' and resid 34 through 37 removed outlier: 4.849A pdb=" N GLU a 35 " --> pdb=" O GLN a 48 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN a 48 " --> pdb=" O GLU a 35 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG a 46 " --> pdb=" O ARG a 37 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR a 97 " --> pdb=" O THR a 49 " (cutoff:3.500A) removed outlier: 9.273A pdb=" N ALA a 51 " --> pdb=" O HIS a 95 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N HIS a 95 " --> pdb=" O ALA a 51 " (cutoff:3.500A) removed outlier: 9.361A pdb=" N PHE a 53 " --> pdb=" O SER a 93 " (cutoff:3.500A) removed outlier: 11.232A pdb=" N SER a 93 " --> pdb=" O PHE a 53 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'a' and resid 82 through 84 removed outlier: 4.962A pdb=" N ASP a 107 " --> pdb=" O HIS a 126 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'a' and resid 147 through 148 Processing sheet with id=AJ6, first strand: chain 'a' and resid 152 through 153 Processing sheet with id=AJ7, first strand: chain 'a' and resid 163 through 164 Processing sheet with id=AJ8, first strand: chain 'a' and resid 166 through 167 Processing sheet with id=AJ9, first strand: chain 'a' and resid 172 through 173 Processing sheet with id=AK1, first strand: chain 'a' and resid 179 through 180 Processing sheet with id=AK2, first strand: chain 'a' and resid 272 through 276 Processing sheet with id=AK3, first strand: chain 'a' and resid 304 through 308 removed outlier: 3.558A pdb=" N LEU a 292 " --> pdb=" O GLN a 306 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU a 323 " --> pdb=" O VAL a 335 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS a 333 " --> pdb=" O TYR a 325 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'b' and resid 33 through 37 removed outlier: 8.038A pdb=" N ILE b 33 " --> pdb=" O SER b 50 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER b 50 " --> pdb=" O ILE b 33 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU b 35 " --> pdb=" O GLN b 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN b 48 " --> pdb=" O GLU b 35 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG b 46 " --> pdb=" O ARG b 37 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N TYR b 97 " --> pdb=" O THR b 49 " (cutoff:3.500A) removed outlier: 9.904A pdb=" N ALA b 51 " --> pdb=" O HIS b 95 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N HIS b 95 " --> pdb=" O ALA b 51 " (cutoff:3.500A) removed outlier: 9.876A pdb=" N PHE b 53 " --> pdb=" O SER b 93 " (cutoff:3.500A) removed outlier: 10.861A pdb=" N SER b 93 " --> pdb=" O PHE b 53 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'b' and resid 64 through 69 removed outlier: 3.519A pdb=" N PHE b 67 " --> pdb=" O LYS b 74 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'b' and resid 82 through 84 removed outlier: 4.719A pdb=" N ASP b 107 " --> pdb=" O HIS b 126 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'b' and resid 146 through 148 Processing sheet with id=AK8, first strand: chain 'b' and resid 152 through 153 Processing sheet with id=AK9, first strand: chain 'b' and resid 163 through 164 Processing sheet with id=AL1, first strand: chain 'b' and resid 166 through 167 Processing sheet with id=AL2, first strand: chain 'b' and resid 172 through 173 Processing sheet with id=AL3, first strand: chain 'b' and resid 178 through 180 Processing sheet with id=AL4, first strand: chain 'b' and resid 272 through 276 removed outlier: 3.840A pdb=" N THR b 279 " --> pdb=" O LYS b 276 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU b 284 " --> pdb=" O THR b 312 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR b 312 " --> pdb=" O LEU b 284 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'b' and resid 304 through 308 Processing sheet with id=AL6, first strand: chain 'c' and resid 33 through 37 removed outlier: 8.257A pdb=" N ILE c 33 " --> pdb=" O SER c 50 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER c 50 " --> pdb=" O ILE c 33 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU c 35 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN c 48 " --> pdb=" O GLU c 35 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N SER c 50 " --> pdb=" O MET c 68 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET c 68 " --> pdb=" O SER c 50 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY c 54 " --> pdb=" O TYR c 64 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR c 64 " --> pdb=" O GLY c 54 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE c 67 " --> pdb=" O LYS c 74 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR c 72 " --> pdb=" O ASN c 69 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'c' and resid 33 through 37 removed outlier: 8.257A pdb=" N ILE c 33 " --> pdb=" O SER c 50 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER c 50 " --> pdb=" O ILE c 33 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU c 35 " --> pdb=" O GLN c 48 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN c 48 " --> pdb=" O GLU c 35 " (cutoff:3.500A) removed outlier: 11.332A pdb=" N ILE c 47 " --> pdb=" O GLN c 102 " (cutoff:3.500A) removed outlier: 11.088A pdb=" N GLN c 102 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 11.171A pdb=" N THR c 49 " --> pdb=" O LEU c 100 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N LEU c 100 " --> pdb=" O THR c 49 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N ALA c 51 " --> pdb=" O TYR c 98 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N TYR c 98 " --> pdb=" O ALA c 51 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'c' and resid 82 through 84 removed outlier: 4.213A pdb=" N THR c 108 " --> pdb=" O HIS c 126 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N HIS c 126 " --> pdb=" O THR c 108 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N THR c 110 " --> pdb=" O VAL c 124 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL c 124 " --> pdb=" O THR c 110 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLY c 112 " --> pdb=" O CYS c 122 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N CYS c 122 " --> pdb=" O GLY c 112 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'c' and resid 147 through 148 Processing sheet with id=AM1, first strand: chain 'c' and resid 152 through 153 Processing sheet with id=AM2, first strand: chain 'c' and resid 163 through 164 Processing sheet with id=AM3, first strand: chain 'c' and resid 172 through 173 removed outlier: 4.065A pdb=" N TYR c 198 " --> pdb=" O ARG c 224 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'c' and resid 178 through 181 removed outlier: 3.719A pdb=" N LYS c 184 " --> pdb=" O HIS c 181 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'c' and resid 272 through 276 Processing sheet with id=AM6, first strand: chain 'c' and resid 304 through 308 removed outlier: 3.718A pdb=" N ILE c 308 " --> pdb=" O THR c 290 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR c 290 " --> pdb=" O ILE c 308 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR c 293 " --> pdb=" O THR c 326 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'd' and resid 33 through 37 removed outlier: 8.178A pdb=" N ILE d 33 " --> pdb=" O SER d 50 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER d 50 " --> pdb=" O ILE d 33 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU d 35 " --> pdb=" O GLN d 48 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN d 48 " --> pdb=" O GLU d 35 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N SER d 50 " --> pdb=" O MET d 68 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N MET d 68 " --> pdb=" O SER d 50 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY d 54 " --> pdb=" O TYR d 64 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR d 64 " --> pdb=" O GLY d 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE d 67 " --> pdb=" O LYS d 74 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'd' and resid 33 through 37 removed outlier: 8.178A pdb=" N ILE d 33 " --> pdb=" O SER d 50 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N SER d 50 " --> pdb=" O ILE d 33 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU d 35 " --> pdb=" O GLN d 48 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN d 48 " --> pdb=" O GLU d 35 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR d 97 " --> pdb=" O THR d 49 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N ALA d 51 " --> pdb=" O HIS d 95 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N HIS d 95 " --> pdb=" O ALA d 51 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N PHE d 53 " --> pdb=" O SER d 93 " (cutoff:3.500A) removed outlier: 11.728A pdb=" N SER d 93 " --> pdb=" O PHE d 53 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'd' and resid 82 through 84 removed outlier: 5.170A pdb=" N ASP d 107 " --> pdb=" O HIS d 126 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'd' and resid 146 through 149 Processing sheet with id=AN2, first strand: chain 'd' and resid 152 through 153 Processing sheet with id=AN3, first strand: chain 'd' and resid 163 through 164 Processing sheet with id=AN4, first strand: chain 'd' and resid 172 through 173 removed outlier: 3.620A pdb=" N TYR d 226 " --> pdb=" O LYS d 196 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'd' and resid 178 through 180 removed outlier: 3.692A pdb=" N SER d 179 " --> pdb=" O LYS d 186 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL d 185 " --> pdb=" O THR d 214 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP d 212 " --> pdb=" O ILE d 187 " (cutoff:3.500A) Processing sheet with id=AN6, first strand: chain 'd' and resid 272 through 276 removed outlier: 3.662A pdb=" N ILE d 281 " --> pdb=" O GLU d 274 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'd' and resid 304 through 305 removed outlier: 3.566A pdb=" N THR d 293 " --> pdb=" O THR d 326 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'e' and resid 33 through 37 removed outlier: 4.823A pdb=" N GLU e 35 " --> pdb=" O GLN e 48 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN e 48 " --> pdb=" O GLU e 35 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG e 46 " --> pdb=" O ARG e 37 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN e 102 " --> pdb=" O LEU e 91 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LEU e 91 " --> pdb=" O GLN e 102 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'e' and resid 52 through 54 removed outlier: 3.611A pdb=" N GLY e 54 " --> pdb=" O TYR e 64 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TYR e 64 " --> pdb=" O GLY e 54 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE e 67 " --> pdb=" O LYS e 74 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'e' and resid 82 through 84 removed outlier: 4.680A pdb=" N ASP e 107 " --> pdb=" O HIS e 126 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'e' and resid 147 through 149 Processing sheet with id=AO3, first strand: chain 'e' and resid 152 through 153 Processing sheet with id=AO4, first strand: chain 'e' and resid 163 through 164 Processing sheet with id=AO5, first strand: chain 'e' and resid 172 through 173 Processing sheet with id=AO6, first strand: chain 'e' and resid 179 through 180 Processing sheet with id=AO7, first strand: chain 'e' and resid 272 through 275 Processing sheet with id=AO8, first strand: chain 'e' and resid 304 through 308 removed outlier: 3.614A pdb=" N LEU e 323 " --> pdb=" O VAL e 335 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'f' and resid 17 through 18 removed outlier: 3.794A pdb=" N ALA f 17 " --> pdb=" O SER f 29 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'f' and resid 33 through 37 removed outlier: 8.221A pdb=" N ILE f 33 " --> pdb=" O SER f 50 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N SER f 50 " --> pdb=" O ILE f 33 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU f 35 " --> pdb=" O GLN f 48 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN f 48 " --> pdb=" O GLU f 35 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG f 46 " --> pdb=" O ARG f 37 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'f' and resid 33 through 37 removed outlier: 8.221A pdb=" N ILE f 33 " --> pdb=" O SER f 50 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N SER f 50 " --> pdb=" O ILE f 33 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLU f 35 " --> pdb=" O GLN f 48 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLN f 48 " --> pdb=" O GLU f 35 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG f 46 " --> pdb=" O ARG f 37 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N ILE f 47 " --> pdb=" O GLN f 102 " (cutoff:3.500A) removed outlier: 10.373A pdb=" N GLN f 102 " --> pdb=" O ILE f 47 " (cutoff:3.500A) removed outlier: 10.765A pdb=" N THR f 49 " --> pdb=" O LEU f 100 " (cutoff:3.500A) removed outlier: 10.203A pdb=" N LEU f 100 " --> pdb=" O THR f 49 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N ALA f 51 " --> pdb=" O TYR f 98 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TYR f 98 " --> pdb=" O ALA f 51 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'f' and resid 82 through 84 removed outlier: 3.572A pdb=" N THR f 108 " --> pdb=" O HIS f 126 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N HIS f 126 " --> pdb=" O THR f 108 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N THR f 110 " --> pdb=" O VAL f 124 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL f 124 " --> pdb=" O THR f 110 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLY f 112 " --> pdb=" O CYS f 122 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N CYS f 122 " --> pdb=" O GLY f 112 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'f' and resid 147 through 148 Processing sheet with id=AP5, first strand: chain 'f' and resid 152 through 153 Processing sheet with id=AP6, first strand: chain 'f' and resid 163 through 164 Processing sheet with id=AP7, first strand: chain 'f' and resid 172 through 173 Processing sheet with id=AP8, first strand: chain 'f' and resid 179 through 180 Processing sheet with id=AP9, first strand: chain 'f' and resid 272 through 276 Processing sheet with id=AQ1, first strand: chain 'f' and resid 304 through 308 removed outlier: 3.757A pdb=" N THR f 293 " --> pdb=" O THR f 326 " (cutoff:3.500A) 1102 hydrogen bonds defined for protein. 2568 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.11 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 6502 1.28 - 1.42: 10322 1.42 - 1.56: 22093 1.56 - 1.70: 3 1.70 - 1.83: 264 Bond restraints: 39184 Sorted by residual: bond pdb=" C TRP C 89 " pdb=" O TRP C 89 " ideal model delta sigma weight residual 1.235 1.142 0.094 1.26e-02 6.30e+03 5.52e+01 bond pdb=" C TRP C 89 " pdb=" N GLY C 90 " ideal model delta sigma weight residual 1.331 1.246 0.084 1.46e-02 4.69e+03 3.33e+01 bond pdb=" N TYR A 391 " pdb=" CA TYR A 391 " ideal model delta sigma weight residual 1.453 1.495 -0.042 8.30e-03 1.45e+04 2.51e+01 bond pdb=" CZ ARG c 46 " pdb=" NH2 ARG c 46 " ideal model delta sigma weight residual 1.330 1.279 0.051 1.30e-02 5.92e+03 1.53e+01 bond pdb=" CE1 HIS C 183 " pdb=" NE2 HIS C 183 " ideal model delta sigma weight residual 1.321 1.283 0.038 1.00e-02 1.00e+04 1.48e+01 ... (remaining 39179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 46403 1.88 - 3.76: 5675 3.76 - 5.65: 835 5.65 - 7.53: 78 7.53 - 9.41: 11 Bond angle restraints: 53002 Sorted by residual: angle pdb=" CA ASP e 287 " pdb=" CB ASP e 287 " pdb=" CG ASP e 287 " ideal model delta sigma weight residual 112.60 117.70 -5.10 1.00e+00 1.00e+00 2.61e+01 angle pdb=" OE1 GLN c 222 " pdb=" CD GLN c 222 " pdb=" NE2 GLN c 222 " ideal model delta sigma weight residual 122.60 117.56 5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" N TYR C 391 " pdb=" CA TYR C 391 " pdb=" C TYR C 391 " ideal model delta sigma weight residual 110.08 116.98 -6.90 1.38e+00 5.25e-01 2.50e+01 angle pdb=" C MET C 88 " pdb=" N TRP C 89 " pdb=" CA TRP C 89 " ideal model delta sigma weight residual 121.54 130.75 -9.21 1.91e+00 2.74e-01 2.33e+01 angle pdb=" O TRP C 89 " pdb=" C TRP C 89 " pdb=" N GLY C 90 " ideal model delta sigma weight residual 122.59 116.23 6.36 1.33e+00 5.65e-01 2.29e+01 ... (remaining 52997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 21506 21.37 - 42.73: 939 42.73 - 64.10: 179 64.10 - 85.47: 49 85.47 - 106.83: 29 Dihedral angle restraints: 22702 sinusoidal: 8964 harmonic: 13738 Sorted by residual: dihedral pdb=" CD ARG f 224 " pdb=" NE ARG f 224 " pdb=" CZ ARG f 224 " pdb=" NH1 ARG f 224 " ideal model delta sinusoidal sigma weight residual 0.00 89.09 -89.09 1 1.00e+01 1.00e-02 9.45e+01 dihedral pdb=" CD ARG f 13 " pdb=" NE ARG f 13 " pdb=" CZ ARG f 13 " pdb=" NH1 ARG f 13 " ideal model delta sinusoidal sigma weight residual 0.00 -64.15 64.15 1 1.00e+01 1.00e-02 5.41e+01 dihedral pdb=" CB CYS F 329 " pdb=" SG CYS F 329 " pdb=" SG CYS F 371 " pdb=" CB CYS F 371 " ideal model delta sinusoidal sigma weight residual 93.00 152.40 -59.40 1 1.00e+01 1.00e-02 4.71e+01 ... (remaining 22699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 4797 0.108 - 0.217: 547 0.217 - 0.325: 69 0.325 - 0.433: 9 0.433 - 0.542: 1 Chirality restraints: 5423 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.84e+02 chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.74e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.04e+01 ... (remaining 5420 not shown) Planarity restraints: 7173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 401 " -0.336 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG c 401 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG c 401 " -0.136 2.00e-02 2.50e+03 pdb=" N2 NAG c 401 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG c 401 " -0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 89 " 0.252 2.00e-02 2.50e+03 1.27e-01 4.01e+02 pdb=" CG TRP A 89 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 89 " -0.092 2.00e-02 2.50e+03 pdb=" CD2 TRP A 89 " -0.086 2.00e-02 2.50e+03 pdb=" NE1 TRP A 89 " -0.078 2.00e-02 2.50e+03 pdb=" CE2 TRP A 89 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 89 " -0.176 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 89 " 0.144 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 89 " -0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP A 89 " 0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 401 " -0.175 2.00e-02 2.50e+03 1.48e-01 2.72e+02 pdb=" C7 NAG e 401 " 0.038 2.00e-02 2.50e+03 pdb=" C8 NAG e 401 " -0.122 2.00e-02 2.50e+03 pdb=" N2 NAG e 401 " 0.249 2.00e-02 2.50e+03 pdb=" O7 NAG e 401 " 0.008 2.00e-02 2.50e+03 ... (remaining 7170 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 271 2.59 - 3.17: 31086 3.17 - 3.74: 55047 3.74 - 4.32: 73121 4.32 - 4.90: 122603 Nonbonded interactions: 282128 Sorted by model distance: nonbonded pdb=" CD1 LEU c 291 " pdb=" CD ARG c 305 " model vdw 2.010 3.860 nonbonded pdb=" O PRO F 8 " pdb=" OH TYR F 15 " model vdw 2.077 3.040 nonbonded pdb=" OD1 ASN F 328 " pdb=" OG1 THR F 346 " model vdw 2.164 3.040 nonbonded pdb=" CZ PHE F 95 " pdb=" CB LYS f 200 " model vdw 2.186 3.740 nonbonded pdb=" OG1 THR f 294 " pdb=" OG1 THR f 304 " model vdw 2.190 3.040 ... (remaining 282123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain '1' selection = chain '3' } ncs_group { reference = chain '2' selection = chain '4' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 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: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.210 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 39291 Z= 0.523 Angle : 1.262 14.511 53239 Z= 0.800 Chirality : 0.072 0.542 5423 Planarity : 0.014 0.492 7162 Dihedral : 13.237 106.834 14206 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.38 % Favored : 90.27 % Rotamer: Outliers : 5.98 % Allowed : 9.87 % Favored : 84.15 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.11), residues: 5280 helix: -4.18 (0.25), residues: 130 sheet: -1.09 (0.13), residues: 1554 loop : -1.64 (0.10), residues: 3596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG e 295 TYR 0.193 0.010 TYR d 15 PHE 0.074 0.006 PHE C 95 TRP 0.252 0.015 TRP A 89 HIS 0.020 0.001 HIS a 213 Details of bonding type rmsd covalent geometry : bond 0.00826 (39184) covalent geometry : angle 1.23908 (53002) SS BOND : bond 0.00830 ( 84) SS BOND : angle 1.93038 ( 168) hydrogen bonds : bond 0.21990 ( 1062) hydrogen bonds : angle 10.03228 ( 2568) link_BETA1-4 : bond 0.04562 ( 12) link_BETA1-4 : angle 7.22124 ( 36) link_NAG-ASN : bond 0.01063 ( 11) link_NAG-ASN : angle 5.28397 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1477 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 1250 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9036 (mttp) cc_final: 0.8830 (mtmm) REVERT: A 28 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7552 (p90) REVERT: A 113 GLU cc_start: 0.8636 (mp0) cc_final: 0.8394 (mp0) REVERT: A 143 ARG cc_start: 0.7400 (tpt170) cc_final: 0.6708 (tpp-160) REVERT: A 163 ILE cc_start: 0.9509 (mt) cc_final: 0.9271 (mm) REVERT: A 205 GLN cc_start: 0.8303 (mt0) cc_final: 0.8000 (mt0) REVERT: A 319 VAL cc_start: 0.8834 (t) cc_final: 0.8487 (t) REVERT: A 343 ASN cc_start: 0.8003 (p0) cc_final: 0.7622 (p0) REVERT: B 3 HIS cc_start: 0.9240 (t70) cc_final: 0.9013 (t-90) REVERT: B 4 THR cc_start: 0.9266 (p) cc_final: 0.9051 (p) REVERT: B 7 MET cc_start: 0.8143 (ttm) cc_final: 0.7575 (ttm) REVERT: B 37 ARG cc_start: 0.7641 (mpp80) cc_final: 0.7425 (mpp80) REVERT: B 79 GLN cc_start: 0.9076 (tt0) cc_final: 0.8858 (tt0) REVERT: B 116 ILE cc_start: 0.9340 (pt) cc_final: 0.9051 (mm) REVERT: B 130 GLN cc_start: 0.8628 (mt0) cc_final: 0.8351 (mt0) REVERT: B 192 GLU cc_start: 0.4709 (tt0) cc_final: 0.3575 (mt-10) REVERT: B 279 ILE cc_start: 0.8142 (mm) cc_final: 0.7877 (mm) REVERT: B 304 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.8744 (mm) REVERT: B 354 THR cc_start: 0.8856 (p) cc_final: 0.8566 (p) REVERT: B 368 LEU cc_start: 0.9355 (tp) cc_final: 0.9143 (tp) REVERT: C 10 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8477 (mtmt) REVERT: C 16 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8435 (ptpp) REVERT: C 30 GLN cc_start: 0.8583 (tt0) cc_final: 0.8346 (tt0) REVERT: C 175 ASP cc_start: 0.8498 (t70) cc_final: 0.8191 (t70) REVERT: C 205 GLN cc_start: 0.8430 (mt0) cc_final: 0.8169 (mt0) REVERT: D 21 ARG cc_start: 0.8660 (tpp-160) cc_final: 0.7922 (mmm-85) REVERT: D 113 GLU cc_start: 0.8832 (mp0) cc_final: 0.8219 (mp0) REVERT: D 143 ARG cc_start: 0.7429 (ttt90) cc_final: 0.7072 (ttt90) REVERT: D 187 ASN cc_start: 0.8750 (p0) cc_final: 0.8393 (m-40) REVERT: D 303 LYS cc_start: 0.8257 (tttt) cc_final: 0.8008 (ttpp) REVERT: D 342 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8080 (mp0) REVERT: D 343 ASN cc_start: 0.8561 (p0) cc_final: 0.8243 (p0) REVERT: E 3 HIS cc_start: 0.8955 (t70) cc_final: 0.8742 (t-170) REVERT: E 11 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8667 (m) REVERT: E 30 GLN cc_start: 0.7873 (mt0) cc_final: 0.7238 (mt0) REVERT: E 37 ARG cc_start: 0.8031 (ptt90) cc_final: 0.7611 (ptt-90) REVERT: E 149 VAL cc_start: 0.8240 (p) cc_final: 0.8027 (p) REVERT: E 159 ASP cc_start: 0.8647 (p0) cc_final: 0.7892 (p0) REVERT: E 192 GLU cc_start: 0.4313 (tt0) cc_final: 0.3240 (mt-10) REVERT: E 203 ASP cc_start: 0.8546 (p0) cc_final: 0.8254 (p0) REVERT: E 214 LEU cc_start: 0.8754 (pt) cc_final: 0.8392 (pp) REVERT: E 312 ASP cc_start: 0.8681 (t0) cc_final: 0.8422 (m-30) REVERT: E 331 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8423 (pt) REVERT: E 341 LYS cc_start: 0.9254 (tttt) cc_final: 0.8881 (ttpp) REVERT: F 30 GLN cc_start: 0.7631 (tt0) cc_final: 0.7416 (tt0) REVERT: F 61 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7840 (tptp) REVERT: F 243 ARG cc_start: 0.9366 (ttt180) cc_final: 0.9082 (ttt180) REVERT: F 321 TYR cc_start: 0.5808 (m-80) cc_final: 0.5359 (m-80) REVERT: a 29 SER cc_start: 0.9437 (t) cc_final: 0.9169 (m) REVERT: a 73 GLN cc_start: 0.8529 (mp10) cc_final: 0.7834 (mm-40) REVERT: a 194 GLN cc_start: 0.8564 (pt0) cc_final: 0.8212 (pm20) REVERT: a 222 GLN cc_start: 0.9054 (mt0) cc_final: 0.8745 (tm-30) REVERT: a 254 VAL cc_start: 0.8766 (t) cc_final: 0.8407 (m) REVERT: a 285 HIS cc_start: 0.8569 (m90) cc_final: 0.8349 (m-70) REVERT: a 302 ASN cc_start: 0.9230 (t0) cc_final: 0.8785 (t0) REVERT: a 306 GLN cc_start: 0.9274 (pp30) cc_final: 0.8237 (pp30) REVERT: a 336 TRP cc_start: 0.5106 (OUTLIER) cc_final: 0.4848 (p-90) REVERT: b 48 GLN cc_start: 0.8887 (tt0) cc_final: 0.7728 (tt0) REVERT: b 71 LYS cc_start: 0.8872 (mtmt) cc_final: 0.8615 (mppt) REVERT: b 97 TYR cc_start: 0.8669 (m-80) cc_final: 0.8345 (m-80) REVERT: b 107 ASP cc_start: 0.7917 (m-30) cc_final: 0.7640 (m-30) REVERT: b 110 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9048 (m) REVERT: b 139 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7327 (ptp90) REVERT: b 235 TYR cc_start: 0.8298 (t80) cc_final: 0.7883 (t80) REVERT: b 324 GLU cc_start: 0.8144 (pp20) cc_final: 0.7942 (pp20) REVERT: c 3 ASP cc_start: 0.8560 (p0) cc_final: 0.8025 (t0) REVERT: c 18 ASP cc_start: 0.7381 (m-30) cc_final: 0.7053 (m-30) REVERT: c 64 TYR cc_start: 0.8478 (m-80) cc_final: 0.7170 (m-80) REVERT: c 73 GLN cc_start: 0.8333 (pt0) cc_final: 0.7655 (pm20) REVERT: c 138 TYR cc_start: 0.5852 (OUTLIER) cc_final: 0.4980 (t80) REVERT: c 151 ASN cc_start: 0.8760 (p0) cc_final: 0.8515 (p0) REVERT: c 317 THR cc_start: 0.9241 (p) cc_final: 0.9018 (t) REVERT: d 11 LEU cc_start: 0.8892 (mp) cc_final: 0.8546 (mm) REVERT: d 31 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9077 (pp) REVERT: d 37 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8327 (mmm-85) REVERT: d 114 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.7014 (t-170) REVERT: d 136 GLU cc_start: 0.7932 (mp0) cc_final: 0.7599 (mp0) REVERT: d 222 GLN cc_start: 0.8448 (mt0) cc_final: 0.8034 (mt0) REVERT: d 224 ARG cc_start: 0.5549 (OUTLIER) cc_final: 0.5266 (mmp-170) REVERT: d 229 ASP cc_start: 0.8546 (t0) cc_final: 0.8137 (t0) REVERT: d 291 LEU cc_start: 0.9512 (tp) cc_final: 0.9135 (tt) REVERT: d 302 ASN cc_start: 0.9194 (t0) cc_final: 0.8855 (t0) REVERT: d 317 THR cc_start: 0.9027 (m) cc_final: 0.8761 (p) REVERT: e 24 HIS cc_start: 0.8516 (OUTLIER) cc_final: 0.8068 (p90) REVERT: e 68 MET cc_start: 0.8121 (ttt) cc_final: 0.7694 (tpp) REVERT: e 69 ASN cc_start: 0.9435 (t0) cc_final: 0.8944 (t0) REVERT: e 165 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8257 (tp30) REVERT: e 174 ASP cc_start: 0.7122 (t0) cc_final: 0.6720 (t0) REVERT: e 178 LEU cc_start: 0.8584 (mt) cc_final: 0.8346 (tp) REVERT: e 254 VAL cc_start: 0.9525 (t) cc_final: 0.9297 (p) REVERT: f 62 LEU cc_start: 0.9023 (pt) cc_final: 0.8630 (tp) REVERT: f 64 TYR cc_start: 0.8860 (m-80) cc_final: 0.8525 (m-10) REVERT: f 98 TYR cc_start: 0.8900 (m-80) cc_final: 0.8589 (m-80) REVERT: f 163 TYR cc_start: 0.8599 (m-80) cc_final: 0.8327 (m-80) REVERT: f 274 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7849 (mt-10) REVERT: f 275 HIS cc_start: 0.4830 (t70) cc_final: 0.3991 (t70) REVERT: f 302 ASN cc_start: 0.9343 (t0) cc_final: 0.9089 (t0) REVERT: f 323 LEU cc_start: 0.9172 (tp) cc_final: 0.8911 (tt) outliers start: 227 outliers final: 87 residues processed: 1404 average time/residue: 0.2078 time to fit residues: 471.8654 Evaluate side-chains 824 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 722 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 100 ASN Chi-restraints excluded: chain C residue 143 ARG Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain D residue 28 HIS Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 100 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 253 ASN Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 387 HIS Chi-restraints excluded: chain a residue 3 ASP Chi-restraints excluded: chain a residue 76 ILE Chi-restraints excluded: chain a residue 99 ILE Chi-restraints excluded: chain a residue 118 ASN Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 133 VAL Chi-restraints excluded: chain a residue 154 THR Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 315 ASN Chi-restraints excluded: chain a residue 336 TRP Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 114 HIS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 248 PHE Chi-restraints excluded: chain b residue 266 THR Chi-restraints excluded: chain b residue 279 THR Chi-restraints excluded: chain b residue 285 HIS Chi-restraints excluded: chain b residue 315 ASN Chi-restraints excluded: chain c residue 22 CYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 138 TYR Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain c residue 338 GLN Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 22 CYS Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 37 ARG Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain d residue 114 HIS Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 224 ARG Chi-restraints excluded: chain d residue 280 LEU Chi-restraints excluded: chain e residue 24 HIS Chi-restraints excluded: chain e residue 27 CYS Chi-restraints excluded: chain e residue 99 ILE Chi-restraints excluded: chain e residue 114 HIS Chi-restraints excluded: chain e residue 167 HIS Chi-restraints excluded: chain e residue 247 THR Chi-restraints excluded: chain e residue 248 PHE Chi-restraints excluded: chain e residue 285 HIS Chi-restraints excluded: chain e residue 290 THR Chi-restraints excluded: chain e residue 315 ASN Chi-restraints excluded: chain f residue 27 CYS Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 55 LEU Chi-restraints excluded: chain f residue 131 ARG Chi-restraints excluded: chain f residue 167 HIS Chi-restraints excluded: chain f residue 224 ARG Chi-restraints excluded: chain f residue 308 ILE Chi-restraints excluded: chain f residue 336 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 394 optimal weight: 0.6980 chunk 430 optimal weight: 3.9990 chunk 41 optimal weight: 50.0000 chunk 265 optimal weight: 0.9990 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 0.8980 chunk 414 optimal weight: 0.9990 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 0.4980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 100 ASN A 102 GLN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 363 HIS A 395 HIS ** B 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 ASN B 356 HIS C 35 ASN C 219 ASN C 363 HIS D 356 HIS D 363 HIS E 28 HIS ** E 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 HIS F 183 HIS F 271 ASN F 369 GLN a 95 HIS a 114 HIS a 167 HIS ** a 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 329 ASN ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 155 HIS b 167 HIS b 194 GLN b 275 HIS b 283 HIS b 302 ASN ** c 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 167 HIS c 175 HIS c 275 HIS d 102 GLN d 155 HIS d 162 HIS d 167 HIS ** e 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 175 HIS ** e 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 102 GLN f 118 ASN f 162 HIS ** f 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 175 HIS f 222 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.111443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.083924 restraints weight = 90457.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086514 restraints weight = 44798.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.088201 restraints weight = 27522.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089246 restraints weight = 19617.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.089985 restraints weight = 15707.751| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 39291 Z= 0.166 Angle : 0.728 10.323 53239 Z= 0.377 Chirality : 0.049 0.340 5423 Planarity : 0.005 0.073 7162 Dihedral : 9.835 79.771 6377 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.24 % Favored : 91.61 % Rotamer: Outliers : 6.29 % Allowed : 16.72 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.96 (0.11), residues: 5280 helix: -3.65 (0.31), residues: 134 sheet: -0.95 (0.13), residues: 1632 loop : -1.42 (0.10), residues: 3514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 207 TYR 0.024 0.002 TYR E 76 PHE 0.040 0.002 PHE F 95 TRP 0.024 0.002 TRP d 233 HIS 0.014 0.001 HIS e 275 Details of bonding type rmsd covalent geometry : bond 0.00378 (39184) covalent geometry : angle 0.71597 (53002) SS BOND : bond 0.00352 ( 84) SS BOND : angle 1.46513 ( 168) hydrogen bonds : bond 0.04216 ( 1062) hydrogen bonds : angle 7.50578 ( 2568) link_BETA1-4 : bond 0.00984 ( 12) link_BETA1-4 : angle 3.49692 ( 36) link_NAG-ASN : bond 0.00491 ( 11) link_NAG-ASN : angle 2.72124 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 788 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LYS cc_start: 0.9132 (mttp) cc_final: 0.8870 (mtmm) REVERT: A 103 MET cc_start: 0.8323 (ttm) cc_final: 0.7793 (tpp) REVERT: A 143 ARG cc_start: 0.7287 (tpt170) cc_final: 0.6407 (tpp-160) REVERT: A 283 ILE cc_start: 0.9446 (mm) cc_final: 0.9244 (mm) REVERT: A 334 PRO cc_start: 0.9172 (Cg_exo) cc_final: 0.8190 (Cg_endo) REVERT: A 343 ASN cc_start: 0.8195 (p0) cc_final: 0.7833 (p0) REVERT: A 367 LYS cc_start: 0.8993 (mmtm) cc_final: 0.8681 (mmtp) REVERT: B 175 ASP cc_start: 0.8676 (m-30) cc_final: 0.8450 (m-30) REVERT: B 192 GLU cc_start: 0.5216 (tt0) cc_final: 0.4901 (tt0) REVERT: B 203 ASP cc_start: 0.8655 (p0) cc_final: 0.8435 (p0) REVERT: B 252 LEU cc_start: 0.9509 (tp) cc_final: 0.9181 (tt) REVERT: B 304 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8928 (mm) REVERT: B 367 LYS cc_start: 0.8756 (tppt) cc_final: 0.8420 (tppt) REVERT: B 369 GLN cc_start: 0.9116 (tt0) cc_final: 0.8774 (tp-100) REVERT: C 10 LYS cc_start: 0.8961 (mtpt) cc_final: 0.8297 (mtmm) REVERT: C 45 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8546 (tp30) REVERT: C 85 TYR cc_start: 0.9336 (t80) cc_final: 0.9119 (t80) REVERT: C 103 MET cc_start: 0.8110 (tmm) cc_final: 0.7707 (tmm) REVERT: C 152 GLU cc_start: 0.3821 (pt0) cc_final: 0.3291 (pt0) REVERT: C 175 ASP cc_start: 0.8530 (t70) cc_final: 0.8127 (t70) REVERT: C 213 ASP cc_start: 0.8678 (t0) cc_final: 0.8240 (t0) REVERT: C 262 ILE cc_start: 0.8752 (mt) cc_final: 0.8531 (mt) REVERT: D 45 GLU cc_start: 0.9033 (tp30) cc_final: 0.8658 (mm-30) REVERT: D 152 GLU cc_start: 0.6567 (tt0) cc_final: 0.6180 (tt0) REVERT: D 171 TRP cc_start: 0.8917 (t60) cc_final: 0.8691 (t60) REVERT: D 297 VAL cc_start: 0.8654 (m) cc_final: 0.8419 (m) REVERT: D 303 LYS cc_start: 0.8372 (tttt) cc_final: 0.8119 (ttpp) REVERT: D 343 ASN cc_start: 0.8476 (p0) cc_final: 0.8120 (p0) REVERT: D 344 ASP cc_start: 0.8394 (t0) cc_final: 0.8156 (p0) REVERT: E 37 ARG cc_start: 0.7928 (ptt90) cc_final: 0.7276 (ptt-90) REVERT: E 102 GLN cc_start: 0.9196 (tt0) cc_final: 0.8805 (tm-30) REVERT: E 149 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7911 (p) REVERT: E 171 TRP cc_start: 0.8883 (t60) cc_final: 0.8345 (t60) REVERT: E 192 GLU cc_start: 0.4153 (tt0) cc_final: 0.3617 (tt0) REVERT: E 290 ARG cc_start: 0.8246 (mmt180) cc_final: 0.7738 (mmt180) REVERT: E 341 LYS cc_start: 0.9392 (tttt) cc_final: 0.9033 (ttpp) REVERT: E 367 LYS cc_start: 0.8549 (ttpp) cc_final: 0.8265 (ttpp) REVERT: F 50 LYS cc_start: 0.9193 (tttt) cc_final: 0.8843 (tttp) REVERT: F 61 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7939 (tptp) REVERT: F 183 HIS cc_start: 0.7555 (t70) cc_final: 0.7335 (t-170) REVERT: F 215 TYR cc_start: 0.8538 (t80) cc_final: 0.8293 (t80) REVERT: F 290 ARG cc_start: 0.9296 (mmm-85) cc_final: 0.9007 (mmm160) REVERT: a 73 GLN cc_start: 0.8519 (mp10) cc_final: 0.8202 (mp10) REVERT: a 194 GLN cc_start: 0.8542 (pt0) cc_final: 0.8124 (pm20) REVERT: a 285 HIS cc_start: 0.8736 (m90) cc_final: 0.8503 (m-70) REVERT: a 302 ASN cc_start: 0.9371 (t0) cc_final: 0.8774 (t0) REVERT: a 306 GLN cc_start: 0.9364 (pp30) cc_final: 0.8121 (pp30) REVERT: a 336 TRP cc_start: 0.4611 (OUTLIER) cc_final: 0.4300 (p-90) REVERT: b 3 ASP cc_start: 0.8472 (m-30) cc_final: 0.7869 (t0) REVERT: b 15 TYR cc_start: 0.6833 (t80) cc_final: 0.6116 (t80) REVERT: b 34 GLU cc_start: 0.8666 (pm20) cc_final: 0.8289 (pm20) REVERT: b 48 GLN cc_start: 0.8613 (tt0) cc_final: 0.8223 (tt0) REVERT: b 80 ASN cc_start: 0.8660 (m-40) cc_final: 0.7568 (t0) REVERT: b 82 HIS cc_start: 0.6675 (m170) cc_final: 0.6284 (m170) REVERT: b 97 TYR cc_start: 0.8562 (m-80) cc_final: 0.8285 (m-80) REVERT: b 110 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.9021 (m) REVERT: b 139 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8164 (ptp-170) REVERT: b 235 TYR cc_start: 0.8638 (t80) cc_final: 0.8430 (t80) REVERT: b 240 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8642 (mm) REVERT: c 3 ASP cc_start: 0.8627 (p0) cc_final: 0.7866 (t0) REVERT: c 64 TYR cc_start: 0.8566 (m-80) cc_final: 0.7473 (m-80) REVERT: c 68 MET cc_start: 0.7569 (tpp) cc_final: 0.7105 (tpp) REVERT: c 97 TYR cc_start: 0.8878 (m-80) cc_final: 0.8523 (m-10) REVERT: c 107 ASP cc_start: 0.7264 (t70) cc_final: 0.7002 (t0) REVERT: c 138 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.5171 (t80) REVERT: c 217 CYS cc_start: 0.4185 (OUTLIER) cc_final: 0.3667 (m) REVERT: c 224 ARG cc_start: 0.5762 (OUTLIER) cc_final: 0.4032 (mtm-85) REVERT: c 327 TRP cc_start: 0.9532 (t-100) cc_final: 0.9242 (t-100) REVERT: c 338 GLN cc_start: 0.4405 (OUTLIER) cc_final: 0.4117 (tt0) REVERT: d 31 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9050 (pp) REVERT: d 98 TYR cc_start: 0.8950 (m-80) cc_final: 0.8693 (m-80) REVERT: d 174 ASP cc_start: 0.7669 (t0) cc_final: 0.7468 (t0) REVERT: d 219 ASP cc_start: 0.8461 (t0) cc_final: 0.8249 (t0) REVERT: d 222 GLN cc_start: 0.8647 (mt0) cc_final: 0.8153 (mt0) REVERT: d 229 ASP cc_start: 0.8570 (t0) cc_final: 0.8243 (t0) REVERT: d 302 ASN cc_start: 0.9279 (t0) cc_final: 0.9008 (t0) REVERT: d 317 THR cc_start: 0.9144 (m) cc_final: 0.8904 (p) REVERT: e 24 HIS cc_start: 0.8743 (OUTLIER) cc_final: 0.8488 (p90) REVERT: e 113 PHE cc_start: 0.8846 (p90) cc_final: 0.8586 (p90) REVERT: e 120 HIS cc_start: 0.8578 (OUTLIER) cc_final: 0.8294 (t-90) REVERT: e 165 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8250 (tp30) REVERT: e 168 GLN cc_start: 0.8841 (pt0) cc_final: 0.8250 (pm20) REVERT: e 333 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7859 (ttpp) REVERT: f 33 ILE cc_start: 0.9290 (mm) cc_final: 0.9087 (mm) REVERT: f 64 TYR cc_start: 0.8894 (m-80) cc_final: 0.8483 (m-10) REVERT: f 98 TYR cc_start: 0.8895 (m-80) cc_final: 0.8413 (m-80) REVERT: f 178 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.7650 (tt) REVERT: f 275 HIS cc_start: 0.4379 (t70) cc_final: 0.3853 (t70) REVERT: f 302 ASN cc_start: 0.9408 (t0) cc_final: 0.9086 (t0) REVERT: f 323 LEU cc_start: 0.9383 (tp) cc_final: 0.9127 (tt) outliers start: 239 outliers final: 126 residues processed: 954 average time/residue: 0.1903 time to fit residues: 299.5696 Evaluate side-chains 790 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 648 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 TRP Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 52 LYS Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 93 TYR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 387 HIS Chi-restraints excluded: chain a residue 76 ILE Chi-restraints excluded: chain a residue 93 SER Chi-restraints excluded: chain a residue 99 ILE Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 154 THR Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 197 TYR Chi-restraints excluded: chain a residue 257 VAL Chi-restraints excluded: chain a residue 290 THR Chi-restraints excluded: chain a residue 315 ASN Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 335 VAL Chi-restraints excluded: chain a residue 336 TRP Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 114 HIS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 151 ASN Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 240 LEU Chi-restraints excluded: chain b residue 248 PHE Chi-restraints excluded: chain b residue 257 VAL Chi-restraints excluded: chain b residue 266 THR Chi-restraints excluded: chain b residue 285 HIS Chi-restraints excluded: chain c residue 22 CYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 65 MET Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 138 TYR Chi-restraints excluded: chain c residue 187 ILE Chi-restraints excluded: chain c residue 217 CYS Chi-restraints excluded: chain c residue 224 ARG Chi-restraints excluded: chain c residue 228 ILE Chi-restraints excluded: chain c residue 275 HIS Chi-restraints excluded: chain c residue 281 ILE Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain c residue 338 GLN Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 22 CYS Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 114 HIS Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 254 VAL Chi-restraints excluded: chain d residue 267 LEU Chi-restraints excluded: chain e residue 24 HIS Chi-restraints excluded: chain e residue 27 CYS Chi-restraints excluded: chain e residue 99 ILE Chi-restraints excluded: chain e residue 114 HIS Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 167 HIS Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain e residue 247 THR Chi-restraints excluded: chain e residue 285 HIS Chi-restraints excluded: chain e residue 290 THR Chi-restraints excluded: chain e residue 315 ASN Chi-restraints excluded: chain e residue 333 LYS Chi-restraints excluded: chain f residue 27 CYS Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 45 ILE Chi-restraints excluded: chain f residue 99 ILE Chi-restraints excluded: chain f residue 108 THR Chi-restraints excluded: chain f residue 131 ARG Chi-restraints excluded: chain f residue 177 LEU Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain f residue 308 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 376 optimal weight: 0.2980 chunk 325 optimal weight: 0.0770 chunk 206 optimal weight: 4.9990 chunk 37 optimal weight: 40.0000 chunk 38 optimal weight: 50.0000 chunk 393 optimal weight: 0.9980 chunk 463 optimal weight: 2.9990 chunk 430 optimal weight: 5.9990 chunk 89 optimal weight: 0.1980 chunk 156 optimal weight: 0.8980 chunk 339 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS C 35 ASN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN F 369 GLN ** a 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 114 HIS a 162 HIS a 167 HIS ** a 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 277 HIS ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 160 GLN b 283 HIS ** c 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 ASN ** c 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 73 GLN d 102 GLN d 151 ASN d 155 HIS ** e 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 HIS e 194 GLN ** e 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 102 GLN f 160 GLN ** f 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 330 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.115290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.087523 restraints weight = 89326.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.090225 restraints weight = 43556.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091950 restraints weight = 26573.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.093065 restraints weight = 18875.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.093806 restraints weight = 15014.368| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39291 Z= 0.131 Angle : 0.679 9.376 53239 Z= 0.346 Chirality : 0.047 0.345 5423 Planarity : 0.005 0.077 7162 Dihedral : 8.347 76.608 6318 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.43 % Favored : 91.46 % Rotamer: Outliers : 5.90 % Allowed : 18.48 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.11), residues: 5280 helix: -3.50 (0.34), residues: 132 sheet: -0.95 (0.12), residues: 1794 loop : -1.36 (0.11), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 26 TYR 0.040 0.002 TYR F 15 PHE 0.039 0.002 PHE F 95 TRP 0.023 0.002 TRP E 89 HIS 0.013 0.001 HIS b 288 Details of bonding type rmsd covalent geometry : bond 0.00301 (39184) covalent geometry : angle 0.66727 (53002) SS BOND : bond 0.00350 ( 84) SS BOND : angle 1.50888 ( 168) hydrogen bonds : bond 0.03466 ( 1062) hydrogen bonds : angle 6.78022 ( 2568) link_BETA1-4 : bond 0.00902 ( 12) link_BETA1-4 : angle 3.24481 ( 36) link_NAG-ASN : bond 0.00545 ( 11) link_NAG-ASN : angle 2.53781 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 722 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.5937 (mmt) cc_final: 0.5641 (mmt) REVERT: A 109 GLU cc_start: 0.8571 (tt0) cc_final: 0.8277 (pt0) REVERT: A 143 ARG cc_start: 0.7279 (tpt170) cc_final: 0.6439 (tpp-160) REVERT: A 203 ASP cc_start: 0.8997 (p0) cc_final: 0.8497 (p0) REVERT: A 343 ASN cc_start: 0.8145 (p0) cc_final: 0.7786 (p0) REVERT: A 385 LYS cc_start: 0.3344 (OUTLIER) cc_final: 0.1709 (mttt) REVERT: B 20 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8060 (tm-30) REVERT: B 270 GLU cc_start: 0.9096 (pt0) cc_final: 0.8787 (mt-10) REVERT: B 367 LYS cc_start: 0.8677 (tppt) cc_final: 0.8361 (tppt) REVERT: B 369 GLN cc_start: 0.9180 (tt0) cc_final: 0.8767 (tp-100) REVERT: C 10 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8551 (mttm) REVERT: C 45 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8333 (tp30) REVERT: C 152 GLU cc_start: 0.3415 (pt0) cc_final: 0.2742 (pt0) REVERT: C 159 ASP cc_start: 0.8174 (p0) cc_final: 0.7967 (p0) REVERT: C 175 ASP cc_start: 0.8448 (t70) cc_final: 0.8068 (t70) REVERT: C 213 ASP cc_start: 0.8680 (t0) cc_final: 0.8222 (t0) REVERT: C 282 ASP cc_start: 0.8831 (t0) cc_final: 0.8450 (p0) REVERT: C 385 LYS cc_start: 0.8575 (mppt) cc_final: 0.8341 (mppt) REVERT: D 143 ARG cc_start: 0.7064 (ttt90) cc_final: 0.6075 (ttt90) REVERT: D 219 ASN cc_start: 0.9481 (OUTLIER) cc_final: 0.9272 (t0) REVERT: D 303 LYS cc_start: 0.8332 (tttt) cc_final: 0.8120 (ttpp) REVERT: D 306 GLU cc_start: 0.4279 (mt-10) cc_final: 0.3380 (pm20) REVERT: D 312 ASP cc_start: 0.7175 (t0) cc_final: 0.6967 (t0) REVERT: D 343 ASN cc_start: 0.8450 (p0) cc_final: 0.8106 (p0) REVERT: D 344 ASP cc_start: 0.8300 (t0) cc_final: 0.8060 (p0) REVERT: E 7 MET cc_start: 0.8532 (ppp) cc_final: 0.7808 (ppp) REVERT: E 37 ARG cc_start: 0.8003 (ptt90) cc_final: 0.7292 (ptt-90) REVERT: E 149 VAL cc_start: 0.8165 (p) cc_final: 0.7870 (p) REVERT: E 161 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8423 (mmmt) REVERT: E 192 GLU cc_start: 0.4411 (tt0) cc_final: 0.4038 (tt0) REVERT: E 341 LYS cc_start: 0.9389 (tttt) cc_final: 0.9041 (ttpp) REVERT: E 367 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8229 (ttpp) REVERT: F 50 LYS cc_start: 0.9134 (tttt) cc_final: 0.8887 (tttp) REVERT: F 61 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7934 (tptp) REVERT: F 183 HIS cc_start: 0.7588 (t70) cc_final: 0.7309 (t-170) REVERT: F 230 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.9050 (m) REVERT: F 239 SER cc_start: 0.9244 (t) cc_final: 0.8720 (p) REVERT: F 283 ILE cc_start: 0.9333 (mt) cc_final: 0.9019 (mt) REVERT: F 290 ARG cc_start: 0.9301 (mmm-85) cc_final: 0.8987 (mmm160) REVERT: F 301 GLU cc_start: 0.8000 (tp30) cc_final: 0.7697 (tp30) REVERT: a 21 ASN cc_start: 0.9164 (t0) cc_final: 0.8958 (t0) REVERT: a 35 GLU cc_start: 0.7484 (tt0) cc_final: 0.7265 (tt0) REVERT: a 50 SER cc_start: 0.9250 (OUTLIER) cc_final: 0.8578 (t) REVERT: a 73 GLN cc_start: 0.8633 (mp10) cc_final: 0.8393 (mt0) REVERT: a 194 GLN cc_start: 0.8506 (pt0) cc_final: 0.8058 (pm20) REVERT: a 233 TRP cc_start: 0.8750 (m-90) cc_final: 0.8501 (m-90) REVERT: a 302 ASN cc_start: 0.9325 (t0) cc_final: 0.8714 (t0) REVERT: b 3 ASP cc_start: 0.8524 (m-30) cc_final: 0.7980 (t0) REVERT: b 15 TYR cc_start: 0.6664 (t80) cc_final: 0.6165 (t80) REVERT: b 80 ASN cc_start: 0.8652 (m-40) cc_final: 0.7539 (t0) REVERT: b 82 HIS cc_start: 0.6749 (m170) cc_final: 0.6258 (m170) REVERT: b 97 TYR cc_start: 0.8636 (m-80) cc_final: 0.8259 (m-80) REVERT: b 110 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9122 (m) REVERT: b 139 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8028 (ptp90) REVERT: b 155 HIS cc_start: 0.8222 (t-170) cc_final: 0.7935 (t-90) REVERT: b 240 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8545 (mm) REVERT: c 3 ASP cc_start: 0.8657 (p0) cc_final: 0.7880 (t0) REVERT: c 18 ASP cc_start: 0.7435 (m-30) cc_final: 0.7172 (m-30) REVERT: c 41 HIS cc_start: 0.9197 (OUTLIER) cc_final: 0.8056 (m170) REVERT: c 68 MET cc_start: 0.7693 (tpp) cc_final: 0.7222 (tpp) REVERT: c 107 ASP cc_start: 0.7279 (t70) cc_final: 0.6986 (t0) REVERT: c 138 TYR cc_start: 0.6029 (OUTLIER) cc_final: 0.5326 (t80) REVERT: c 165 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: c 174 ASP cc_start: 0.7790 (t0) cc_final: 0.7580 (t0) REVERT: d 49 THR cc_start: 0.9238 (OUTLIER) cc_final: 0.8962 (t) REVERT: d 82 HIS cc_start: 0.6398 (m170) cc_final: 0.6048 (m170) REVERT: d 98 TYR cc_start: 0.8957 (m-80) cc_final: 0.8602 (m-80) REVERT: d 174 ASP cc_start: 0.7817 (t0) cc_final: 0.7418 (t0) REVERT: d 222 GLN cc_start: 0.8661 (mt0) cc_final: 0.8125 (mt0) REVERT: d 229 ASP cc_start: 0.8599 (t0) cc_final: 0.8184 (t0) REVERT: d 248 PHE cc_start: 0.7160 (t80) cc_final: 0.6029 (t80) REVERT: d 302 ASN cc_start: 0.9259 (t0) cc_final: 0.8756 (t0) REVERT: d 317 THR cc_start: 0.9174 (m) cc_final: 0.8972 (p) REVERT: e 24 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.8548 (p90) REVERT: e 91 LEU cc_start: 0.9439 (tp) cc_final: 0.9186 (tt) REVERT: e 165 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8269 (tp30) REVERT: e 333 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7836 (ttpp) REVERT: f 21 ASN cc_start: 0.9344 (t0) cc_final: 0.9134 (t0) REVERT: f 39 ASP cc_start: 0.8134 (t0) cc_final: 0.7690 (t0) REVERT: f 45 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9195 (pt) REVERT: f 64 TYR cc_start: 0.8890 (m-80) cc_final: 0.8395 (m-10) REVERT: f 65 MET cc_start: 0.8674 (ptm) cc_final: 0.8171 (ptm) REVERT: f 98 TYR cc_start: 0.8899 (m-80) cc_final: 0.8404 (m-80) REVERT: f 166 MET cc_start: 0.8730 (ptm) cc_final: 0.8487 (ptm) REVERT: f 251 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8828 (ptmm) REVERT: f 275 HIS cc_start: 0.4217 (t70) cc_final: 0.3695 (t70) REVERT: f 302 ASN cc_start: 0.9409 (t0) cc_final: 0.9061 (t0) REVERT: f 323 LEU cc_start: 0.9395 (tp) cc_final: 0.9123 (tt) outliers start: 224 outliers final: 130 residues processed: 886 average time/residue: 0.1977 time to fit residues: 291.0088 Evaluate side-chains 773 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 626 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 TRP Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 219 ASN Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 142 TRP Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 230 VAL Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 387 HIS Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 50 SER Chi-restraints excluded: chain a residue 76 ILE Chi-restraints excluded: chain a residue 99 ILE Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 213 HIS Chi-restraints excluded: chain a residue 264 ILE Chi-restraints excluded: chain a residue 290 THR Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 336 TRP Chi-restraints excluded: chain b residue 16 ILE Chi-restraints excluded: chain b residue 27 CYS Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 114 HIS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 175 HIS Chi-restraints excluded: chain b residue 240 LEU Chi-restraints excluded: chain b residue 248 PHE Chi-restraints excluded: chain b residue 257 VAL Chi-restraints excluded: chain b residue 285 HIS Chi-restraints excluded: chain b residue 288 HIS Chi-restraints excluded: chain c residue 22 CYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 41 HIS Chi-restraints excluded: chain c residue 65 MET Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 138 TYR Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 22 CYS Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 254 VAL Chi-restraints excluded: chain d residue 267 LEU Chi-restraints excluded: chain e residue 24 HIS Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 99 ILE Chi-restraints excluded: chain e residue 114 HIS Chi-restraints excluded: chain e residue 167 HIS Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain e residue 247 THR Chi-restraints excluded: chain e residue 257 VAL Chi-restraints excluded: chain e residue 285 HIS Chi-restraints excluded: chain e residue 290 THR Chi-restraints excluded: chain e residue 315 ASN Chi-restraints excluded: chain e residue 333 LYS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 27 CYS Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 45 ILE Chi-restraints excluded: chain f residue 99 ILE Chi-restraints excluded: chain f residue 131 ARG Chi-restraints excluded: chain f residue 177 LEU Chi-restraints excluded: chain f residue 217 CYS Chi-restraints excluded: chain f residue 251 LYS Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 308 ILE Chi-restraints excluded: chain f residue 318 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 470 optimal weight: 0.9990 chunk 418 optimal weight: 3.9990 chunk 271 optimal weight: 0.7980 chunk 280 optimal weight: 0.7980 chunk 80 optimal weight: 50.0000 chunk 134 optimal weight: 1.9990 chunk 340 optimal weight: 0.0010 chunk 278 optimal weight: 5.9990 chunk 497 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS E 30 GLN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN F 369 GLN ** a 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 167 HIS ** a 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 114 HIS ** b 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 283 HIS c 162 HIS d 102 GLN ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 151 ASN ** e 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.113821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.086402 restraints weight = 88950.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.089058 restraints weight = 43265.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.090770 restraints weight = 26356.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.091875 restraints weight = 18679.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.092593 restraints weight = 14838.304| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39291 Z= 0.138 Angle : 0.649 9.206 53239 Z= 0.330 Chirality : 0.046 0.252 5423 Planarity : 0.005 0.075 7162 Dihedral : 7.320 59.826 6299 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.64 % Favored : 91.27 % Rotamer: Outliers : 6.03 % Allowed : 19.12 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.11), residues: 5280 helix: -3.43 (0.36), residues: 132 sheet: -0.67 (0.13), residues: 1734 loop : -1.43 (0.10), residues: 3414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 290 TYR 0.037 0.002 TYR E 321 PHE 0.039 0.001 PHE F 95 TRP 0.037 0.002 TRP d 233 HIS 0.010 0.001 HIS b 288 Details of bonding type rmsd covalent geometry : bond 0.00318 (39184) covalent geometry : angle 0.63958 (53002) SS BOND : bond 0.00316 ( 84) SS BOND : angle 1.18409 ( 168) hydrogen bonds : bond 0.03101 ( 1062) hydrogen bonds : angle 6.33109 ( 2568) link_BETA1-4 : bond 0.00743 ( 12) link_BETA1-4 : angle 2.97085 ( 36) link_NAG-ASN : bond 0.00352 ( 11) link_NAG-ASN : angle 2.39976 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 674 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7428 (mm-30) REVERT: A 7 MET cc_start: 0.5842 (mmt) cc_final: 0.5516 (mmt) REVERT: A 109 GLU cc_start: 0.8563 (tt0) cc_final: 0.8302 (pt0) REVERT: A 143 ARG cc_start: 0.7237 (tpt170) cc_final: 0.6354 (tpp-160) REVERT: A 171 TRP cc_start: 0.8348 (t60) cc_final: 0.8010 (t60) REVERT: A 203 ASP cc_start: 0.8981 (p0) cc_final: 0.8462 (p0) REVERT: A 271 ASN cc_start: 0.9247 (m110) cc_final: 0.9000 (m110) REVERT: A 343 ASN cc_start: 0.8309 (p0) cc_final: 0.7952 (p0) REVERT: A 385 LYS cc_start: 0.3333 (OUTLIER) cc_final: 0.1600 (mptt) REVERT: B 126 THR cc_start: 0.8766 (m) cc_final: 0.8527 (p) REVERT: B 143 ARG cc_start: 0.8070 (ttt180) cc_final: 0.7697 (ttt180) REVERT: B 161 LYS cc_start: 0.9351 (ptmt) cc_final: 0.9083 (ptmm) REVERT: B 163 ILE cc_start: 0.9661 (OUTLIER) cc_final: 0.9361 (tp) REVERT: B 200 SER cc_start: 0.9210 (t) cc_final: 0.8809 (p) REVERT: B 203 ASP cc_start: 0.8480 (p0) cc_final: 0.8073 (p0) REVERT: B 270 GLU cc_start: 0.9119 (pt0) cc_final: 0.8833 (mt-10) REVERT: B 363 HIS cc_start: 0.8886 (m-70) cc_final: 0.8529 (m-70) REVERT: B 367 LYS cc_start: 0.8639 (tppt) cc_final: 0.8330 (tppt) REVERT: C 10 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8587 (mttm) REVERT: C 45 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8581 (tp30) REVERT: C 103 MET cc_start: 0.8195 (tmm) cc_final: 0.7900 (tmm) REVERT: C 152 GLU cc_start: 0.3406 (pt0) cc_final: 0.2454 (pt0) REVERT: C 175 ASP cc_start: 0.8476 (t70) cc_final: 0.8184 (t0) REVERT: C 213 ASP cc_start: 0.8719 (t0) cc_final: 0.8259 (t0) REVERT: D 143 ARG cc_start: 0.7318 (ttt90) cc_final: 0.6511 (ttt90) REVERT: D 303 LYS cc_start: 0.8374 (tttt) cc_final: 0.8173 (ttpp) REVERT: D 306 GLU cc_start: 0.3904 (mt-10) cc_final: 0.3135 (pm20) REVERT: D 312 ASP cc_start: 0.7424 (t0) cc_final: 0.7185 (t0) REVERT: D 343 ASN cc_start: 0.8565 (p0) cc_final: 0.8228 (p0) REVERT: D 344 ASP cc_start: 0.8257 (t0) cc_final: 0.8028 (p0) REVERT: E 7 MET cc_start: 0.8990 (ppp) cc_final: 0.8140 (ppp) REVERT: E 37 ARG cc_start: 0.7932 (ptt90) cc_final: 0.7504 (ptt-90) REVERT: E 149 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7903 (p) REVERT: E 192 GLU cc_start: 0.4429 (tt0) cc_final: 0.4135 (tt0) REVERT: E 341 LYS cc_start: 0.9387 (tttt) cc_final: 0.9063 (ttpp) REVERT: E 367 LYS cc_start: 0.8618 (ttpp) cc_final: 0.8213 (ttpp) REVERT: F 50 LYS cc_start: 0.9078 (tttt) cc_final: 0.8825 (tttp) REVERT: F 150 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8134 (p0) REVERT: F 159 ASP cc_start: 0.8671 (p0) cc_final: 0.8423 (p0) REVERT: F 239 SER cc_start: 0.9261 (t) cc_final: 0.8781 (p) REVERT: F 290 ARG cc_start: 0.9289 (mmm-85) cc_final: 0.9051 (mmm160) REVERT: F 301 GLU cc_start: 0.8044 (tp30) cc_final: 0.7790 (tp30) REVERT: a 21 ASN cc_start: 0.9144 (t0) cc_final: 0.8840 (t0) REVERT: a 72 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8289 (t) REVERT: a 194 GLN cc_start: 0.8379 (pt0) cc_final: 0.8002 (pm20) REVERT: a 233 TRP cc_start: 0.8748 (m-90) cc_final: 0.8411 (m-90) REVERT: a 288 HIS cc_start: 0.8375 (m90) cc_final: 0.8065 (m90) REVERT: a 302 ASN cc_start: 0.9326 (t0) cc_final: 0.8686 (t0) REVERT: b 3 ASP cc_start: 0.8583 (m-30) cc_final: 0.8156 (t0) REVERT: b 15 TYR cc_start: 0.6729 (t80) cc_final: 0.6296 (t80) REVERT: b 52 MET cc_start: 0.8434 (ptm) cc_final: 0.8159 (ptm) REVERT: b 80 ASN cc_start: 0.8651 (m-40) cc_final: 0.7326 (t0) REVERT: b 82 HIS cc_start: 0.6855 (m170) cc_final: 0.6425 (m170) REVERT: b 97 TYR cc_start: 0.8686 (m-80) cc_final: 0.8259 (m-80) REVERT: b 110 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9175 (m) REVERT: b 139 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8082 (ptp90) REVERT: b 155 HIS cc_start: 0.8239 (t-170) cc_final: 0.7983 (t-90) REVERT: b 187 ILE cc_start: 0.8704 (tt) cc_final: 0.8473 (tp) REVERT: b 198 TYR cc_start: 0.6399 (t80) cc_final: 0.6166 (t80) REVERT: b 240 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8372 (mm) REVERT: c 3 ASP cc_start: 0.8725 (p0) cc_final: 0.7951 (t0) REVERT: c 18 ASP cc_start: 0.7233 (m-30) cc_final: 0.6956 (m-30) REVERT: c 21 ASN cc_start: 0.9331 (t0) cc_final: 0.9129 (t0) REVERT: c 41 HIS cc_start: 0.9161 (OUTLIER) cc_final: 0.8178 (m170) REVERT: c 68 MET cc_start: 0.7620 (tpp) cc_final: 0.7125 (tpp) REVERT: c 107 ASP cc_start: 0.7404 (t70) cc_final: 0.6997 (t0) REVERT: c 138 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.5487 (t80) REVERT: c 174 ASP cc_start: 0.7843 (t0) cc_final: 0.7525 (t0) REVERT: d 174 ASP cc_start: 0.7909 (t0) cc_final: 0.7439 (t0) REVERT: d 181 HIS cc_start: 0.6757 (p90) cc_final: 0.6535 (p90) REVERT: d 219 ASP cc_start: 0.8293 (t0) cc_final: 0.7894 (t0) REVERT: d 221 LYS cc_start: 0.9244 (ptmt) cc_final: 0.9017 (pttp) REVERT: d 222 GLN cc_start: 0.8689 (mt0) cc_final: 0.8102 (mt0) REVERT: d 229 ASP cc_start: 0.8608 (t0) cc_final: 0.8204 (t0) REVERT: d 248 PHE cc_start: 0.7273 (t80) cc_final: 0.5878 (t80) REVERT: d 302 ASN cc_start: 0.9272 (t0) cc_final: 0.8759 (t0) REVERT: e 24 HIS cc_start: 0.8870 (OUTLIER) cc_final: 0.8616 (p90) REVERT: e 50 SER cc_start: 0.9402 (OUTLIER) cc_final: 0.9043 (p) REVERT: e 165 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8241 (tp30) REVERT: e 168 GLN cc_start: 0.8961 (pt0) cc_final: 0.8710 (tt0) REVERT: e 194 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7374 (mm-40) REVERT: e 287 ASP cc_start: 0.7919 (p0) cc_final: 0.7691 (p0) REVERT: e 333 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7929 (ttpp) REVERT: e 338 GLN cc_start: 0.4350 (tm-30) cc_final: 0.3956 (tm-30) REVERT: f 35 GLU cc_start: 0.8367 (tt0) cc_final: 0.7935 (tt0) REVERT: f 45 ILE cc_start: 0.9531 (OUTLIER) cc_final: 0.9303 (pt) REVERT: f 65 MET cc_start: 0.8761 (ptm) cc_final: 0.8106 (ptm) REVERT: f 68 MET cc_start: 0.8235 (tpp) cc_final: 0.7971 (tpp) REVERT: f 98 TYR cc_start: 0.8900 (m-80) cc_final: 0.8334 (m-80) REVERT: f 166 MET cc_start: 0.8703 (ptm) cc_final: 0.8334 (ptm) REVERT: f 240 LEU cc_start: 0.9240 (tp) cc_final: 0.8941 (mp) REVERT: f 275 HIS cc_start: 0.4115 (t70) cc_final: 0.3884 (t70) REVERT: f 302 ASN cc_start: 0.9420 (t0) cc_final: 0.9047 (t0) REVERT: f 323 LEU cc_start: 0.9337 (tp) cc_final: 0.9112 (tt) outliers start: 229 outliers final: 153 residues processed: 844 average time/residue: 0.1857 time to fit residues: 262.8017 Evaluate side-chains 786 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 619 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 162 LEU Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 316 ILE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 387 HIS Chi-restraints excluded: chain a residue 22 CYS Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 50 SER Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 76 ILE Chi-restraints excluded: chain a residue 99 ILE Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 197 TYR Chi-restraints excluded: chain a residue 213 HIS Chi-restraints excluded: chain a residue 217 CYS Chi-restraints excluded: chain a residue 254 VAL Chi-restraints excluded: chain a residue 257 VAL Chi-restraints excluded: chain a residue 264 ILE Chi-restraints excluded: chain a residue 290 THR Chi-restraints excluded: chain a residue 308 ILE Chi-restraints excluded: chain a residue 315 ASN Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 336 TRP Chi-restraints excluded: chain b residue 16 ILE Chi-restraints excluded: chain b residue 27 CYS Chi-restraints excluded: chain b residue 53 PHE Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 114 HIS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 175 HIS Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 240 LEU Chi-restraints excluded: chain b residue 257 VAL Chi-restraints excluded: chain b residue 285 HIS Chi-restraints excluded: chain c residue 22 CYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 41 HIS Chi-restraints excluded: chain c residue 65 MET Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 138 TYR Chi-restraints excluded: chain c residue 197 TYR Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 299 SER Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 22 CYS Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 247 THR Chi-restraints excluded: chain d residue 254 VAL Chi-restraints excluded: chain d residue 267 LEU Chi-restraints excluded: chain d residue 318 VAL Chi-restraints excluded: chain e residue 24 HIS Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 50 SER Chi-restraints excluded: chain e residue 99 ILE Chi-restraints excluded: chain e residue 114 HIS Chi-restraints excluded: chain e residue 167 HIS Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain e residue 247 THR Chi-restraints excluded: chain e residue 257 VAL Chi-restraints excluded: chain e residue 285 HIS Chi-restraints excluded: chain e residue 315 ASN Chi-restraints excluded: chain e residue 333 LYS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 22 CYS Chi-restraints excluded: chain f residue 27 CYS Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 45 ILE Chi-restraints excluded: chain f residue 99 ILE Chi-restraints excluded: chain f residue 131 ARG Chi-restraints excluded: chain f residue 177 LEU Chi-restraints excluded: chain f residue 217 CYS Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 308 ILE Chi-restraints excluded: chain f residue 310 ARG Chi-restraints excluded: chain f residue 318 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 196 optimal weight: 1.9990 chunk 19 optimal weight: 50.0000 chunk 349 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 516 optimal weight: 0.7980 chunk 405 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 444 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 chunk 281 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN B 226 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 223 GLN E 183 HIS ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS F 369 GLN ** a 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 167 HIS a 222 GLN b 167 HIS ** b 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 275 HIS d 102 GLN d 151 ASN ** e 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 277 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.082995 restraints weight = 89325.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.085574 restraints weight = 43903.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.087243 restraints weight = 26984.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.088340 restraints weight = 19262.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.089043 restraints weight = 15340.582| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 39291 Z= 0.223 Angle : 0.684 14.267 53239 Z= 0.351 Chirality : 0.046 0.203 5423 Planarity : 0.005 0.077 7162 Dihedral : 7.225 59.423 6293 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.17 % Favored : 90.70 % Rotamer: Outliers : 6.74 % Allowed : 19.14 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % 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 aren not related in a simple way. whole: -1.86 (0.11), residues: 5280 helix: -3.12 (0.36), residues: 134 sheet: -0.71 (0.13), residues: 1674 loop : -1.48 (0.10), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG c 13 TYR 0.028 0.002 TYR F 15 PHE 0.040 0.002 PHE F 95 TRP 0.056 0.003 TRP d 233 HIS 0.015 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00498 (39184) covalent geometry : angle 0.67453 (53002) SS BOND : bond 0.00810 ( 84) SS BOND : angle 1.41167 ( 168) hydrogen bonds : bond 0.03170 ( 1062) hydrogen bonds : angle 6.17138 ( 2568) link_BETA1-4 : bond 0.00645 ( 12) link_BETA1-4 : angle 2.53776 ( 36) link_NAG-ASN : bond 0.00351 ( 11) link_NAG-ASN : angle 2.50652 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 624 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 MET cc_start: 0.6263 (mmt) cc_final: 0.5997 (mmt) REVERT: A 79 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7205 (tm-30) REVERT: A 109 GLU cc_start: 0.8655 (tt0) cc_final: 0.8424 (pt0) REVERT: A 143 ARG cc_start: 0.7403 (tpt170) cc_final: 0.6087 (tpp-160) REVERT: A 171 TRP cc_start: 0.8544 (t60) cc_final: 0.8075 (t60) REVERT: A 203 ASP cc_start: 0.8998 (p0) cc_final: 0.8503 (p0) REVERT: A 271 ASN cc_start: 0.9243 (m110) cc_final: 0.8679 (m110) REVERT: A 343 ASN cc_start: 0.8445 (p0) cc_final: 0.8131 (p0) REVERT: B 15 TYR cc_start: 0.8596 (t80) cc_final: 0.8214 (t80) REVERT: B 203 ASP cc_start: 0.8637 (p0) cc_final: 0.8299 (p0) REVERT: B 369 GLN cc_start: 0.9408 (tt0) cc_final: 0.8932 (mt0) REVERT: B 378 LYS cc_start: 0.8688 (tptt) cc_final: 0.8405 (tptt) REVERT: C 10 LYS cc_start: 0.9065 (mtpt) cc_final: 0.8655 (mttm) REVERT: C 175 ASP cc_start: 0.8479 (t70) cc_final: 0.8168 (t70) REVERT: C 213 ASP cc_start: 0.8715 (t0) cc_final: 0.8233 (t0) REVERT: C 262 ILE cc_start: 0.8914 (mt) cc_final: 0.8686 (mt) REVERT: C 282 ASP cc_start: 0.8746 (t0) cc_final: 0.8481 (p0) REVERT: D 7 MET cc_start: 0.9190 (ppp) cc_final: 0.8229 (ppp) REVERT: D 143 ARG cc_start: 0.7403 (ttt90) cc_final: 0.6867 (ttt90) REVERT: D 150 ASN cc_start: 0.8532 (t0) cc_final: 0.8262 (t0) REVERT: D 187 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8627 (m-40) REVERT: D 203 ASP cc_start: 0.8764 (p0) cc_final: 0.8504 (p0) REVERT: D 306 GLU cc_start: 0.4528 (mt-10) cc_final: 0.3573 (pm20) REVERT: E 7 MET cc_start: 0.9031 (ppp) cc_final: 0.8307 (ppp) REVERT: E 37 ARG cc_start: 0.8148 (ptt90) cc_final: 0.7712 (ptt-90) REVERT: E 192 GLU cc_start: 0.4491 (tt0) cc_final: 0.4088 (tt0) REVERT: E 341 LYS cc_start: 0.9377 (tttt) cc_final: 0.9100 (ttpp) REVERT: E 367 LYS cc_start: 0.8710 (ttpp) cc_final: 0.8246 (ttpp) REVERT: F 61 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8043 (tptp) REVERT: F 150 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8241 (p0) REVERT: F 239 SER cc_start: 0.9293 (t) cc_final: 0.9064 (p) REVERT: F 290 ARG cc_start: 0.9282 (mmm-85) cc_final: 0.9021 (mmm160) REVERT: F 301 GLU cc_start: 0.8150 (tp30) cc_final: 0.7869 (tp30) REVERT: a 21 ASN cc_start: 0.9167 (t0) cc_final: 0.8795 (t0) REVERT: a 160 GLN cc_start: 0.8339 (mm110) cc_final: 0.8079 (mm-40) REVERT: a 194 GLN cc_start: 0.8597 (pt0) cc_final: 0.8161 (mp10) REVERT: a 288 HIS cc_start: 0.8284 (m90) cc_final: 0.7972 (m90) REVERT: a 302 ASN cc_start: 0.9318 (t0) cc_final: 0.8652 (t0) REVERT: a 335 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8318 (m) REVERT: b 3 ASP cc_start: 0.8522 (m-30) cc_final: 0.8190 (t0) REVERT: b 15 TYR cc_start: 0.6939 (t80) cc_final: 0.6350 (t80) REVERT: b 52 MET cc_start: 0.8379 (ptm) cc_final: 0.8153 (ptm) REVERT: b 80 ASN cc_start: 0.8702 (m-40) cc_final: 0.7304 (t0) REVERT: b 82 HIS cc_start: 0.6872 (m170) cc_final: 0.6500 (m170) REVERT: b 110 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.9156 (m) REVERT: b 139 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8351 (ptp90) REVERT: b 155 HIS cc_start: 0.8228 (t-170) cc_final: 0.7994 (t-90) REVERT: b 198 TYR cc_start: 0.6481 (t80) cc_final: 0.6141 (t80) REVERT: b 240 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8210 (mm) REVERT: c 3 ASP cc_start: 0.8878 (p0) cc_final: 0.7991 (t0) REVERT: c 18 ASP cc_start: 0.7282 (m-30) cc_final: 0.6986 (m-30) REVERT: c 41 HIS cc_start: 0.9266 (OUTLIER) cc_final: 0.8251 (m170) REVERT: c 68 MET cc_start: 0.7512 (tpp) cc_final: 0.7116 (tpp) REVERT: c 107 ASP cc_start: 0.7391 (t70) cc_final: 0.7045 (t0) REVERT: c 138 TYR cc_start: 0.6387 (OUTLIER) cc_final: 0.5732 (t80) REVERT: c 171 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8205 (pp) REVERT: c 174 ASP cc_start: 0.8178 (t0) cc_final: 0.7878 (t0) REVERT: d 80 ASN cc_start: 0.8519 (t0) cc_final: 0.8295 (t0) REVERT: d 98 TYR cc_start: 0.8886 (m-80) cc_final: 0.8672 (m-80) REVERT: d 174 ASP cc_start: 0.8079 (t0) cc_final: 0.7561 (t0) REVERT: d 219 ASP cc_start: 0.8416 (t0) cc_final: 0.8169 (t0) REVERT: d 221 LYS cc_start: 0.9248 (ptmt) cc_final: 0.9044 (pttp) REVERT: d 222 GLN cc_start: 0.8687 (mt0) cc_final: 0.8126 (mt0) REVERT: d 229 ASP cc_start: 0.8617 (t0) cc_final: 0.8242 (t0) REVERT: d 248 PHE cc_start: 0.7718 (t80) cc_final: 0.6775 (t80) REVERT: d 302 ASN cc_start: 0.9282 (t0) cc_final: 0.8971 (t0) REVERT: e 24 HIS cc_start: 0.8852 (OUTLIER) cc_final: 0.8610 (p90) REVERT: e 35 GLU cc_start: 0.7694 (tt0) cc_final: 0.7427 (tt0) REVERT: e 73 GLN cc_start: 0.7838 (tm-30) cc_final: 0.7620 (tm-30) REVERT: e 113 PHE cc_start: 0.8868 (p90) cc_final: 0.8384 (p90) REVERT: e 120 HIS cc_start: 0.8732 (OUTLIER) cc_final: 0.8039 (t-170) REVERT: e 165 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8334 (mt-10) REVERT: e 168 GLN cc_start: 0.8991 (pt0) cc_final: 0.8753 (tt0) REVERT: e 194 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7223 (mm-40) REVERT: e 217 CYS cc_start: 0.4887 (OUTLIER) cc_final: 0.3451 (m) REVERT: e 333 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8052 (ttpp) REVERT: e 338 GLN cc_start: 0.5419 (tm-30) cc_final: 0.4926 (tm-30) REVERT: f 33 ILE cc_start: 0.9437 (mm) cc_final: 0.9213 (mm) REVERT: f 35 GLU cc_start: 0.8380 (tt0) cc_final: 0.7919 (tt0) REVERT: f 39 ASP cc_start: 0.8399 (t0) cc_final: 0.7854 (t0) REVERT: f 65 MET cc_start: 0.8920 (ptm) cc_final: 0.8629 (ptm) REVERT: f 68 MET cc_start: 0.8147 (tpp) cc_final: 0.7819 (tpp) REVERT: f 98 TYR cc_start: 0.8965 (m-80) cc_final: 0.8412 (m-80) REVERT: f 171 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8144 (pp) REVERT: f 178 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8569 (tt) REVERT: f 240 LEU cc_start: 0.9405 (tp) cc_final: 0.9179 (mp) REVERT: f 275 HIS cc_start: 0.4474 (t70) cc_final: 0.4184 (t70) REVERT: f 278 ARG cc_start: 0.9024 (mtp180) cc_final: 0.8769 (ttm110) REVERT: f 302 ASN cc_start: 0.9460 (t0) cc_final: 0.9068 (t0) REVERT: f 323 LEU cc_start: 0.9304 (tp) cc_final: 0.9021 (tt) outliers start: 256 outliers final: 181 residues processed: 818 average time/residue: 0.1985 time to fit residues: 270.7992 Evaluate side-chains 774 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 576 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 183 HIS Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 316 ILE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 347 LEU Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 142 TRP Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 387 HIS Chi-restraints excluded: chain a residue 22 CYS Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 50 SER Chi-restraints excluded: chain a residue 68 MET Chi-restraints excluded: chain a residue 76 ILE Chi-restraints excluded: chain a residue 93 SER Chi-restraints excluded: chain a residue 99 ILE Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 148 LEU Chi-restraints excluded: chain a residue 154 THR Chi-restraints excluded: chain a residue 155 HIS Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 197 TYR Chi-restraints excluded: chain a residue 213 HIS Chi-restraints excluded: chain a residue 254 VAL Chi-restraints excluded: chain a residue 264 ILE Chi-restraints excluded: chain a residue 290 THR Chi-restraints excluded: chain a residue 308 ILE Chi-restraints excluded: chain a residue 315 ASN Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 335 VAL Chi-restraints excluded: chain a residue 336 TRP Chi-restraints excluded: chain b residue 27 CYS Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 114 HIS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 175 HIS Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 240 LEU Chi-restraints excluded: chain b residue 248 PHE Chi-restraints excluded: chain b residue 257 VAL Chi-restraints excluded: chain b residue 264 ILE Chi-restraints excluded: chain b residue 281 ILE Chi-restraints excluded: chain b residue 285 HIS Chi-restraints excluded: chain b residue 288 HIS Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 22 CYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 41 HIS Chi-restraints excluded: chain c residue 65 MET Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 138 TYR Chi-restraints excluded: chain c residue 171 LEU Chi-restraints excluded: chain c residue 197 TYR Chi-restraints excluded: chain c residue 275 HIS Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 299 SER Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 22 CYS Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 146 VAL Chi-restraints excluded: chain d residue 213 HIS Chi-restraints excluded: chain d residue 247 THR Chi-restraints excluded: chain d residue 254 VAL Chi-restraints excluded: chain d residue 257 VAL Chi-restraints excluded: chain d residue 264 ILE Chi-restraints excluded: chain d residue 267 LEU Chi-restraints excluded: chain d residue 318 VAL Chi-restraints excluded: chain e residue 24 HIS Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 50 SER Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 99 ILE Chi-restraints excluded: chain e residue 114 HIS Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 167 HIS Chi-restraints excluded: chain e residue 172 VAL Chi-restraints excluded: chain e residue 195 VAL Chi-restraints excluded: chain e residue 216 THR Chi-restraints excluded: chain e residue 217 CYS Chi-restraints excluded: chain e residue 247 THR Chi-restraints excluded: chain e residue 257 VAL Chi-restraints excluded: chain e residue 273 VAL Chi-restraints excluded: chain e residue 281 ILE Chi-restraints excluded: chain e residue 285 HIS Chi-restraints excluded: chain e residue 290 THR Chi-restraints excluded: chain e residue 292 LEU Chi-restraints excluded: chain e residue 315 ASN Chi-restraints excluded: chain e residue 333 LYS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 22 CYS Chi-restraints excluded: chain f residue 27 CYS Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 99 ILE Chi-restraints excluded: chain f residue 131 ARG Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain f residue 177 LEU Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain f residue 197 TYR Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 267 LEU Chi-restraints excluded: chain f residue 308 ILE Chi-restraints excluded: chain f residue 310 ARG Chi-restraints excluded: chain f residue 318 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 295 optimal weight: 4.9990 chunk 322 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 439 optimal weight: 0.9990 chunk 398 optimal weight: 0.9990 chunk 334 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 329 optimal weight: 0.3980 chunk 418 optimal weight: 0.9990 chunk 225 optimal weight: 0.0270 overall best weight: 0.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN B 73 HIS ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN ** E 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS a 94 HIS ** a 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 222 GLN d 102 GLN d 151 ASN ** e 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 175 HIS f 277 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.111938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.084091 restraints weight = 89315.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.086720 restraints weight = 43738.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.088423 restraints weight = 26826.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089535 restraints weight = 19093.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.090240 restraints weight = 15190.562| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39291 Z= 0.134 Angle : 0.648 13.318 53239 Z= 0.329 Chirality : 0.045 0.193 5423 Planarity : 0.005 0.076 7162 Dihedral : 6.982 59.060 6290 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.33 % Rotamer: Outliers : 5.66 % Allowed : 20.85 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.11), residues: 5280 helix: -3.33 (0.36), residues: 134 sheet: -0.53 (0.13), residues: 1626 loop : -1.42 (0.10), residues: 3520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG c 13 TYR 0.028 0.002 TYR E 321 PHE 0.037 0.002 PHE F 95 TRP 0.045 0.002 TRP d 233 HIS 0.029 0.001 HIS c 275 Details of bonding type rmsd covalent geometry : bond 0.00310 (39184) covalent geometry : angle 0.63940 (53002) SS BOND : bond 0.00259 ( 84) SS BOND : angle 1.36069 ( 168) hydrogen bonds : bond 0.02895 ( 1062) hydrogen bonds : angle 5.97780 ( 2568) link_BETA1-4 : bond 0.00606 ( 12) link_BETA1-4 : angle 2.24179 ( 36) link_NAG-ASN : bond 0.00256 ( 11) link_NAG-ASN : angle 2.38337 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 622 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: A 103 MET cc_start: 0.8016 (tpp) cc_final: 0.7706 (tpp) REVERT: A 109 GLU cc_start: 0.8594 (tt0) cc_final: 0.8367 (pt0) REVERT: A 143 ARG cc_start: 0.7545 (tpt170) cc_final: 0.6604 (tpp-160) REVERT: A 171 TRP cc_start: 0.8529 (t60) cc_final: 0.8201 (t60) REVERT: A 203 ASP cc_start: 0.8987 (p0) cc_final: 0.8481 (p0) REVERT: A 271 ASN cc_start: 0.9140 (m110) cc_final: 0.8893 (m110) REVERT: A 322 LYS cc_start: 0.9402 (tptp) cc_final: 0.9065 (tppp) REVERT: A 343 ASN cc_start: 0.8461 (p0) cc_final: 0.8113 (p0) REVERT: A 385 LYS cc_start: 0.3246 (OUTLIER) cc_final: 0.1507 (mptt) REVERT: B 15 TYR cc_start: 0.8586 (t80) cc_final: 0.8140 (t80) REVERT: B 126 THR cc_start: 0.8730 (m) cc_final: 0.8519 (p) REVERT: B 161 LYS cc_start: 0.9352 (ptmt) cc_final: 0.9104 (ptmm) REVERT: B 200 SER cc_start: 0.9263 (t) cc_final: 0.8837 (p) REVERT: B 203 ASP cc_start: 0.8623 (p0) cc_final: 0.8412 (p0) REVERT: B 270 GLU cc_start: 0.9155 (pt0) cc_final: 0.8839 (mt-10) REVERT: B 369 GLN cc_start: 0.9379 (tt0) cc_final: 0.8783 (tp-100) REVERT: B 378 LYS cc_start: 0.8708 (tptt) cc_final: 0.8472 (tptp) REVERT: C 10 LYS cc_start: 0.8960 (mtpt) cc_final: 0.8592 (mttm) REVERT: C 175 ASP cc_start: 0.8466 (t70) cc_final: 0.8220 (t0) REVERT: C 213 ASP cc_start: 0.8746 (t0) cc_final: 0.8264 (t0) REVERT: C 282 ASP cc_start: 0.8714 (t0) cc_final: 0.8434 (p0) REVERT: D 7 MET cc_start: 0.9279 (ppp) cc_final: 0.8417 (ppp) REVERT: D 143 ARG cc_start: 0.7290 (ttt90) cc_final: 0.6982 (ttt90) REVERT: D 150 ASN cc_start: 0.8527 (t0) cc_final: 0.8273 (t0) REVERT: D 187 ASN cc_start: 0.9158 (OUTLIER) cc_final: 0.8847 (m-40) REVERT: D 203 ASP cc_start: 0.8703 (p0) cc_final: 0.8142 (p0) REVERT: D 230 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8965 (m) REVERT: D 306 GLU cc_start: 0.4315 (mt-10) cc_final: 0.3541 (pm20) REVERT: D 397 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6875 (tm-30) REVERT: E 7 MET cc_start: 0.8987 (ppp) cc_final: 0.8235 (ppp) REVERT: E 37 ARG cc_start: 0.8104 (ptt90) cc_final: 0.7675 (ptt-90) REVERT: E 149 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.8064 (p) REVERT: E 192 GLU cc_start: 0.4494 (tt0) cc_final: 0.4216 (tt0) REVERT: E 341 LYS cc_start: 0.9421 (tttt) cc_final: 0.9099 (ttpp) REVERT: F 61 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8000 (tptp) REVERT: F 150 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8236 (p0) REVERT: F 188 TYR cc_start: 0.8941 (t80) cc_final: 0.8649 (t80) REVERT: F 213 ASP cc_start: 0.9035 (t0) cc_final: 0.8678 (t0) REVERT: F 239 SER cc_start: 0.9264 (t) cc_final: 0.9054 (p) REVERT: F 290 ARG cc_start: 0.9320 (mmm-85) cc_final: 0.9063 (mmm160) REVERT: F 301 GLU cc_start: 0.8133 (tp30) cc_final: 0.7832 (tp30) REVERT: a 21 ASN cc_start: 0.9116 (t0) cc_final: 0.8685 (t0) REVERT: a 160 GLN cc_start: 0.8316 (mm110) cc_final: 0.8051 (mm-40) REVERT: a 194 GLN cc_start: 0.8546 (pt0) cc_final: 0.8127 (mp10) REVERT: a 233 TRP cc_start: 0.8715 (m-90) cc_final: 0.8436 (m-90) REVERT: a 242 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8491 (ttp80) REVERT: a 288 HIS cc_start: 0.8185 (m90) cc_final: 0.7936 (m90) REVERT: a 302 ASN cc_start: 0.9362 (t0) cc_final: 0.8725 (t0) REVERT: b 3 ASP cc_start: 0.8523 (m-30) cc_final: 0.8188 (t0) REVERT: b 15 TYR cc_start: 0.6747 (t80) cc_final: 0.6320 (t80) REVERT: b 80 ASN cc_start: 0.8648 (m-40) cc_final: 0.7309 (t0) REVERT: b 82 HIS cc_start: 0.6899 (m170) cc_final: 0.6547 (m170) REVERT: b 139 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8245 (ptp90) REVERT: b 155 HIS cc_start: 0.8122 (t-170) cc_final: 0.7873 (t-90) REVERT: b 198 TYR cc_start: 0.6540 (t80) cc_final: 0.5856 (t80) REVERT: b 240 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8070 (mm) REVERT: b 304 THR cc_start: 0.9433 (m) cc_final: 0.9097 (p) REVERT: c 3 ASP cc_start: 0.8872 (p0) cc_final: 0.7996 (t0) REVERT: c 18 ASP cc_start: 0.7144 (m-30) cc_final: 0.6900 (m-30) REVERT: c 41 HIS cc_start: 0.9207 (OUTLIER) cc_final: 0.8291 (m170) REVERT: c 56 LYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5633 (pptt) REVERT: c 64 TYR cc_start: 0.8264 (m-10) cc_final: 0.8025 (m-10) REVERT: c 68 MET cc_start: 0.7430 (tpp) cc_final: 0.7025 (tpp) REVERT: c 98 TYR cc_start: 0.8573 (m-80) cc_final: 0.7956 (m-80) REVERT: c 107 ASP cc_start: 0.7494 (t70) cc_final: 0.7040 (t0) REVERT: c 138 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.5794 (t80) REVERT: c 171 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8172 (pp) REVERT: c 174 ASP cc_start: 0.8187 (t0) cc_final: 0.7852 (t0) REVERT: d 80 ASN cc_start: 0.8471 (t0) cc_final: 0.8172 (t0) REVERT: d 98 TYR cc_start: 0.8938 (m-80) cc_final: 0.8673 (m-80) REVERT: d 135 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7837 (mmm-85) REVERT: d 166 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7169 (mtm) REVERT: d 174 ASP cc_start: 0.8137 (t0) cc_final: 0.7634 (t0) REVERT: d 219 ASP cc_start: 0.8371 (t0) cc_final: 0.8164 (t0) REVERT: d 222 GLN cc_start: 0.8684 (mt0) cc_final: 0.8105 (mt0) REVERT: d 229 ASP cc_start: 0.8564 (t0) cc_final: 0.8175 (t0) REVERT: d 248 PHE cc_start: 0.7756 (t80) cc_final: 0.6817 (t80) REVERT: d 302 ASN cc_start: 0.9290 (t0) cc_final: 0.8751 (t0) REVERT: e 24 HIS cc_start: 0.8901 (OUTLIER) cc_final: 0.8671 (p90) REVERT: e 113 PHE cc_start: 0.8864 (p90) cc_final: 0.8490 (p90) REVERT: e 120 HIS cc_start: 0.8733 (OUTLIER) cc_final: 0.8159 (t-170) REVERT: e 165 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8275 (mt-10) REVERT: e 168 GLN cc_start: 0.8966 (pt0) cc_final: 0.8263 (pm20) REVERT: e 194 GLN cc_start: 0.7982 (mm-40) cc_final: 0.7483 (mm-40) REVERT: e 287 ASP cc_start: 0.8365 (p0) cc_final: 0.8151 (p0) REVERT: e 288 HIS cc_start: 0.8085 (m90) cc_final: 0.7864 (m90) REVERT: e 333 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8058 (ttpp) REVERT: e 338 GLN cc_start: 0.5301 (tm-30) cc_final: 0.5062 (tm-30) REVERT: f 35 GLU cc_start: 0.8341 (tt0) cc_final: 0.7960 (tt0) REVERT: f 39 ASP cc_start: 0.8390 (t0) cc_final: 0.7869 (t0) REVERT: f 52 MET cc_start: 0.7985 (mmm) cc_final: 0.7664 (mmm) REVERT: f 68 MET cc_start: 0.8111 (tpp) cc_final: 0.7816 (tpp) REVERT: f 98 TYR cc_start: 0.8906 (m-80) cc_final: 0.8320 (m-80) REVERT: f 166 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8173 (ptm) REVERT: f 171 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8255 (pp) REVERT: f 240 LEU cc_start: 0.9386 (tp) cc_final: 0.9162 (mp) REVERT: f 275 HIS cc_start: 0.4159 (t70) cc_final: 0.3935 (t70) REVERT: f 302 ASN cc_start: 0.9475 (t0) cc_final: 0.9063 (t0) REVERT: f 323 LEU cc_start: 0.9411 (tp) cc_final: 0.9080 (tt) outliers start: 215 outliers final: 156 residues processed: 780 average time/residue: 0.2112 time to fit residues: 273.6612 Evaluate side-chains 743 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 566 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 142 TRP Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 183 HIS Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 316 ILE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 347 LEU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 142 TRP Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 387 HIS Chi-restraints excluded: chain a residue 22 CYS Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 50 SER Chi-restraints excluded: chain a residue 68 MET Chi-restraints excluded: chain a residue 76 ILE Chi-restraints excluded: chain a residue 99 ILE Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 213 HIS Chi-restraints excluded: chain a residue 242 ARG Chi-restraints excluded: chain a residue 254 VAL Chi-restraints excluded: chain a residue 264 ILE Chi-restraints excluded: chain a residue 290 THR Chi-restraints excluded: chain a residue 315 ASN Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 335 VAL Chi-restraints excluded: chain a residue 336 TRP Chi-restraints excluded: chain b residue 27 CYS Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 114 HIS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 175 HIS Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 240 LEU Chi-restraints excluded: chain b residue 248 PHE Chi-restraints excluded: chain b residue 257 VAL Chi-restraints excluded: chain b residue 285 HIS Chi-restraints excluded: chain b residue 288 HIS Chi-restraints excluded: chain c residue 22 CYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 41 HIS Chi-restraints excluded: chain c residue 56 LYS Chi-restraints excluded: chain c residue 65 MET Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 138 TYR Chi-restraints excluded: chain c residue 171 LEU Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 197 TYR Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 22 CYS Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 47 ILE Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 135 ARG Chi-restraints excluded: chain d residue 166 MET Chi-restraints excluded: chain d residue 175 HIS Chi-restraints excluded: chain d residue 185 VAL Chi-restraints excluded: chain d residue 247 THR Chi-restraints excluded: chain d residue 254 VAL Chi-restraints excluded: chain d residue 264 ILE Chi-restraints excluded: chain d residue 267 LEU Chi-restraints excluded: chain e residue 24 HIS Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 99 ILE Chi-restraints excluded: chain e residue 114 HIS Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 167 HIS Chi-restraints excluded: chain e residue 257 VAL Chi-restraints excluded: chain e residue 273 VAL Chi-restraints excluded: chain e residue 285 HIS Chi-restraints excluded: chain e residue 292 LEU Chi-restraints excluded: chain e residue 315 ASN Chi-restraints excluded: chain e residue 333 LYS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 22 CYS Chi-restraints excluded: chain f residue 27 CYS Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 99 ILE Chi-restraints excluded: chain f residue 131 ARG Chi-restraints excluded: chain f residue 166 MET Chi-restraints excluded: chain f residue 171 LEU Chi-restraints excluded: chain f residue 177 LEU Chi-restraints excluded: chain f residue 178 LEU Chi-restraints excluded: chain f residue 197 TYR Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 308 ILE Chi-restraints excluded: chain f residue 310 ARG Chi-restraints excluded: chain f residue 318 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 419 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 401 optimal weight: 2.9990 chunk 444 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 65 optimal weight: 40.0000 chunk 242 optimal weight: 0.0970 chunk 399 optimal weight: 0.8980 chunk 441 optimal weight: 5.9990 chunk 431 optimal weight: 2.9990 chunk 499 optimal weight: 0.2980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS E 183 HIS ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 114 HIS ** a 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 160 GLN d 102 GLN ** d 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.112120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.084557 restraints weight = 88863.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.087193 restraints weight = 43619.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.088897 restraints weight = 26741.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.090016 restraints weight = 19000.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.090694 restraints weight = 15092.349| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 39291 Z= 0.130 Angle : 0.648 13.988 53239 Z= 0.327 Chirality : 0.045 0.245 5423 Planarity : 0.005 0.081 7162 Dihedral : 6.831 58.754 6288 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.75 % Favored : 91.16 % Rotamer: Outliers : 5.58 % Allowed : 21.72 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.12), residues: 5280 helix: -3.28 (0.36), residues: 132 sheet: -0.46 (0.13), residues: 1688 loop : -1.45 (0.10), residues: 3460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG c 13 TYR 0.026 0.001 TYR E 321 PHE 0.045 0.002 PHE a 248 TRP 0.051 0.002 TRP d 233 HIS 0.013 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00301 (39184) covalent geometry : angle 0.64038 (53002) SS BOND : bond 0.00242 ( 84) SS BOND : angle 1.26119 ( 168) hydrogen bonds : bond 0.02825 ( 1062) hydrogen bonds : angle 5.82145 ( 2568) link_BETA1-4 : bond 0.00591 ( 12) link_BETA1-4 : angle 2.09782 ( 36) link_NAG-ASN : bond 0.00256 ( 11) link_NAG-ASN : angle 2.28292 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 630 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7373 (tm-30) REVERT: A 103 MET cc_start: 0.8093 (tpp) cc_final: 0.7867 (tpp) REVERT: A 109 GLU cc_start: 0.8604 (tt0) cc_final: 0.8357 (pt0) REVERT: A 143 ARG cc_start: 0.7521 (tpt170) cc_final: 0.6559 (tpp-160) REVERT: A 171 TRP cc_start: 0.8519 (t60) cc_final: 0.8186 (t60) REVERT: A 203 ASP cc_start: 0.9004 (p0) cc_final: 0.8551 (p0) REVERT: A 271 ASN cc_start: 0.9074 (m110) cc_final: 0.8833 (m110) REVERT: A 322 LYS cc_start: 0.9431 (tptp) cc_final: 0.9064 (tppp) REVERT: A 343 ASN cc_start: 0.8462 (p0) cc_final: 0.8150 (p0) REVERT: A 385 LYS cc_start: 0.3261 (OUTLIER) cc_final: 0.1506 (mptt) REVERT: B 15 TYR cc_start: 0.8471 (t80) cc_final: 0.8170 (t80) REVERT: B 126 THR cc_start: 0.8694 (m) cc_final: 0.8494 (p) REVERT: B 200 SER cc_start: 0.9258 (t) cc_final: 0.8821 (p) REVERT: B 230 VAL cc_start: 0.9330 (OUTLIER) cc_final: 0.8980 (m) REVERT: B 270 GLU cc_start: 0.9132 (pt0) cc_final: 0.8807 (mt-10) REVERT: B 369 GLN cc_start: 0.9354 (tt0) cc_final: 0.8974 (mm-40) REVERT: C 10 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8582 (mttm) REVERT: C 103 MET cc_start: 0.8146 (tmm) cc_final: 0.7660 (tmm) REVERT: C 175 ASP cc_start: 0.8452 (t70) cc_final: 0.8242 (t0) REVERT: C 213 ASP cc_start: 0.8743 (t0) cc_final: 0.8256 (t0) REVERT: C 230 VAL cc_start: 0.9311 (t) cc_final: 0.9013 (p) REVERT: C 378 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.9031 (tmtt) REVERT: D 7 MET cc_start: 0.9362 (ppp) cc_final: 0.8417 (ppp) REVERT: D 143 ARG cc_start: 0.7479 (ttt90) cc_final: 0.7036 (ttt90) REVERT: D 150 ASN cc_start: 0.8532 (t0) cc_final: 0.8272 (t0) REVERT: D 187 ASN cc_start: 0.9165 (OUTLIER) cc_final: 0.8924 (m-40) REVERT: D 230 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9035 (m) REVERT: D 306 GLU cc_start: 0.4191 (mt-10) cc_final: 0.3533 (pm20) REVERT: D 397 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6912 (tm-30) REVERT: E 7 MET cc_start: 0.9035 (ppp) cc_final: 0.8277 (ppp) REVERT: E 37 ARG cc_start: 0.8068 (ptt90) cc_final: 0.7672 (ptt-90) REVERT: E 149 VAL cc_start: 0.8383 (OUTLIER) cc_final: 0.8105 (p) REVERT: E 192 GLU cc_start: 0.4465 (tt0) cc_final: 0.4208 (tt0) REVERT: F 7 MET cc_start: 0.9188 (ptm) cc_final: 0.8882 (ppp) REVERT: F 61 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8008 (tptp) REVERT: F 150 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8328 (p0) REVERT: F 177 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8375 (mttp) REVERT: F 188 TYR cc_start: 0.8958 (t80) cc_final: 0.8672 (t80) REVERT: F 239 SER cc_start: 0.9242 (t) cc_final: 0.9032 (p) REVERT: F 290 ARG cc_start: 0.9319 (mmm-85) cc_final: 0.9073 (mmm160) REVERT: F 301 GLU cc_start: 0.8140 (tp30) cc_final: 0.7836 (tp30) REVERT: a 114 HIS cc_start: 0.6640 (OUTLIER) cc_final: 0.6312 (t-90) REVERT: a 194 GLN cc_start: 0.8525 (pt0) cc_final: 0.8120 (mp10) REVERT: a 233 TRP cc_start: 0.8758 (m-90) cc_final: 0.8474 (m-90) REVERT: a 242 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8463 (ttp80) REVERT: a 288 HIS cc_start: 0.8210 (m90) cc_final: 0.7950 (m90) REVERT: a 302 ASN cc_start: 0.9344 (t0) cc_final: 0.8669 (t0) REVERT: a 335 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8292 (m) REVERT: b 3 ASP cc_start: 0.8529 (m-30) cc_final: 0.8197 (t0) REVERT: b 15 TYR cc_start: 0.6642 (t80) cc_final: 0.6163 (t80) REVERT: b 80 ASN cc_start: 0.8588 (m-40) cc_final: 0.7228 (t0) REVERT: b 82 HIS cc_start: 0.6851 (m170) cc_final: 0.6494 (m170) REVERT: b 139 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8165 (ptp90) REVERT: b 155 HIS cc_start: 0.8095 (t-170) cc_final: 0.7870 (t-90) REVERT: b 198 TYR cc_start: 0.6628 (t80) cc_final: 0.5996 (t80) REVERT: b 240 LEU cc_start: 0.8453 (mm) cc_final: 0.7983 (mm) REVERT: b 304 THR cc_start: 0.9474 (m) cc_final: 0.9051 (p) REVERT: c 3 ASP cc_start: 0.8880 (p0) cc_final: 0.8016 (t0) REVERT: c 41 HIS cc_start: 0.9202 (OUTLIER) cc_final: 0.8302 (m170) REVERT: c 68 MET cc_start: 0.7422 (tpp) cc_final: 0.7013 (tpp) REVERT: c 98 TYR cc_start: 0.8593 (m-80) cc_final: 0.7963 (m-80) REVERT: c 107 ASP cc_start: 0.7496 (t70) cc_final: 0.6985 (t0) REVERT: c 138 TYR cc_start: 0.6453 (OUTLIER) cc_final: 0.5731 (t80) REVERT: c 171 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8084 (pp) REVERT: c 174 ASP cc_start: 0.8080 (t0) cc_final: 0.7747 (t0) REVERT: d 80 ASN cc_start: 0.8391 (t0) cc_final: 0.7464 (t0) REVERT: d 82 HIS cc_start: 0.6749 (m170) cc_final: 0.6399 (m170) REVERT: d 98 TYR cc_start: 0.8895 (m-80) cc_final: 0.8599 (m-80) REVERT: d 135 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7756 (mmm-85) REVERT: d 166 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7195 (mtm) REVERT: d 174 ASP cc_start: 0.8205 (t0) cc_final: 0.7961 (t0) REVERT: d 222 GLN cc_start: 0.8652 (mt0) cc_final: 0.8026 (mt0) REVERT: d 248 PHE cc_start: 0.7321 (t80) cc_final: 0.6674 (t80) REVERT: d 302 ASN cc_start: 0.9281 (t0) cc_final: 0.8749 (t0) REVERT: e 24 HIS cc_start: 0.8922 (OUTLIER) cc_final: 0.8716 (p90) REVERT: e 113 PHE cc_start: 0.8775 (p90) cc_final: 0.8456 (p90) REVERT: e 120 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8228 (t-170) REVERT: e 165 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8307 (mt-10) REVERT: e 168 GLN cc_start: 0.8972 (pt0) cc_final: 0.8279 (pm20) REVERT: e 194 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7637 (mm-40) REVERT: e 287 ASP cc_start: 0.8374 (p0) cc_final: 0.8100 (p0) REVERT: e 288 HIS cc_start: 0.8007 (m90) cc_final: 0.7786 (m90) REVERT: e 333 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8071 (ttpp) REVERT: e 338 GLN cc_start: 0.5368 (tm-30) cc_final: 0.4927 (tm-30) REVERT: f 35 GLU cc_start: 0.8323 (tt0) cc_final: 0.7935 (tt0) REVERT: f 39 ASP cc_start: 0.8362 (t0) cc_final: 0.7816 (t0) REVERT: f 65 MET cc_start: 0.8725 (ptm) cc_final: 0.8465 (ptm) REVERT: f 98 TYR cc_start: 0.8854 (m-80) cc_final: 0.8236 (m-80) REVERT: f 166 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8087 (ptm) REVERT: f 240 LEU cc_start: 0.9382 (tp) cc_final: 0.9164 (mp) REVERT: f 275 HIS cc_start: 0.4238 (t70) cc_final: 0.4007 (t70) REVERT: f 302 ASN cc_start: 0.9462 (t0) cc_final: 0.9040 (t0) REVERT: f 323 LEU cc_start: 0.9421 (tp) cc_final: 0.9161 (tt) outliers start: 212 outliers final: 163 residues processed: 784 average time/residue: 0.2160 time to fit residues: 279.9329 Evaluate side-chains 768 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 582 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 316 ILE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 347 LEU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 142 TRP Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 177 LYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 387 HIS Chi-restraints excluded: chain a residue 22 CYS Chi-restraints excluded: chain a residue 24 HIS Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 50 SER Chi-restraints excluded: chain a residue 68 MET Chi-restraints excluded: chain a residue 76 ILE Chi-restraints excluded: chain a residue 99 ILE Chi-restraints excluded: chain a residue 114 HIS Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 197 TYR Chi-restraints excluded: chain a residue 213 HIS Chi-restraints excluded: chain a residue 242 ARG Chi-restraints excluded: chain a residue 254 VAL Chi-restraints excluded: chain a residue 264 ILE Chi-restraints excluded: chain a residue 290 THR Chi-restraints excluded: chain a residue 315 ASN Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 335 VAL Chi-restraints excluded: chain a residue 336 TRP Chi-restraints excluded: chain b residue 27 CYS Chi-restraints excluded: chain b residue 53 PHE Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 114 HIS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 175 HIS Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 248 PHE Chi-restraints excluded: chain b residue 257 VAL Chi-restraints excluded: chain b residue 285 HIS Chi-restraints excluded: chain b residue 292 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 22 CYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 41 HIS Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 138 TYR Chi-restraints excluded: chain c residue 171 LEU Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 197 TYR Chi-restraints excluded: chain c residue 275 HIS Chi-restraints excluded: chain c residue 291 LEU Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 22 CYS Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 114 HIS Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 135 ARG Chi-restraints excluded: chain d residue 166 MET Chi-restraints excluded: chain d residue 175 HIS Chi-restraints excluded: chain d residue 185 VAL Chi-restraints excluded: chain d residue 187 ILE Chi-restraints excluded: chain d residue 247 THR Chi-restraints excluded: chain d residue 254 VAL Chi-restraints excluded: chain d residue 264 ILE Chi-restraints excluded: chain d residue 267 LEU Chi-restraints excluded: chain d residue 318 VAL Chi-restraints excluded: chain e residue 24 HIS Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 99 ILE Chi-restraints excluded: chain e residue 114 HIS Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 167 HIS Chi-restraints excluded: chain e residue 257 VAL Chi-restraints excluded: chain e residue 285 HIS Chi-restraints excluded: chain e residue 292 LEU Chi-restraints excluded: chain e residue 315 ASN Chi-restraints excluded: chain e residue 318 VAL Chi-restraints excluded: chain e residue 333 LYS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 22 CYS Chi-restraints excluded: chain f residue 27 CYS Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 99 ILE Chi-restraints excluded: chain f residue 131 ARG Chi-restraints excluded: chain f residue 166 MET Chi-restraints excluded: chain f residue 177 LEU Chi-restraints excluded: chain f residue 197 TYR Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 294 THR Chi-restraints excluded: chain f residue 308 ILE Chi-restraints excluded: chain f residue 310 ARG Chi-restraints excluded: chain f residue 318 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 449 optimal weight: 0.0970 chunk 258 optimal weight: 1.9990 chunk 434 optimal weight: 0.8980 chunk 330 optimal weight: 3.9990 chunk 1 optimal weight: 50.0000 chunk 397 optimal weight: 0.9990 chunk 93 optimal weight: 0.0970 chunk 84 optimal weight: 20.0000 chunk 444 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 351 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS D 231 HIS ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 387 HIS ** a 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 114 HIS d 102 GLN ** d 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 277 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.113490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.085718 restraints weight = 88603.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.088490 restraints weight = 42157.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.090278 restraints weight = 25388.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.091443 restraints weight = 17836.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.092197 restraints weight = 14050.124| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 39291 Z= 0.123 Angle : 0.646 12.747 53239 Z= 0.325 Chirality : 0.045 0.192 5423 Planarity : 0.005 0.079 7162 Dihedral : 6.744 58.660 6286 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.48 % Favored : 91.42 % Rotamer: Outliers : 5.37 % Allowed : 22.54 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.12), residues: 5280 helix: -3.20 (0.37), residues: 132 sheet: -0.36 (0.13), residues: 1674 loop : -1.44 (0.10), residues: 3474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG c 13 TYR 0.025 0.001 TYR E 321 PHE 0.039 0.002 PHE a 248 TRP 0.065 0.002 TRP d 233 HIS 0.012 0.001 HIS a 114 Details of bonding type rmsd covalent geometry : bond 0.00283 (39184) covalent geometry : angle 0.63942 (53002) SS BOND : bond 0.00234 ( 84) SS BOND : angle 1.19741 ( 168) hydrogen bonds : bond 0.02723 ( 1062) hydrogen bonds : angle 5.71398 ( 2568) link_BETA1-4 : bond 0.00580 ( 12) link_BETA1-4 : angle 2.01386 ( 36) link_NAG-ASN : bond 0.00250 ( 11) link_NAG-ASN : angle 2.21481 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 613 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: A 103 MET cc_start: 0.8077 (tpp) cc_final: 0.7839 (tpp) REVERT: A 109 GLU cc_start: 0.8595 (tt0) cc_final: 0.8371 (pt0) REVERT: A 143 ARG cc_start: 0.7484 (tpt170) cc_final: 0.6555 (tpp-160) REVERT: A 171 TRP cc_start: 0.8552 (t60) cc_final: 0.8302 (t60) REVERT: A 203 ASP cc_start: 0.8982 (p0) cc_final: 0.8543 (p0) REVERT: A 271 ASN cc_start: 0.9010 (m110) cc_final: 0.8761 (m110) REVERT: A 322 LYS cc_start: 0.9395 (tptp) cc_final: 0.9042 (tppp) REVERT: A 343 ASN cc_start: 0.8476 (p0) cc_final: 0.8155 (p0) REVERT: A 385 LYS cc_start: 0.3279 (OUTLIER) cc_final: 0.1512 (mptt) REVERT: B 15 TYR cc_start: 0.8459 (t80) cc_final: 0.8197 (t80) REVERT: B 184 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7508 (mp0) REVERT: B 200 SER cc_start: 0.9255 (t) cc_final: 0.8824 (p) REVERT: B 230 VAL cc_start: 0.9240 (OUTLIER) cc_final: 0.9015 (m) REVERT: B 270 GLU cc_start: 0.9080 (pt0) cc_final: 0.8763 (mt-10) REVERT: B 306 GLU cc_start: 0.8711 (tp30) cc_final: 0.8362 (tp30) REVERT: B 321 TYR cc_start: 0.4365 (m-80) cc_final: 0.3591 (m-80) REVERT: B 369 GLN cc_start: 0.9336 (tt0) cc_final: 0.8991 (mm-40) REVERT: C 10 LYS cc_start: 0.8868 (mtpt) cc_final: 0.8538 (mttm) REVERT: C 54 LYS cc_start: 0.9468 (tttt) cc_final: 0.9071 (ttmm) REVERT: C 103 MET cc_start: 0.8155 (tmm) cc_final: 0.7675 (tmm) REVERT: C 175 ASP cc_start: 0.8463 (t70) cc_final: 0.8250 (t0) REVERT: C 230 VAL cc_start: 0.9310 (t) cc_final: 0.9020 (p) REVERT: D 7 MET cc_start: 0.9342 (ppp) cc_final: 0.8430 (ppp) REVERT: D 45 GLU cc_start: 0.9092 (tp30) cc_final: 0.8703 (tp30) REVERT: D 143 ARG cc_start: 0.7353 (ttt90) cc_final: 0.6995 (ttt90) REVERT: D 150 ASN cc_start: 0.8527 (t0) cc_final: 0.8278 (t0) REVERT: D 187 ASN cc_start: 0.9200 (OUTLIER) cc_final: 0.8951 (m-40) REVERT: D 230 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9020 (m) REVERT: D 276 SER cc_start: 0.9208 (OUTLIER) cc_final: 0.8968 (p) REVERT: D 306 GLU cc_start: 0.4111 (mt-10) cc_final: 0.3340 (pm20) REVERT: D 397 GLU cc_start: 0.7257 (tm-30) cc_final: 0.6910 (tm-30) REVERT: E 7 MET cc_start: 0.9040 (ppp) cc_final: 0.8300 (ppp) REVERT: E 37 ARG cc_start: 0.8021 (ptt90) cc_final: 0.7621 (ptt-90) REVERT: E 149 VAL cc_start: 0.8349 (OUTLIER) cc_final: 0.8062 (p) REVERT: E 192 GLU cc_start: 0.4452 (tt0) cc_final: 0.4191 (tt0) REVERT: E 322 LYS cc_start: 0.9446 (mmtt) cc_final: 0.9145 (mmmt) REVERT: E 367 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8238 (ttpp) REVERT: F 7 MET cc_start: 0.9142 (ptm) cc_final: 0.8941 (ppp) REVERT: F 61 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8026 (tptp) REVERT: F 150 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8335 (p0) REVERT: F 175 ASP cc_start: 0.8630 (m-30) cc_final: 0.8419 (m-30) REVERT: F 177 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8403 (mttp) REVERT: F 188 TYR cc_start: 0.8998 (t80) cc_final: 0.8738 (t80) REVERT: F 213 ASP cc_start: 0.8969 (t0) cc_final: 0.8626 (t0) REVERT: F 290 ARG cc_start: 0.9369 (mmm-85) cc_final: 0.9156 (mmm160) REVERT: F 301 GLU cc_start: 0.8089 (tp30) cc_final: 0.7792 (tp30) REVERT: a 119 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.8066 (mmm-85) REVERT: a 160 GLN cc_start: 0.8463 (mm-40) cc_final: 0.7692 (mm110) REVERT: a 194 GLN cc_start: 0.8503 (pt0) cc_final: 0.8122 (mp10) REVERT: a 233 TRP cc_start: 0.8757 (m-90) cc_final: 0.8482 (m-90) REVERT: a 242 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8503 (ttp80) REVERT: a 287 ASP cc_start: 0.7876 (p0) cc_final: 0.7386 (p0) REVERT: a 288 HIS cc_start: 0.8198 (m90) cc_final: 0.7987 (m90) REVERT: a 302 ASN cc_start: 0.9331 (t0) cc_final: 0.8674 (t0) REVERT: a 335 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8235 (m) REVERT: b 3 ASP cc_start: 0.8489 (m-30) cc_final: 0.8149 (t0) REVERT: b 80 ASN cc_start: 0.8552 (m-40) cc_final: 0.7197 (t0) REVERT: b 82 HIS cc_start: 0.6853 (m170) cc_final: 0.6509 (m170) REVERT: b 139 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8197 (ptp90) REVERT: b 155 HIS cc_start: 0.8045 (t-170) cc_final: 0.7821 (t-90) REVERT: b 198 TYR cc_start: 0.6632 (t80) cc_final: 0.6039 (t80) REVERT: c 3 ASP cc_start: 0.8864 (p0) cc_final: 0.7942 (t0) REVERT: c 13 ARG cc_start: 0.7617 (tpp-160) cc_final: 0.7355 (tpp-160) REVERT: c 41 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8335 (m170) REVERT: c 68 MET cc_start: 0.7402 (tpp) cc_final: 0.7005 (tpp) REVERT: c 98 TYR cc_start: 0.8596 (m-80) cc_final: 0.8013 (m-80) REVERT: c 138 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5707 (t80) REVERT: c 171 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8244 (pp) REVERT: c 174 ASP cc_start: 0.8064 (t0) cc_final: 0.7745 (t0) REVERT: c 194 GLN cc_start: 0.7741 (mm110) cc_final: 0.7466 (mm110) REVERT: d 80 ASN cc_start: 0.8341 (t0) cc_final: 0.7461 (t0) REVERT: d 82 HIS cc_start: 0.6808 (m170) cc_final: 0.6389 (m170) REVERT: d 135 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7753 (mmm-85) REVERT: d 166 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.7137 (mtm) REVERT: d 174 ASP cc_start: 0.8189 (t0) cc_final: 0.7930 (t0) REVERT: d 222 GLN cc_start: 0.8504 (mt0) cc_final: 0.8050 (mt0) REVERT: d 229 ASP cc_start: 0.8602 (t0) cc_final: 0.8202 (t0) REVERT: d 302 ASN cc_start: 0.9266 (t0) cc_final: 0.8741 (t0) REVERT: e 24 HIS cc_start: 0.8862 (OUTLIER) cc_final: 0.8648 (p90) REVERT: e 52 MET cc_start: 0.8968 (tpp) cc_final: 0.7639 (tpp) REVERT: e 113 PHE cc_start: 0.8656 (p90) cc_final: 0.8384 (p90) REVERT: e 120 HIS cc_start: 0.8738 (OUTLIER) cc_final: 0.8237 (t-170) REVERT: e 168 GLN cc_start: 0.8965 (pt0) cc_final: 0.8334 (pm20) REVERT: e 194 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7892 (mm-40) REVERT: e 287 ASP cc_start: 0.8314 (p0) cc_final: 0.8059 (p0) REVERT: e 333 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8075 (ttpp) REVERT: f 33 ILE cc_start: 0.9415 (mm) cc_final: 0.9199 (mm) REVERT: f 35 GLU cc_start: 0.8294 (tt0) cc_final: 0.7924 (tt0) REVERT: f 39 ASP cc_start: 0.8325 (t0) cc_final: 0.7816 (t0) REVERT: f 65 MET cc_start: 0.8803 (ptm) cc_final: 0.8584 (ptm) REVERT: f 98 TYR cc_start: 0.8848 (m-80) cc_final: 0.8227 (m-80) REVERT: f 166 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8075 (ptm) REVERT: f 240 LEU cc_start: 0.9357 (tp) cc_final: 0.9154 (mp) REVERT: f 275 HIS cc_start: 0.4219 (t70) cc_final: 0.3992 (t70) REVERT: f 302 ASN cc_start: 0.9442 (t0) cc_final: 0.9003 (t0) REVERT: f 323 LEU cc_start: 0.9394 (tp) cc_final: 0.9115 (tt) outliers start: 204 outliers final: 155 residues processed: 761 average time/residue: 0.2157 time to fit residues: 270.7404 Evaluate side-chains 764 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 587 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 316 ILE Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 347 LEU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 381 CYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 142 TRP Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 177 LYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 387 HIS Chi-restraints excluded: chain a residue 22 CYS Chi-restraints excluded: chain a residue 24 HIS Chi-restraints excluded: chain a residue 26 ARG Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 33 ILE Chi-restraints excluded: chain a residue 50 SER Chi-restraints excluded: chain a residue 68 MET Chi-restraints excluded: chain a residue 76 ILE Chi-restraints excluded: chain a residue 99 ILE Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 213 HIS Chi-restraints excluded: chain a residue 242 ARG Chi-restraints excluded: chain a residue 264 ILE Chi-restraints excluded: chain a residue 290 THR Chi-restraints excluded: chain a residue 315 ASN Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 335 VAL Chi-restraints excluded: chain a residue 336 TRP Chi-restraints excluded: chain b residue 27 CYS Chi-restraints excluded: chain b residue 53 PHE Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 114 HIS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 175 HIS Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 248 PHE Chi-restraints excluded: chain b residue 257 VAL Chi-restraints excluded: chain b residue 285 HIS Chi-restraints excluded: chain b residue 292 LEU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 22 CYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 41 HIS Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 138 TYR Chi-restraints excluded: chain c residue 171 LEU Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 197 TYR Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 22 CYS Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 114 HIS Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 135 ARG Chi-restraints excluded: chain d residue 166 MET Chi-restraints excluded: chain d residue 185 VAL Chi-restraints excluded: chain d residue 254 VAL Chi-restraints excluded: chain d residue 264 ILE Chi-restraints excluded: chain d residue 267 LEU Chi-restraints excluded: chain d residue 318 VAL Chi-restraints excluded: chain e residue 24 HIS Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 99 ILE Chi-restraints excluded: chain e residue 114 HIS Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 167 HIS Chi-restraints excluded: chain e residue 257 VAL Chi-restraints excluded: chain e residue 285 HIS Chi-restraints excluded: chain e residue 292 LEU Chi-restraints excluded: chain e residue 315 ASN Chi-restraints excluded: chain e residue 333 LYS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 22 CYS Chi-restraints excluded: chain f residue 27 CYS Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 99 ILE Chi-restraints excluded: chain f residue 131 ARG Chi-restraints excluded: chain f residue 166 MET Chi-restraints excluded: chain f residue 177 LEU Chi-restraints excluded: chain f residue 197 TYR Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 294 THR Chi-restraints excluded: chain f residue 308 ILE Chi-restraints excluded: chain f residue 310 ARG Chi-restraints excluded: chain f residue 318 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 371 optimal weight: 2.9990 chunk 227 optimal weight: 0.1980 chunk 491 optimal weight: 0.9990 chunk 224 optimal weight: 0.0170 chunk 291 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 358 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 50.0000 chunk 136 optimal weight: 0.8980 chunk 461 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN B 176 ASN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 102 GLN ** d 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.112845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.085048 restraints weight = 89156.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.087809 restraints weight = 42439.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.089583 restraints weight = 25589.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.090750 restraints weight = 17974.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.091487 restraints weight = 14158.646| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 39291 Z= 0.124 Angle : 0.652 11.969 53239 Z= 0.327 Chirality : 0.045 0.191 5423 Planarity : 0.005 0.077 7162 Dihedral : 6.669 58.673 6286 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.81 % Favored : 91.10 % Rotamer: Outliers : 5.19 % Allowed : 22.70 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.12), residues: 5280 helix: -3.08 (0.38), residues: 132 sheet: -0.34 (0.13), residues: 1680 loop : -1.43 (0.10), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG c 13 TYR 0.022 0.001 TYR b 235 PHE 0.038 0.002 PHE d 248 TRP 0.063 0.002 TRP d 233 HIS 0.006 0.001 HIS E 183 Details of bonding type rmsd covalent geometry : bond 0.00289 (39184) covalent geometry : angle 0.64625 (53002) SS BOND : bond 0.00229 ( 84) SS BOND : angle 1.22553 ( 168) hydrogen bonds : bond 0.02692 ( 1062) hydrogen bonds : angle 5.61059 ( 2568) link_BETA1-4 : bond 0.00621 ( 12) link_BETA1-4 : angle 1.93199 ( 36) link_NAG-ASN : bond 0.00227 ( 11) link_NAG-ASN : angle 2.06981 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 617 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8776 (m) REVERT: A 79 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: A 143 ARG cc_start: 0.7495 (tpt170) cc_final: 0.6565 (tpp-160) REVERT: A 171 TRP cc_start: 0.8541 (t60) cc_final: 0.8305 (t60) REVERT: A 203 ASP cc_start: 0.8985 (p0) cc_final: 0.8562 (p0) REVERT: A 271 ASN cc_start: 0.8937 (m110) cc_final: 0.8690 (m110) REVERT: A 343 ASN cc_start: 0.8410 (p0) cc_final: 0.8099 (p0) REVERT: A 385 LYS cc_start: 0.3242 (OUTLIER) cc_final: 0.1483 (mptt) REVERT: B 15 TYR cc_start: 0.8501 (t80) cc_final: 0.8261 (t80) REVERT: B 200 SER cc_start: 0.9255 (t) cc_final: 0.8829 (p) REVERT: B 270 GLU cc_start: 0.9071 (pt0) cc_final: 0.8799 (mt-10) REVERT: B 306 GLU cc_start: 0.8709 (tp30) cc_final: 0.8374 (tp30) REVERT: B 369 GLN cc_start: 0.9314 (tt0) cc_final: 0.8953 (mm-40) REVERT: C 10 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8584 (mttm) REVERT: C 54 LYS cc_start: 0.9473 (tttt) cc_final: 0.9147 (ttmm) REVERT: C 103 MET cc_start: 0.8126 (tmm) cc_final: 0.7630 (tmm) REVERT: C 175 ASP cc_start: 0.8482 (t70) cc_final: 0.8261 (t0) REVERT: C 213 ASP cc_start: 0.8678 (t0) cc_final: 0.8260 (t0) REVERT: C 230 VAL cc_start: 0.9311 (t) cc_final: 0.9023 (p) REVERT: C 369 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7172 (tm-30) REVERT: D 7 MET cc_start: 0.9357 (ppp) cc_final: 0.8483 (ppp) REVERT: D 143 ARG cc_start: 0.7347 (ttt90) cc_final: 0.6921 (ttt90) REVERT: D 150 ASN cc_start: 0.8539 (t0) cc_final: 0.8296 (t0) REVERT: D 187 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.8973 (m-40) REVERT: D 230 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.9011 (m) REVERT: D 276 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8990 (p) REVERT: D 306 GLU cc_start: 0.4235 (mt-10) cc_final: 0.3470 (pm20) REVERT: D 397 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6918 (tm-30) REVERT: E 7 MET cc_start: 0.9032 (ppp) cc_final: 0.8311 (ppp) REVERT: E 37 ARG cc_start: 0.8001 (ptt90) cc_final: 0.7636 (ptt-90) REVERT: E 117 ASP cc_start: 0.8875 (t0) cc_final: 0.8604 (t70) REVERT: E 149 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8055 (p) REVERT: E 192 GLU cc_start: 0.4463 (tt0) cc_final: 0.4206 (tt0) REVERT: E 322 LYS cc_start: 0.9452 (mmtt) cc_final: 0.9221 (mptt) REVERT: E 367 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8309 (ttpp) REVERT: F 61 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8034 (tptp) REVERT: F 150 ASN cc_start: 0.8666 (OUTLIER) cc_final: 0.8407 (p0) REVERT: F 175 ASP cc_start: 0.8627 (m-30) cc_final: 0.8419 (m-30) REVERT: F 177 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8382 (mttp) REVERT: F 188 TYR cc_start: 0.9025 (t80) cc_final: 0.8813 (t80) REVERT: F 213 ASP cc_start: 0.8991 (t0) cc_final: 0.8624 (t0) REVERT: F 290 ARG cc_start: 0.9366 (mmm-85) cc_final: 0.9156 (mmm160) REVERT: F 301 GLU cc_start: 0.8116 (tp30) cc_final: 0.7828 (tp30) REVERT: a 73 GLN cc_start: 0.8282 (mt0) cc_final: 0.8034 (mt0) REVERT: a 194 GLN cc_start: 0.8494 (pt0) cc_final: 0.8125 (mp10) REVERT: a 233 TRP cc_start: 0.8778 (m-90) cc_final: 0.8530 (m-90) REVERT: a 242 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8514 (ttp80) REVERT: a 287 ASP cc_start: 0.7883 (p0) cc_final: 0.7368 (p0) REVERT: a 302 ASN cc_start: 0.9333 (t0) cc_final: 0.8656 (t0) REVERT: a 335 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8315 (m) REVERT: b 3 ASP cc_start: 0.8481 (m-30) cc_final: 0.8095 (t0) REVERT: b 80 ASN cc_start: 0.8517 (m-40) cc_final: 0.7165 (t0) REVERT: b 82 HIS cc_start: 0.6823 (m170) cc_final: 0.6469 (m170) REVERT: b 139 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8245 (ptp-170) REVERT: b 155 HIS cc_start: 0.8040 (t-170) cc_final: 0.7811 (t-90) REVERT: b 198 TYR cc_start: 0.6543 (t80) cc_final: 0.5978 (t80) REVERT: b 304 THR cc_start: 0.9464 (m) cc_final: 0.8940 (p) REVERT: b 321 GLU cc_start: 0.8180 (mp0) cc_final: 0.7508 (mp0) REVERT: c 3 ASP cc_start: 0.8828 (p0) cc_final: 0.8320 (t0) REVERT: c 13 ARG cc_start: 0.7531 (tpp-160) cc_final: 0.7079 (tpp-160) REVERT: c 35 GLU cc_start: 0.8119 (tt0) cc_final: 0.7898 (tt0) REVERT: c 41 HIS cc_start: 0.9165 (OUTLIER) cc_final: 0.8380 (m170) REVERT: c 68 MET cc_start: 0.7439 (tpp) cc_final: 0.7072 (tmm) REVERT: c 98 TYR cc_start: 0.8593 (m-80) cc_final: 0.7995 (m-80) REVERT: c 138 TYR cc_start: 0.6427 (OUTLIER) cc_final: 0.5713 (t80) REVERT: c 168 GLN cc_start: 0.8097 (pm20) cc_final: 0.7776 (mp10) REVERT: c 171 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8255 (pp) REVERT: c 174 ASP cc_start: 0.8049 (t0) cc_final: 0.7754 (t0) REVERT: d 80 ASN cc_start: 0.8178 (t0) cc_final: 0.7329 (t0) REVERT: d 82 HIS cc_start: 0.6802 (m170) cc_final: 0.6358 (m170) REVERT: d 98 TYR cc_start: 0.8875 (m-80) cc_final: 0.8528 (m-80) REVERT: d 135 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7791 (mmm-85) REVERT: d 166 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7075 (mtm) REVERT: d 174 ASP cc_start: 0.8203 (t0) cc_final: 0.7941 (t0) REVERT: d 222 GLN cc_start: 0.8493 (mt0) cc_final: 0.8048 (mt0) REVERT: d 302 ASN cc_start: 0.9267 (t0) cc_final: 0.8751 (t0) REVERT: e 52 MET cc_start: 0.9015 (tpp) cc_final: 0.7808 (tpp) REVERT: e 113 PHE cc_start: 0.8598 (p90) cc_final: 0.8387 (p90) REVERT: e 120 HIS cc_start: 0.8736 (OUTLIER) cc_final: 0.8241 (t-170) REVERT: e 168 GLN cc_start: 0.8953 (pt0) cc_final: 0.8333 (pm20) REVERT: e 194 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7988 (mm-40) REVERT: e 287 ASP cc_start: 0.8286 (p0) cc_final: 0.7944 (p0) REVERT: e 333 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8043 (ttpp) REVERT: f 35 GLU cc_start: 0.8322 (tt0) cc_final: 0.7916 (tt0) REVERT: f 39 ASP cc_start: 0.8338 (t0) cc_final: 0.7801 (t0) REVERT: f 65 MET cc_start: 0.8880 (ptm) cc_final: 0.8658 (ptm) REVERT: f 98 TYR cc_start: 0.8842 (m-80) cc_final: 0.8241 (m-80) REVERT: f 240 LEU cc_start: 0.9325 (tp) cc_final: 0.9094 (mp) REVERT: f 302 ASN cc_start: 0.9436 (t0) cc_final: 0.8987 (t0) REVERT: f 323 LEU cc_start: 0.9370 (tp) cc_final: 0.9114 (tt) outliers start: 197 outliers final: 157 residues processed: 761 average time/residue: 0.1886 time to fit residues: 238.8354 Evaluate side-chains 762 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 585 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 4 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 347 LEU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 142 TRP Chi-restraints excluded: chain F residue 150 ASN Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 177 LYS Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 387 HIS Chi-restraints excluded: chain a residue 22 CYS Chi-restraints excluded: chain a residue 24 HIS Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 50 SER Chi-restraints excluded: chain a residue 68 MET Chi-restraints excluded: chain a residue 76 ILE Chi-restraints excluded: chain a residue 99 ILE Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 197 TYR Chi-restraints excluded: chain a residue 213 HIS Chi-restraints excluded: chain a residue 242 ARG Chi-restraints excluded: chain a residue 264 ILE Chi-restraints excluded: chain a residue 290 THR Chi-restraints excluded: chain a residue 315 ASN Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 335 VAL Chi-restraints excluded: chain a residue 336 TRP Chi-restraints excluded: chain b residue 27 CYS Chi-restraints excluded: chain b residue 53 PHE Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 114 HIS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 175 HIS Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 248 PHE Chi-restraints excluded: chain b residue 257 VAL Chi-restraints excluded: chain b residue 285 HIS Chi-restraints excluded: chain b residue 292 LEU Chi-restraints excluded: chain c residue 22 CYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 41 HIS Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 138 TYR Chi-restraints excluded: chain c residue 171 LEU Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 197 TYR Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 22 CYS Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 114 HIS Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 135 ARG Chi-restraints excluded: chain d residue 166 MET Chi-restraints excluded: chain d residue 175 HIS Chi-restraints excluded: chain d residue 185 VAL Chi-restraints excluded: chain d residue 187 ILE Chi-restraints excluded: chain d residue 254 VAL Chi-restraints excluded: chain d residue 264 ILE Chi-restraints excluded: chain d residue 267 LEU Chi-restraints excluded: chain d residue 318 VAL Chi-restraints excluded: chain e residue 27 CYS Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 47 ILE Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 99 ILE Chi-restraints excluded: chain e residue 114 HIS Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 167 HIS Chi-restraints excluded: chain e residue 257 VAL Chi-restraints excluded: chain e residue 285 HIS Chi-restraints excluded: chain e residue 290 THR Chi-restraints excluded: chain e residue 292 LEU Chi-restraints excluded: chain e residue 315 ASN Chi-restraints excluded: chain e residue 333 LYS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 22 CYS Chi-restraints excluded: chain f residue 27 CYS Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 99 ILE Chi-restraints excluded: chain f residue 131 ARG Chi-restraints excluded: chain f residue 177 LEU Chi-restraints excluded: chain f residue 197 TYR Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 294 THR Chi-restraints excluded: chain f residue 308 ILE Chi-restraints excluded: chain f residue 310 ARG Chi-restraints excluded: chain f residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 346 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 14 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 301 optimal weight: 0.6980 chunk 147 optimal weight: 0.9990 chunk 142 optimal weight: 0.0970 chunk 481 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 HIS d 102 GLN ** d 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 ASN ** f 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.111695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.083967 restraints weight = 88630.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.086689 restraints weight = 42315.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.088449 restraints weight = 25563.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.089607 restraints weight = 17993.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.090345 restraints weight = 14176.325| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 39291 Z= 0.153 Angle : 0.666 12.286 53239 Z= 0.336 Chirality : 0.045 0.180 5423 Planarity : 0.005 0.086 7162 Dihedral : 6.696 59.857 6284 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.11 % Favored : 90.80 % Rotamer: Outliers : 5.03 % Allowed : 22.93 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.12), residues: 5280 helix: -2.70 (0.39), residues: 134 sheet: -0.36 (0.13), residues: 1710 loop : -1.48 (0.10), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG c 13 TYR 0.025 0.001 TYR D 107 PHE 0.036 0.002 PHE a 248 TRP 0.069 0.002 TRP d 233 HIS 0.010 0.001 HIS b 288 Details of bonding type rmsd covalent geometry : bond 0.00354 (39184) covalent geometry : angle 0.65980 (53002) SS BOND : bond 0.00369 ( 84) SS BOND : angle 1.22335 ( 168) hydrogen bonds : bond 0.02742 ( 1062) hydrogen bonds : angle 5.60359 ( 2568) link_BETA1-4 : bond 0.00587 ( 12) link_BETA1-4 : angle 1.89038 ( 36) link_NAG-ASN : bond 0.00180 ( 11) link_NAG-ASN : angle 2.07465 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 590 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 VAL cc_start: 0.9036 (OUTLIER) cc_final: 0.8771 (m) REVERT: A 79 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7238 (tm-30) REVERT: A 143 ARG cc_start: 0.7594 (tpt170) cc_final: 0.6598 (tpp-160) REVERT: A 171 TRP cc_start: 0.8645 (t60) cc_final: 0.8437 (t60) REVERT: A 203 ASP cc_start: 0.9003 (p0) cc_final: 0.8563 (p0) REVERT: A 271 ASN cc_start: 0.8988 (m110) cc_final: 0.8748 (m110) REVERT: A 343 ASN cc_start: 0.8436 (p0) cc_final: 0.8074 (p0) REVERT: A 385 LYS cc_start: 0.3285 (OUTLIER) cc_final: 0.0804 (pttt) REVERT: B 200 SER cc_start: 0.9275 (t) cc_final: 0.8853 (p) REVERT: B 270 GLU cc_start: 0.9103 (pt0) cc_final: 0.8819 (mt-10) REVERT: B 290 ARG cc_start: 0.9037 (mmt-90) cc_final: 0.8294 (mmp80) REVERT: B 306 GLU cc_start: 0.8748 (tp30) cc_final: 0.8421 (tp30) REVERT: B 369 GLN cc_start: 0.9316 (tt0) cc_final: 0.9027 (mt0) REVERT: C 10 LYS cc_start: 0.8917 (mtpt) cc_final: 0.8534 (mttm) REVERT: C 175 ASP cc_start: 0.8502 (t70) cc_final: 0.8258 (t0) REVERT: C 213 ASP cc_start: 0.8658 (t0) cc_final: 0.8234 (t0) REVERT: C 369 GLN cc_start: 0.7855 (tm-30) cc_final: 0.6736 (tm-30) REVERT: D 7 MET cc_start: 0.9369 (ppp) cc_final: 0.8543 (ppp) REVERT: D 143 ARG cc_start: 0.7468 (ttt90) cc_final: 0.6960 (ttt90) REVERT: D 150 ASN cc_start: 0.8509 (t0) cc_final: 0.8267 (t0) REVERT: D 184 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8030 (mt-10) REVERT: D 187 ASN cc_start: 0.9174 (OUTLIER) cc_final: 0.8938 (m-40) REVERT: D 230 VAL cc_start: 0.9257 (OUTLIER) cc_final: 0.9038 (m) REVERT: D 276 SER cc_start: 0.9243 (OUTLIER) cc_final: 0.9019 (p) REVERT: D 306 GLU cc_start: 0.4384 (mt-10) cc_final: 0.3635 (pm20) REVERT: D 397 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6944 (tm-30) REVERT: E 7 MET cc_start: 0.9046 (ppp) cc_final: 0.8300 (ppp) REVERT: E 37 ARG cc_start: 0.8058 (ptt90) cc_final: 0.7678 (ptt-90) REVERT: E 117 ASP cc_start: 0.8936 (t0) cc_final: 0.8643 (t70) REVERT: E 149 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7946 (p) REVERT: E 192 GLU cc_start: 0.4564 (tt0) cc_final: 0.4305 (tt0) REVERT: E 213 ASP cc_start: 0.8539 (t0) cc_final: 0.8316 (t0) REVERT: E 322 LYS cc_start: 0.9438 (mmtt) cc_final: 0.9089 (mmmt) REVERT: E 367 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8499 (ttpp) REVERT: F 61 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8121 (tptp) REVERT: F 175 ASP cc_start: 0.8646 (m-30) cc_final: 0.8430 (m-30) REVERT: F 183 HIS cc_start: 0.7732 (t70) cc_final: 0.7500 (t-170) REVERT: F 188 TYR cc_start: 0.9047 (t80) cc_final: 0.8839 (t80) REVERT: F 290 ARG cc_start: 0.9335 (mmm-85) cc_final: 0.9105 (mmm160) REVERT: F 301 GLU cc_start: 0.8160 (tp30) cc_final: 0.7856 (tp30) REVERT: a 160 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8244 (mm110) REVERT: a 194 GLN cc_start: 0.8510 (pt0) cc_final: 0.8154 (mp10) REVERT: a 233 TRP cc_start: 0.8779 (m-90) cc_final: 0.8512 (m-90) REVERT: a 242 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8521 (ttp80) REVERT: a 302 ASN cc_start: 0.9316 (t0) cc_final: 0.8665 (t0) REVERT: b 3 ASP cc_start: 0.8529 (m-30) cc_final: 0.8146 (t0) REVERT: b 80 ASN cc_start: 0.8491 (m-40) cc_final: 0.7150 (t0) REVERT: b 82 HIS cc_start: 0.6836 (m170) cc_final: 0.6543 (m170) REVERT: b 198 TYR cc_start: 0.6560 (t80) cc_final: 0.6018 (t80) REVERT: b 321 GLU cc_start: 0.8270 (mp0) cc_final: 0.7529 (mp0) REVERT: c 3 ASP cc_start: 0.8802 (p0) cc_final: 0.8290 (t0) REVERT: c 41 HIS cc_start: 0.9190 (OUTLIER) cc_final: 0.8355 (m170) REVERT: c 64 TYR cc_start: 0.8090 (m-10) cc_final: 0.7386 (m-80) REVERT: c 98 TYR cc_start: 0.8647 (m-80) cc_final: 0.8079 (m-80) REVERT: c 138 TYR cc_start: 0.6490 (OUTLIER) cc_final: 0.5788 (t80) REVERT: c 171 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8321 (pp) REVERT: c 174 ASP cc_start: 0.8095 (t0) cc_final: 0.7801 (t0) REVERT: d 80 ASN cc_start: 0.8159 (t0) cc_final: 0.7329 (t0) REVERT: d 82 HIS cc_start: 0.6811 (m170) cc_final: 0.6358 (m170) REVERT: d 135 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7815 (mmm-85) REVERT: d 166 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7112 (mtm) REVERT: d 174 ASP cc_start: 0.8222 (t0) cc_final: 0.7945 (t0) REVERT: d 222 GLN cc_start: 0.8512 (mt0) cc_final: 0.7998 (mt0) REVERT: d 302 ASN cc_start: 0.9282 (t0) cc_final: 0.8761 (t0) REVERT: e 52 MET cc_start: 0.9064 (tpp) cc_final: 0.7878 (tpp) REVERT: e 113 PHE cc_start: 0.8641 (p90) cc_final: 0.8420 (p90) REVERT: e 120 HIS cc_start: 0.8737 (OUTLIER) cc_final: 0.8229 (t-170) REVERT: e 165 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8258 (mt-10) REVERT: e 168 GLN cc_start: 0.8943 (pt0) cc_final: 0.8343 (pm20) REVERT: e 194 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8116 (mm-40) REVERT: e 333 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8075 (ttpp) REVERT: f 35 GLU cc_start: 0.8318 (tt0) cc_final: 0.7911 (tt0) REVERT: f 39 ASP cc_start: 0.8361 (t0) cc_final: 0.7890 (t0) REVERT: f 62 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8358 (tp) REVERT: f 65 MET cc_start: 0.8896 (ptm) cc_final: 0.8688 (ptm) REVERT: f 98 TYR cc_start: 0.8884 (m-80) cc_final: 0.8312 (m-80) REVERT: f 302 ASN cc_start: 0.9458 (t0) cc_final: 0.9149 (t0) outliers start: 191 outliers final: 157 residues processed: 732 average time/residue: 0.1887 time to fit residues: 231.1022 Evaluate side-chains 746 residues out of total 4556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 572 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 387 HIS Chi-restraints excluded: chain A residue 394 GLN Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 231 HIS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 272 CYS Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 391 TYR Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain C residue 272 CYS Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 387 HIS Chi-restraints excluded: chain C residue 391 TYR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 ASN Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 230 VAL Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 161 LYS Chi-restraints excluded: chain E residue 164 ILE Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 185 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 307 CYS Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 347 LEU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 381 CYS Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 42 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 61 LYS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 142 TRP Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain F residue 343 ASN Chi-restraints excluded: chain F residue 387 HIS Chi-restraints excluded: chain a residue 22 CYS Chi-restraints excluded: chain a residue 27 CYS Chi-restraints excluded: chain a residue 50 SER Chi-restraints excluded: chain a residue 68 MET Chi-restraints excluded: chain a residue 76 ILE Chi-restraints excluded: chain a residue 99 ILE Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 164 VAL Chi-restraints excluded: chain a residue 171 LEU Chi-restraints excluded: chain a residue 172 VAL Chi-restraints excluded: chain a residue 185 VAL Chi-restraints excluded: chain a residue 197 TYR Chi-restraints excluded: chain a residue 213 HIS Chi-restraints excluded: chain a residue 242 ARG Chi-restraints excluded: chain a residue 264 ILE Chi-restraints excluded: chain a residue 290 THR Chi-restraints excluded: chain a residue 315 ASN Chi-restraints excluded: chain a residue 318 VAL Chi-restraints excluded: chain a residue 336 TRP Chi-restraints excluded: chain b residue 27 CYS Chi-restraints excluded: chain b residue 53 PHE Chi-restraints excluded: chain b residue 58 ASP Chi-restraints excluded: chain b residue 99 ILE Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 114 HIS Chi-restraints excluded: chain b residue 139 ARG Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 172 VAL Chi-restraints excluded: chain b residue 175 HIS Chi-restraints excluded: chain b residue 197 TYR Chi-restraints excluded: chain b residue 216 THR Chi-restraints excluded: chain b residue 257 VAL Chi-restraints excluded: chain b residue 285 HIS Chi-restraints excluded: chain b residue 292 LEU Chi-restraints excluded: chain c residue 22 CYS Chi-restraints excluded: chain c residue 27 CYS Chi-restraints excluded: chain c residue 41 HIS Chi-restraints excluded: chain c residue 109 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 131 ARG Chi-restraints excluded: chain c residue 138 TYR Chi-restraints excluded: chain c residue 171 LEU Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 197 TYR Chi-restraints excluded: chain c residue 275 HIS Chi-restraints excluded: chain c residue 315 ASN Chi-restraints excluded: chain d residue 22 CYS Chi-restraints excluded: chain d residue 27 CYS Chi-restraints excluded: chain d residue 29 SER Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 72 THR Chi-restraints excluded: chain d residue 114 HIS Chi-restraints excluded: chain d residue 131 ARG Chi-restraints excluded: chain d residue 135 ARG Chi-restraints excluded: chain d residue 166 MET Chi-restraints excluded: chain d residue 175 HIS Chi-restraints excluded: chain d residue 185 VAL Chi-restraints excluded: chain d residue 213 HIS Chi-restraints excluded: chain d residue 254 VAL Chi-restraints excluded: chain d residue 264 ILE Chi-restraints excluded: chain d residue 267 LEU Chi-restraints excluded: chain d residue 318 VAL Chi-restraints excluded: chain e residue 27 CYS Chi-restraints excluded: chain e residue 44 VAL Chi-restraints excluded: chain e residue 91 LEU Chi-restraints excluded: chain e residue 99 ILE Chi-restraints excluded: chain e residue 114 HIS Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 167 HIS Chi-restraints excluded: chain e residue 257 VAL Chi-restraints excluded: chain e residue 281 ILE Chi-restraints excluded: chain e residue 285 HIS Chi-restraints excluded: chain e residue 290 THR Chi-restraints excluded: chain e residue 292 LEU Chi-restraints excluded: chain e residue 333 LYS Chi-restraints excluded: chain f residue 11 LEU Chi-restraints excluded: chain f residue 21 ASN Chi-restraints excluded: chain f residue 22 CYS Chi-restraints excluded: chain f residue 27 CYS Chi-restraints excluded: chain f residue 31 ILE Chi-restraints excluded: chain f residue 62 LEU Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 99 ILE Chi-restraints excluded: chain f residue 131 ARG Chi-restraints excluded: chain f residue 177 LEU Chi-restraints excluded: chain f residue 197 TYR Chi-restraints excluded: chain f residue 254 VAL Chi-restraints excluded: chain f residue 294 THR Chi-restraints excluded: chain f residue 308 ILE Chi-restraints excluded: chain f residue 310 ARG Chi-restraints excluded: chain f residue 318 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 524 random chunks: chunk 162 optimal weight: 0.8980 chunk 115 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 436 optimal weight: 1.9990 chunk 375 optimal weight: 0.5980 chunk 238 optimal weight: 5.9990 chunk 421 optimal weight: 2.9990 chunk 522 optimal weight: 0.0570 chunk 352 optimal weight: 0.6980 chunk 306 optimal weight: 1.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 21 ASN ** f 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 275 HIS f 277 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.113305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.084717 restraints weight = 89468.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.087452 restraints weight = 43325.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.089227 restraints weight = 26354.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.090386 restraints weight = 18617.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.091125 restraints weight = 14725.020| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 39291 Z= 0.134 Angle : 0.675 13.219 53239 Z= 0.339 Chirality : 0.045 0.213 5423 Planarity : 0.005 0.082 7162 Dihedral : 6.636 60.096 6280 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.94 % Favored : 90.97 % Rotamer: Outliers : 4.74 % Allowed : 23.54 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.12), residues: 5280 helix: -2.64 (0.40), residues: 134 sheet: -0.33 (0.13), residues: 1710 loop : -1.47 (0.10), residues: 3436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG c 13 TYR 0.034 0.001 TYR d 138 PHE 0.034 0.001 PHE a 248 TRP 0.070 0.002 TRP d 233 HIS 0.016 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00312 (39184) covalent geometry : angle 0.66893 (53002) SS BOND : bond 0.00252 ( 84) SS BOND : angle 1.23912 ( 168) hydrogen bonds : bond 0.02691 ( 1062) hydrogen bonds : angle 5.57555 ( 2568) link_BETA1-4 : bond 0.00551 ( 12) link_BETA1-4 : angle 1.83295 ( 36) link_NAG-ASN : bond 0.00178 ( 11) link_NAG-ASN : angle 2.00432 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9380.44 seconds wall clock time: 161 minutes 40.79 seconds (9700.79 seconds total)