Starting phenix.real_space_refine on Sat Mar 7 10:08:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eu3_31307/03_2026/7eu3_31307.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eu3_31307/03_2026/7eu3_31307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eu3_31307/03_2026/7eu3_31307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eu3_31307/03_2026/7eu3_31307.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eu3_31307/03_2026/7eu3_31307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eu3_31307/03_2026/7eu3_31307.map" } resolution = 3.7 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 1 5.49 5 S 204 5.16 5 C 26574 2.51 5 N 6641 2.21 5 O 7351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 140 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40775 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2608 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 330} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 4, 'TYR:plan': 3, 'GLN:plan1': 1, 'ARG:plan': 5, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 3646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3646 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 4, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 841 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 110} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 2, 'ASP:plan': 1, 'GLU:plan': 4, 'TRP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "D" Number of atoms: 3874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3874 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 24, 'TRANS': 474} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 4, 'GLU:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 750 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 5124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5124 Classifications: {'peptide': 671} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 24, 'TRANS': 646} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 175 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 3, 'PHE:plan': 2, 'ASN:plan1': 7, 'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1260 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 170} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "H" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2991 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 21, 'TRANS': 361} Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 8, 'ASN:plan1': 2, 'GLN:plan1': 4, 'TYR:plan': 2, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 96 Chain: "I" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1229 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 31} Link IDs: {'PTRANS': 7, 'TRANS': 157} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'GLU:plan': 6, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "J" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1258 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 150} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 4, 'TYR:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "K" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1474 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "L" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 572 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 61} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 876 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "N" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1154 Classifications: {'peptide': 145} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "T" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 305 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'TRANS': 60} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'UNK:plan-1': 61} Unresolved non-hydrogen planarities: 61 Chain: "1" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 143} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "2" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 915 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 8, 'TRANS': 120} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 4, 'TRP:plan': 1, 'TYR:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "3" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 989 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 129} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 42 Chain: "4" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 878 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 10, 'TRANS': 119} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 5, 'GLU:plan': 2, 'PHE:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "5" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1289 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 164} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "6" Number of atoms: 2541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2541 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 18, 'TRANS': 324} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 7, 'TYR:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 78 Chain: "7" Number of atoms: 2311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2311 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 18, 'TRANS': 298} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 1, 'TYR:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "8" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 828 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 8, 'TRANS': 110} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'ASP:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 62 Chain: "9" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 617 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 48 Chain: "0" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1089 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 11, 'TRANS': 137} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'TRP:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 8, 'PHE:plan': 3, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 113 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 139 Unusual residues: {'BCR': 1, 'SQD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen planarities: 1 Chain: "8" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 38434 SG CYS 8 132 75.038 177.624 129.984 1.00 78.19 S Time building chain proxies: 8.58, per 1000 atoms: 0.21 Number of scatterers: 40775 At special positions: 0 Unit cell: (172.524, 230.032, 186.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 204 16.00 P 1 15.00 O 7351 8.00 N 6641 7.00 C 26574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 6 410 " - pdb=" SG CYS 6 433 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 8 201 " pdb="FE3 SF4 8 201 " - pdb=" SG CYS 8 132 " pdb="FE4 SF4 8 201 " - pdb=" SG CYS 8 168 " pdb="FE4 SF4 8 201 " - pdb=" SG CYS 8 135 " Number of angles added : 9 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: 9972 Finding SS restraints... Secondary structure from input PDB file: 203 helices and 25 sheets defined 49.1% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 29 through 54 removed outlier: 3.580A pdb=" N LEU A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 57 No H-bonds generated for 'chain 'A' and resid 55 through 57' Processing helix chain 'A' and resid 72 through 84 removed outlier: 3.755A pdb=" N PHE A 83 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS A 84 " --> pdb=" O LYS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 110 removed outlier: 4.169A pdb=" N SER A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.579A pdb=" N SER A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.702A pdb=" N GLY A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 151 " --> pdb=" O ALA A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 removed outlier: 4.266A pdb=" N ALA A 163 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.079A pdb=" N ALA A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 181 " --> pdb=" O CYS A 177 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 210 through 225 removed outlier: 3.688A pdb=" N VAL A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 223 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 275 Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.886A pdb=" N ASP A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 290' Processing helix chain 'A' and resid 296 through 324 removed outlier: 4.265A pdb=" N LEU A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 342 through 358 removed outlier: 3.928A pdb=" N ILE A 346 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 52 removed outlier: 4.098A pdb=" N LEU B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 78 removed outlier: 4.305A pdb=" N SER B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 77 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 121 removed outlier: 3.512A pdb=" N PHE B 100 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 105 " --> pdb=" O GLN B 101 " (cutoff:3.500A) Proline residue: B 113 - end of helix removed outlier: 4.045A pdb=" N GLU B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 144 Processing helix chain 'B' and resid 150 through 161 Proline residue: B 156 - end of helix Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 174 through 205 removed outlier: 3.562A pdb=" N GLU B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N TYR B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N MET B 186 " --> pdb=" O LYS B 182 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 245 removed outlier: 3.833A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLY B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.603A pdb=" N ASP B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU B 258 " --> pdb=" O PRO B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 286 removed outlier: 5.036A pdb=" N LYS B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 317 removed outlier: 4.488A pdb=" N LEU B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LEU B 298 " --> pdb=" O GLU B 294 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ASN B 311 " --> pdb=" O MET B 307 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA B 314 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR B 316 " --> pdb=" O LEU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.961A pdb=" N ILE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 336 through 341' Processing helix chain 'B' and resid 347 through 377 removed outlier: 3.851A pdb=" N SER B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.521A pdb=" N ASP B 383 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 407 removed outlier: 3.665A pdb=" N ALA B 395 " --> pdb=" O ASP B 391 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 423 removed outlier: 4.267A pdb=" N PHE B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS B 423 " --> pdb=" O TYR B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 removed outlier: 4.186A pdb=" N TYR B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N TYR B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 489 removed outlier: 3.761A pdb=" N ILE B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 490 through 492 No H-bonds generated for 'chain 'B' and resid 490 through 492' Processing helix chain 'B' and resid 497 through 506 removed outlier: 4.569A pdb=" N ILE B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 31 Proline residue: C 21 - end of helix removed outlier: 3.505A pdb=" N LEU C 31 " --> pdb=" O ILE C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 85 removed outlier: 4.042A pdb=" N TYR C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N MET C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE C 65 " --> pdb=" O ARG C 61 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL C 74 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU C 75 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR C 76 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N VAL C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Proline residue: C 81 - end of helix Processing helix chain 'C' and resid 91 through 114 removed outlier: 3.565A pdb=" N LEU C 104 " --> pdb=" O PHE C 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 19 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 29 through 54 removed outlier: 3.758A pdb=" N ARG D 33 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TRP D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 104 removed outlier: 4.125A pdb=" N GLY D 88 " --> pdb=" O GLY D 84 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER D 89 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 130 removed outlier: 3.558A pdb=" N PHE D 116 " --> pdb=" O ARG D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 144 removed outlier: 4.141A pdb=" N GLU D 144 " --> pdb=" O MET D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 removed outlier: 3.509A pdb=" N TYR D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 187 removed outlier: 3.826A pdb=" N SER D 163 " --> pdb=" O ARG D 159 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE D 178 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 225 removed outlier: 3.897A pdb=" N ALA D 220 " --> pdb=" O GLY D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 233 through 240 Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.999A pdb=" N LEU D 248 " --> pdb=" O SER D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 265 removed outlier: 4.208A pdb=" N GLY D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 274 Processing helix chain 'D' and resid 276 through 296 removed outlier: 3.563A pdb=" N LEU D 280 " --> pdb=" O PHE D 276 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA D 292 " --> pdb=" O ILE D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 321 removed outlier: 3.774A pdb=" N MET D 313 " --> pdb=" O SER D 309 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY D 314 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE D 316 " --> pdb=" O HIS D 312 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE D 317 " --> pdb=" O MET D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 353 removed outlier: 3.588A pdb=" N LEU D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE D 332 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 341 " --> pdb=" O SER D 337 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA D 343 " --> pdb=" O GLY D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 386 removed outlier: 3.871A pdb=" N PHE D 375 " --> pdb=" O MET D 371 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE D 381 " --> pdb=" O MET D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 406 Processing helix chain 'D' and resid 413 through 441 removed outlier: 3.817A pdb=" N LEU D 417 " --> pdb=" O MET D 413 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY D 425 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET D 426 " --> pdb=" O MET D 422 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 427 " --> pdb=" O ALA D 423 " (cutoff:3.500A) Proline residue: D 430 - end of helix removed outlier: 3.685A pdb=" N SER D 435 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET D 436 " --> pdb=" O TYR D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 478 Proline residue: D 471 - end of helix removed outlier: 3.755A pdb=" N TYR D 478 " --> pdb=" O GLY D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.699A pdb=" N VAL E 6 " --> pdb=" O MET E 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2 through 6' Processing helix chain 'E' and resid 6 through 23 removed outlier: 3.794A pdb=" N VAL E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR E 12 " --> pdb=" O PHE E 8 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE E 16 " --> pdb=" O TYR E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 47 removed outlier: 3.754A pdb=" N THR E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 3.738A pdb=" N PHE E 52 " --> pdb=" O PHE E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 88 removed outlier: 3.626A pdb=" N LEU E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 96 removed outlier: 3.614A pdb=" N GLN E 95 " --> pdb=" O ARG E 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 53 removed outlier: 3.622A pdb=" N VAL F 52 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 70 removed outlier: 3.713A pdb=" N ILE F 61 " --> pdb=" O PRO F 57 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER F 63 " --> pdb=" O PRO F 59 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE F 66 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 76 removed outlier: 3.661A pdb=" N THR F 75 " --> pdb=" O ILE F 71 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS F 76 " --> pdb=" O PRO F 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 71 through 76' Processing helix chain 'F' and resid 82 through 107 removed outlier: 4.047A pdb=" N SER F 86 " --> pdb=" O TRP F 82 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU F 89 " --> pdb=" O PRO F 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 93 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN F 99 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU F 100 " --> pdb=" O PHE F 96 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN F 103 " --> pdb=" O GLN F 99 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 157 removed outlier: 3.902A pdb=" N VAL F 145 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE F 151 " --> pdb=" O ILE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 182 removed outlier: 3.524A pdb=" N GLY F 179 " --> pdb=" O THR F 175 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR F 182 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 205 removed outlier: 3.996A pdb=" N PHE F 192 " --> pdb=" O GLN F 188 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU F 194 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU F 195 " --> pdb=" O PHE F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 243 removed outlier: 3.888A pdb=" N CYS F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLN F 218 " --> pdb=" O ALA F 214 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN F 224 " --> pdb=" O ALA F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 256 removed outlier: 4.287A pdb=" N GLN F 252 " --> pdb=" O ARG F 248 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN F 255 " --> pdb=" O PHE F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 283 removed outlier: 3.737A pdb=" N LEU F 267 " --> pdb=" O ILE F 263 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA F 272 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE F 273 " --> pdb=" O THR F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 299 through 306 Processing helix chain 'F' and resid 312 through 327 removed outlier: 4.484A pdb=" N LEU F 318 " --> pdb=" O ALA F 314 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU F 319 " --> pdb=" O GLY F 315 " (cutoff:3.500A) Proline residue: F 324 - end of helix removed outlier: 3.613A pdb=" N ILE F 327 " --> pdb=" O LEU F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 349 removed outlier: 3.681A pdb=" N SER F 337 " --> pdb=" O MET F 333 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE F 345 " --> pdb=" O THR F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 377 removed outlier: 4.329A pdb=" N ALA F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR F 371 " --> pdb=" O SER F 367 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY F 377 " --> pdb=" O MET F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 410 removed outlier: 3.752A pdb=" N ALA F 384 " --> pdb=" O SER F 380 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE F 386 " --> pdb=" O GLN F 382 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N TYR F 393 " --> pdb=" O ILE F 389 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU F 398 " --> pdb=" O SER F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 449 removed outlier: 4.193A pdb=" N THR F 439 " --> pdb=" O ILE F 435 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE F 440 " --> pdb=" O THR F 436 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER F 446 " --> pdb=" O TRP F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 470 removed outlier: 3.705A pdb=" N GLU F 461 " --> pdb=" O TRP F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 497 removed outlier: 4.952A pdb=" N ILE F 476 " --> pdb=" O PHE F 472 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY F 482 " --> pdb=" O SER F 478 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA F 485 " --> pdb=" O ALA F 481 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE F 489 " --> pdb=" O ALA F 485 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR F 492 " --> pdb=" O MET F 488 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY F 497 " --> pdb=" O LEU F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 592 Processing helix chain 'F' and resid 592 through 597 removed outlier: 3.855A pdb=" N PHE F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 600 No H-bonds generated for 'chain 'F' and resid 598 through 600' Processing helix chain 'F' and resid 640 through 665 Processing helix chain 'F' and resid 687 through 704 removed outlier: 4.606A pdb=" N GLN F 693 " --> pdb=" O GLU F 689 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER F 700 " --> pdb=" O LYS F 696 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN F 704 " --> pdb=" O SER F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 707 through 716 removed outlier: 3.521A pdb=" N THR F 713 " --> pdb=" O ASP F 709 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 730 removed outlier: 3.930A pdb=" N GLU F 725 " --> pdb=" O ARG F 721 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 755 removed outlier: 4.124A pdb=" N GLY F 743 " --> pdb=" O THR F 739 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER F 746 " --> pdb=" O VAL F 742 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE F 747 " --> pdb=" O GLY F 743 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU F 751 " --> pdb=" O PHE F 747 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 775 removed outlier: 3.829A pdb=" N TYR F 771 " --> pdb=" O PHE F 767 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL F 772 " --> pdb=" O PHE F 768 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 29 removed outlier: 3.500A pdb=" N LEU G 21 " --> pdb=" O PHE G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 53 removed outlier: 3.562A pdb=" N LEU G 53 " --> pdb=" O PHE G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 66 removed outlier: 3.977A pdb=" N GLN G 62 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 78 Processing helix chain 'G' and resid 79 through 81 No H-bonds generated for 'chain 'G' and resid 79 through 81' Processing helix chain 'G' and resid 95 through 115 removed outlier: 4.015A pdb=" N ILE G 105 " --> pdb=" O SER G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 118 No H-bonds generated for 'chain 'G' and resid 116 through 118' Processing helix chain 'G' and resid 119 through 124 Processing helix chain 'G' and resid 141 through 148 Processing helix chain 'G' and resid 152 through 175 removed outlier: 3.764A pdb=" N PHE G 156 " --> pdb=" O PHE G 152 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER G 160 " --> pdb=" O PHE G 156 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE G 161 " --> pdb=" O GLU G 157 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE G 162 " --> pdb=" O LEU G 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 55 removed outlier: 3.698A pdb=" N ILE H 54 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 67 removed outlier: 3.540A pdb=" N VAL H 67 " --> pdb=" O LEU H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 88 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 95 through 126 removed outlier: 3.936A pdb=" N ILE H 111 " --> pdb=" O GLU H 107 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Proline residue: H 120 - end of helix Processing helix chain 'H' and resid 129 through 149 removed outlier: 4.431A pdb=" N TYR H 133 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU H 140 " --> pdb=" O ARG H 136 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR H 142 " --> pdb=" O ARG H 138 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR H 149 " --> pdb=" O PHE H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 173 removed outlier: 3.922A pdb=" N ILE H 172 " --> pdb=" O PRO H 168 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP H 173 " --> pdb=" O TYR H 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 168 through 173' Processing helix chain 'H' and resid 175 through 194 removed outlier: 4.671A pdb=" N LEU H 183 " --> pdb=" O CYS H 179 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG H 184 " --> pdb=" O ASP H 180 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL H 187 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU H 188 " --> pdb=" O ARG H 184 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR H 189 " --> pdb=" O GLY H 185 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR H 194 " --> pdb=" O GLN H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 204 removed outlier: 3.776A pdb=" N ARG H 202 " --> pdb=" O ILE H 198 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL H 203 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 217 Processing helix chain 'H' and resid 221 through 226 Processing helix chain 'H' and resid 238 through 242 Processing helix chain 'H' and resid 256 through 266 Processing helix chain 'H' and resid 268 through 282 removed outlier: 4.092A pdb=" N ILE H 272 " --> pdb=" O MET H 268 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS H 273 " --> pdb=" O SER H 269 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU H 280 " --> pdb=" O GLN H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 294 Processing helix chain 'H' and resid 357 through 361 Processing helix chain 'H' and resid 364 through 369 removed outlier: 3.515A pdb=" N VAL H 369 " --> pdb=" O LEU H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 384 Processing helix chain 'I' and resid 4 through 34 removed outlier: 5.184A pdb=" N GLY I 12 " --> pdb=" O PHE I 8 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN I 13 " --> pdb=" O MET I 9 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER I 31 " --> pdb=" O ILE I 27 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS I 32 " --> pdb=" O THR I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 114 removed outlier: 3.945A pdb=" N TYR I 113 " --> pdb=" O ASN I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 152 removed outlier: 3.556A pdb=" N ASP I 152 " --> pdb=" O ILE I 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 11 Processing helix chain 'J' and resid 12 through 14 No H-bonds generated for 'chain 'J' and resid 12 through 14' Processing helix chain 'J' and resid 36 through 48 removed outlier: 4.142A pdb=" N ILE J 40 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA J 41 " --> pdb=" O TRP J 37 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL J 46 " --> pdb=" O VAL J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 116 removed outlier: 3.544A pdb=" N GLU J 114 " --> pdb=" O PHE J 110 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SER J 115 " --> pdb=" O GLN J 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 52 removed outlier: 4.838A pdb=" N LEU K 42 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN K 43 " --> pdb=" O SER K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 71 removed outlier: 4.085A pdb=" N SER K 70 " --> pdb=" O ILE K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 removed outlier: 3.590A pdb=" N ARG K 80 " --> pdb=" O ASP K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 115 removed outlier: 4.003A pdb=" N LEU K 112 " --> pdb=" O SER K 108 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR K 113 " --> pdb=" O LEU K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 131 Processing helix chain 'K' and resid 132 through 136 removed outlier: 3.609A pdb=" N SER K 136 " --> pdb=" O GLY K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 179 removed outlier: 3.907A pdb=" N LYS K 175 " --> pdb=" O THR K 171 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS K 176 " --> pdb=" O LYS K 172 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE K 177 " --> pdb=" O LEU K 173 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER K 178 " --> pdb=" O ARG K 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 110 removed outlier: 3.726A pdb=" N ALA L 104 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU L 108 " --> pdb=" O ALA L 104 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL L 110 " --> pdb=" O PHE L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 122 removed outlier: 3.684A pdb=" N ILE L 114 " --> pdb=" O VAL L 110 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET L 116 " --> pdb=" O PRO L 112 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN L 117 " --> pdb=" O PRO L 113 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG L 122 " --> pdb=" O TRP L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 141 removed outlier: 3.712A pdb=" N PHE L 135 " --> pdb=" O THR L 131 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET L 136 " --> pdb=" O TYR L 132 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE L 137 " --> pdb=" O LEU L 133 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR L 139 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU L 140 " --> pdb=" O MET L 136 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE L 141 " --> pdb=" O PHE L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 146 removed outlier: 3.578A pdb=" N MET L 146 " --> pdb=" O PHE L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 149 No H-bonds generated for 'chain 'L' and resid 147 through 149' Processing helix chain 'M' and resid 136 through 152 removed outlier: 3.997A pdb=" N MET M 142 " --> pdb=" O GLU M 138 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL M 143 " --> pdb=" O THR M 139 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN M 148 " --> pdb=" O TYR M 144 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP M 149 " --> pdb=" O ASN M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 181 removed outlier: 4.335A pdb=" N ASP M 170 " --> pdb=" O LEU M 166 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS M 173 " --> pdb=" O SER M 169 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE M 175 " --> pdb=" O LEU M 171 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG M 176 " --> pdb=" O GLU M 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 88 removed outlier: 3.542A pdb=" N LEU N 85 " --> pdb=" O GLU N 81 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG N 87 " --> pdb=" O ARG N 83 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU N 88 " --> pdb=" O TYR N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 111 Processing helix chain 'N' and resid 135 through 142 Processing helix chain 'N' and resid 185 through 191 Processing helix chain 'N' and resid 193 through 198 removed outlier: 4.008A pdb=" N ASP N 197 " --> pdb=" O ALA N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 218 through 223 removed outlier: 3.701A pdb=" N ILE N 222 " --> pdb=" O PRO N 218 " (cutoff:3.500A) Processing helix chain '1' and resid 128 through 132 Processing helix chain '1' and resid 134 through 139 Processing helix chain '1' and resid 139 through 144 Processing helix chain '1' and resid 204 through 208 Processing helix chain '1' and resid 211 through 220 removed outlier: 4.167A pdb=" N VAL 1 217 " --> pdb=" O ASN 1 213 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N VAL 1 218 " --> pdb=" O LYS 1 214 " (cutoff:3.500A) Processing helix chain '2' and resid 114 through 126 removed outlier: 3.651A pdb=" N ARG 2 118 " --> pdb=" O GLU 2 114 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG 2 120 " --> pdb=" O ALA 2 116 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA 2 123 " --> pdb=" O ILE 2 119 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU 2 124 " --> pdb=" O ARG 2 120 " (cutoff:3.500A) Processing helix chain '2' and resid 129 through 135 Processing helix chain '2' and resid 139 through 153 removed outlier: 3.917A pdb=" N PHE 2 143 " --> pdb=" O LYS 2 139 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL 2 145 " --> pdb=" O VAL 2 141 " (cutoff:3.500A) Processing helix chain '2' and resid 154 through 159 Processing helix chain '2' and resid 174 through 186 removed outlier: 4.643A pdb=" N MET 2 182 " --> pdb=" O LEU 2 178 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR 2 183 " --> pdb=" O VAL 2 179 " (cutoff:3.500A) Processing helix chain '2' and resid 186 through 191 removed outlier: 3.615A pdb=" N ARG 2 190 " --> pdb=" O ASP 2 186 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR 2 191 " --> pdb=" O ARG 2 187 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 186 through 191' Processing helix chain '2' and resid 194 through 204 removed outlier: 3.764A pdb=" N LYS 2 203 " --> pdb=" O LEU 2 199 " (cutoff:3.500A) Processing helix chain '2' and resid 204 through 212 removed outlier: 3.520A pdb=" N LEU 2 208 " --> pdb=" O THR 2 204 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP 2 210 " --> pdb=" O LYS 2 206 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA 2 212 " --> pdb=" O LEU 2 208 " (cutoff:3.500A) Processing helix chain '3' and resid 128 through 135 Processing helix chain '3' and resid 135 through 140 Processing helix chain '3' and resid 151 through 173 removed outlier: 4.727A pdb=" N ARG 3 157 " --> pdb=" O ASN 3 153 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU 3 158 " --> pdb=" O LYS 3 154 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE 3 162 " --> pdb=" O LEU 3 158 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE 3 163 " --> pdb=" O LYS 3 159 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP 3 168 " --> pdb=" O TYR 3 164 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA 3 173 " --> pdb=" O LYS 3 169 " (cutoff:3.500A) Processing helix chain '3' and resid 178 through 201 removed outlier: 4.023A pdb=" N GLU 3 194 " --> pdb=" O PHE 3 190 " (cutoff:3.500A) Processing helix chain '3' and resid 205 through 226 removed outlier: 3.922A pdb=" N GLY 3 209 " --> pdb=" O ASP 3 205 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP 3 214 " --> pdb=" O SER 3 210 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU 3 221 " --> pdb=" O LEU 3 217 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N MET 3 223 " --> pdb=" O LEU 3 219 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THR 3 224 " --> pdb=" O GLN 3 220 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET 3 226 " --> pdb=" O VAL 3 222 " (cutoff:3.500A) Processing helix chain '4' and resid 184 through 186 No H-bonds generated for 'chain '4' and resid 184 through 186' Processing helix chain '4' and resid 200 through 207 Processing helix chain '5' and resid 104 through 115 Processing helix chain '5' and resid 210 through 219 Processing helix chain '6' and resid 126 through 131 removed outlier: 3.990A pdb=" N LEU 6 131 " --> pdb=" O TYR 6 127 " (cutoff:3.500A) Processing helix chain '6' and resid 132 through 143 Processing helix chain '6' and resid 153 through 158 removed outlier: 3.856A pdb=" N GLN 6 158 " --> pdb=" O ALA 6 154 " (cutoff:3.500A) Processing helix chain '6' and resid 159 through 162 Processing helix chain '6' and resid 182 through 192 Processing helix chain '6' and resid 193 through 195 No H-bonds generated for 'chain '6' and resid 193 through 195' Processing helix chain '6' and resid 208 through 216 removed outlier: 3.720A pdb=" N PHE 6 212 " --> pdb=" O GLY 6 208 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER 6 216 " --> pdb=" O PHE 6 212 " (cutoff:3.500A) Processing helix chain '6' and resid 256 through 261 Processing helix chain '6' and resid 284 through 298 removed outlier: 3.945A pdb=" N VAL 6 291 " --> pdb=" O LEU 6 287 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU 6 292 " --> pdb=" O ARG 6 288 " (cutoff:3.500A) Processing helix chain '6' and resid 331 through 340 removed outlier: 4.107A pdb=" N GLU 6 340 " --> pdb=" O GLU 6 336 " (cutoff:3.500A) Processing helix chain '6' and resid 358 through 366 removed outlier: 4.925A pdb=" N ILE 6 363 " --> pdb=" O ARG 6 360 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU 6 364 " --> pdb=" O GLU 6 361 " (cutoff:3.500A) Processing helix chain '6' and resid 382 through 388 Processing helix chain '6' and resid 397 through 406 removed outlier: 3.850A pdb=" N GLN 6 401 " --> pdb=" O THR 6 397 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG 6 406 " --> pdb=" O LEU 6 402 " (cutoff:3.500A) Processing helix chain '6' and resid 418 through 423 Processing helix chain '6' and resid 447 through 456 Processing helix chain '8' and resid 103 through 109 Processing helix chain '8' and resid 150 through 157 removed outlier: 3.678A pdb=" N LYS 8 154 " --> pdb=" O ASN 8 150 " (cutoff:3.500A) Processing helix chain '9' and resid 107 through 115 removed outlier: 3.812A pdb=" N PHE 9 112 " --> pdb=" O PHE 9 108 " (cutoff:3.500A) Processing helix chain '9' and resid 117 through 121 Processing helix chain '9' and resid 143 through 148 Processing helix chain '9' and resid 150 through 165 removed outlier: 3.740A pdb=" N GLU 9 154 " --> pdb=" O TYR 9 150 " (cutoff:3.500A) Processing helix chain '0' and resid 108 through 113 Processing helix chain '0' and resid 124 through 132 removed outlier: 3.518A pdb=" N LEU 0 128 " --> pdb=" O GLY 0 124 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER 0 130 " --> pdb=" O GLN 0 126 " (cutoff:3.500A) Processing helix chain '0' and resid 133 through 138 Processing helix chain '0' and resid 139 through 142 Processing helix chain '0' and resid 146 through 166 removed outlier: 3.600A pdb=" N ALA 0 155 " --> pdb=" O TYR 0 151 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS 0 162 " --> pdb=" O ILE 0 158 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE 0 164 " --> pdb=" O VAL 0 160 " (cutoff:3.500A) Processing helix chain '0' and resid 171 through 175 removed outlier: 3.512A pdb=" N PHE 0 175 " --> pdb=" O PRO 0 172 " (cutoff:3.500A) Processing helix chain '0' and resid 176 through 181 removed outlier: 3.582A pdb=" N MET 0 181 " --> pdb=" O PRO 0 177 " (cutoff:3.500A) Processing helix chain '0' and resid 185 through 191 Processing helix chain '0' and resid 193 through 197 removed outlier: 3.886A pdb=" N SER 0 196 " --> pdb=" O ASP 0 193 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET 0 197 " --> pdb=" O TYR 0 194 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 193 through 197' Processing sheet with id=AA1, first strand: chain 'D' and resid 63 through 66 removed outlier: 4.244A pdb=" N LYS D 65 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU D 80 " --> pdb=" O LYS D 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 123 through 131 removed outlier: 7.558A pdb=" N PHE F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL F 119 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU F 125 " --> pdb=" O TRP F 117 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR F 111 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLN F 112 " --> pdb=" O SER 9 98 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR 9 100 " --> pdb=" O GLN F 112 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU F 114 " --> pdb=" O THR 9 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 12 through 14 removed outlier: 3.888A pdb=" N ARG H 27 " --> pdb=" O ILE H 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 330 through 331 Processing sheet with id=AA5, first strand: chain 'J' and resid 51 through 56 removed outlier: 4.537A pdb=" N GLN J 55 " --> pdb=" O VAL J 69 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL J 69 " --> pdb=" O GLN J 55 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL J 85 " --> pdb=" O LEU J 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 97 through 98 removed outlier: 3.706A pdb=" N ILE J 98 " --> pdb=" O SER J 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'K' and resid 56 through 57 Processing sheet with id=AA8, first strand: chain 'M' and resid 97 through 98 removed outlier: 4.408A pdb=" N ARG M 102 " --> pdb=" O MET M 126 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET M 126 " --> pdb=" O ARG M 102 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 96 through 97 removed outlier: 6.902A pdb=" N LEU N 96 " --> pdb=" O TRP N 152 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU N 70 " --> pdb=" O VAL N 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '1' and resid 78 through 80 removed outlier: 3.501A pdb=" N TYR 1 89 " --> pdb=" O TYR 1 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1' and resid 118 through 120 removed outlier: 3.622A pdb=" N THR 1 188 " --> pdb=" O LEU 1 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '1' and resid 153 through 161 removed outlier: 6.431A pdb=" N GLU 1 177 " --> pdb=" O PRO 1 154 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ILE 1 156 " --> pdb=" O ASP 1 175 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP 1 175 " --> pdb=" O ILE 1 156 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU 1 158 " --> pdb=" O GLU 1 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '4' and resid 153 through 155 removed outlier: 4.946A pdb=" N VAL 4 153 " --> pdb=" O LYS 4 223 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS 4 223 " --> pdb=" O VAL 4 153 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL 4 164 " --> pdb=" O ILE 4 194 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '4' and resid 171 through 173 removed outlier: 3.945A pdb=" N ASP 4 181 " --> pdb=" O ALA 4 172 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '5' and resid 126 through 127 removed outlier: 3.999A pdb=" N SER 5 126 " --> pdb=" O ILE 5 234 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL 5 78 " --> pdb=" O VAL 5 96 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL 5 96 " --> pdb=" O VAL 5 78 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE 5 80 " --> pdb=" O ARG 5 94 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG 5 94 " --> pdb=" O PHE 5 80 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE 5 82 " --> pdb=" O VAL 5 92 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL 5 96 " --> pdb=" O LEU 5 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN 5 206 " --> pdb=" O GLY 5 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '5' and resid 126 through 127 removed outlier: 3.999A pdb=" N SER 5 126 " --> pdb=" O ILE 5 234 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '5' and resid 130 through 132 removed outlier: 3.669A pdb=" N ARG 5 130 " --> pdb=" O GLN 5 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '6' and resid 147 through 150 removed outlier: 6.426A pdb=" N VAL 6 118 " --> pdb=" O ASP 6 149 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N MET 6 198 " --> pdb=" O ARG 6 117 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS 6 119 " --> pdb=" O MET 6 198 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '6' and resid 307 through 308 removed outlier: 6.056A pdb=" N VAL 6 307 " --> pdb=" O VAL 6 393 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '7' and resid 52 through 54 removed outlier: 3.816A pdb=" N SER 7 81 " --> pdb=" O GLN 7 71 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG 7 73 " --> pdb=" O VAL 7 79 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL 7 79 " --> pdb=" O ARG 7 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '7' and resid 137 through 142 removed outlier: 3.858A pdb=" N GLU 7 152 " --> pdb=" O ALA 7 139 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL 7 141 " --> pdb=" O GLN 7 150 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLN 7 150 " --> pdb=" O VAL 7 141 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET 7 173 " --> pdb=" O ILE 7 356 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY 7 352 " --> pdb=" O VAL 7 177 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '7' and resid 196 through 198 Processing sheet with id=AC5, first strand: chain '7' and resid 205 through 206 removed outlier: 3.537A pdb=" N ALA 7 206 " --> pdb=" O ILE 7 295 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '7' and resid 269 through 272 removed outlier: 4.107A pdb=" N VAL 7 269 " --> pdb=" O SER 7 317 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU 7 315 " --> pdb=" O ARG 7 271 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA 7 336 " --> pdb=" O ASP 7 312 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '8' and resid 80 through 84 removed outlier: 6.551A pdb=" N VAL 8 182 " --> pdb=" O VAL 8 140 " (cutoff:3.500A) 1622 hydrogen bonds defined for protein. 4704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.32 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.38: 14916 1.38 - 1.57: 26508 1.57 - 1.76: 7 1.76 - 1.95: 324 1.95 - 2.14: 12 Bond restraints: 41767 Sorted by residual: bond pdb=" C6 SQD F 803 " pdb=" S SQD F 803 " ideal model delta sigma weight residual 1.840 1.660 0.180 2.00e-02 2.50e+03 8.09e+01 bond pdb=" C6 SQD F 802 " pdb=" S SQD F 802 " ideal model delta sigma weight residual 1.840 1.662 0.178 2.00e-02 2.50e+03 7.96e+01 bond pdb=" C7 LHG D 601 " pdb=" O7 LHG D 601 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" C23 LHG D 601 " pdb=" O8 LHG D 601 " ideal model delta sigma weight residual 1.328 1.450 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" O8 SQD F 802 " pdb=" S SQD F 802 " ideal model delta sigma weight residual 1.514 1.634 -0.120 2.00e-02 2.50e+03 3.62e+01 ... (remaining 41762 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 56611 4.58 - 9.16: 220 9.16 - 13.74: 20 13.74 - 18.32: 26 18.32 - 22.90: 1 Bond angle restraints: 56878 Sorted by residual: angle pdb=" N LYS N 157 " pdb=" CA LYS N 157 " pdb=" C LYS N 157 " ideal model delta sigma weight residual 108.34 131.24 -22.90 1.31e+00 5.83e-01 3.06e+02 angle pdb=" C GLU C 49 " pdb=" N PRO C 50 " pdb=" CA PRO C 50 " ideal model delta sigma weight residual 119.90 102.80 17.10 1.02e+00 9.61e-01 2.81e+02 angle pdb=" C GLN 6 274 " pdb=" N PRO 6 275 " pdb=" CA PRO 6 275 " ideal model delta sigma weight residual 119.84 135.69 -15.85 1.25e+00 6.40e-01 1.61e+02 angle pdb="FE2 SF4 8 201 " pdb=" S1 SF4 8 201 " pdb="FE4 SF4 8 201 " ideal model delta sigma weight residual 73.70 90.89 -17.19 1.50e+00 4.44e-01 1.31e+02 angle pdb="FE2 SF4 8 201 " pdb=" S3 SF4 8 201 " pdb="FE4 SF4 8 201 " ideal model delta sigma weight residual 73.70 90.87 -17.17 1.50e+00 4.44e-01 1.31e+02 ... (remaining 56873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.00: 22698 23.00 - 46.01: 1490 46.01 - 69.01: 124 69.01 - 92.02: 32 92.02 - 115.02: 2 Dihedral angle restraints: 24346 sinusoidal: 8770 harmonic: 15576 Sorted by residual: dihedral pdb=" CA ASN 5 86 " pdb=" C ASN 5 86 " pdb=" N PRO 5 87 " pdb=" CA PRO 5 87 " ideal model delta harmonic sigma weight residual 180.00 134.90 45.10 0 5.00e+00 4.00e-02 8.14e+01 dihedral pdb=" CA PRO N 125 " pdb=" C PRO N 125 " pdb=" N VAL N 126 " pdb=" CA VAL N 126 " ideal model delta harmonic sigma weight residual 180.00 -135.13 -44.87 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA TRP 6 178 " pdb=" C TRP 6 178 " pdb=" N PRO 6 179 " pdb=" CA PRO 6 179 " ideal model delta harmonic sigma weight residual -180.00 -136.93 -43.07 0 5.00e+00 4.00e-02 7.42e+01 ... (remaining 24343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 6468 0.170 - 0.341: 23 0.341 - 0.511: 0 0.511 - 0.681: 2 0.681 - 0.852: 4 Chirality restraints: 6497 Sorted by residual: chirality pdb="FE4 SF4 8 201 " pdb=" S1 SF4 8 201 " pdb=" S2 SF4 8 201 " pdb=" S3 SF4 8 201 " both_signs ideal model delta sigma weight residual False 10.55 9.70 0.85 2.00e-01 2.50e+01 1.81e+01 chirality pdb="FE1 SF4 8 201 " pdb=" S2 SF4 8 201 " pdb=" S3 SF4 8 201 " pdb=" S4 SF4 8 201 " both_signs ideal model delta sigma weight residual False -10.55 -9.71 -0.84 2.00e-01 2.50e+01 1.78e+01 chirality pdb="FE2 SF4 8 201 " pdb=" S1 SF4 8 201 " pdb=" S3 SF4 8 201 " pdb=" S4 SF4 8 201 " both_signs ideal model delta sigma weight residual False 10.55 9.72 0.83 2.00e-01 2.50e+01 1.73e+01 ... (remaining 6494 not shown) Planarity restraints: 7182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN 6 274 " 0.034 2.00e-02 2.50e+03 6.75e-02 4.55e+01 pdb=" C GLN 6 274 " -0.117 2.00e-02 2.50e+03 pdb=" O GLN 6 274 " 0.044 2.00e-02 2.50e+03 pdb=" N PRO 6 275 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 122 " 0.031 2.00e-02 2.50e+03 5.97e-02 3.56e+01 pdb=" C THR I 122 " -0.103 2.00e-02 2.50e+03 pdb=" O THR I 122 " 0.038 2.00e-02 2.50e+03 pdb=" N GLU I 123 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 480 " -0.019 2.00e-02 2.50e+03 3.81e-02 1.45e+01 pdb=" C ASP D 480 " 0.066 2.00e-02 2.50e+03 pdb=" O ASP D 480 " -0.024 2.00e-02 2.50e+03 pdb=" N PHE D 481 " -0.022 2.00e-02 2.50e+03 ... (remaining 7179 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 145 2.43 - 3.05: 28092 3.05 - 3.67: 60895 3.67 - 4.28: 86537 4.28 - 4.90: 139702 Nonbonded interactions: 315371 Sorted by model distance: nonbonded pdb=" O LEU 8 123 " pdb=" O LEU 8 124 " model vdw 1.818 3.040 nonbonded pdb=" O GLU C 49 " pdb=" C PRO C 50 " model vdw 2.080 3.270 nonbonded pdb=" C LEU 8 123 " pdb=" O LEU 8 124 " model vdw 2.146 3.270 nonbonded pdb=" CA GLY C 47 " pdb=" ND2 ASN H 14 " model vdw 2.174 3.520 nonbonded pdb=" OG SER J 68 " pdb=" OH TYR J 123 " model vdw 2.210 3.040 ... (remaining 315366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.760 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: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 37.600 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 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 : 0.010 1.205 41771 Z= 0.342 Angle : 0.982 56.846 56889 Z= 0.497 Chirality : 0.052 0.852 6497 Planarity : 0.005 0.092 7182 Dihedral : 14.842 115.021 14371 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.45 % Allowed : 14.98 % Favored : 84.56 % Rotamer: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 2.38 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.09), residues: 5280 helix: -2.25 (0.09), residues: 2399 sheet: -3.25 (0.25), residues: 335 loop : -4.52 (0.10), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 25 TYR 0.026 0.001 TYR F 516 PHE 0.030 0.001 PHE 9 105 TRP 0.040 0.001 TRP 8 164 HIS 0.007 0.001 HIS F 407 Details of bonding type rmsd covalent geometry : bond 0.00488 (41767) covalent geometry : angle 0.87726 (56878) SS BOND : bond 0.00842 ( 1) SS BOND : angle 1.20400 ( 2) hydrogen bonds : bond 0.16557 ( 1619) hydrogen bonds : angle 6.97960 ( 4704) metal coordination : bond 1.01018 ( 3) metal coordination : angle 35.09358 ( 9) *********************** 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 738 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 736 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8794 (t60) cc_final: 0.8439 (t60) REVERT: A 166 GLN cc_start: 0.8472 (pp30) cc_final: 0.8084 (pp30) REVERT: A 302 MET cc_start: 0.2849 (tpt) cc_final: 0.2461 (tmm) REVERT: A 325 TRP cc_start: 0.6831 (m100) cc_final: 0.6357 (m100) REVERT: B 47 MET cc_start: 0.8016 (tmm) cc_final: 0.7461 (mtp) REVERT: B 124 MET cc_start: 0.7728 (mmm) cc_final: 0.7421 (ttm) REVERT: B 320 MET cc_start: 0.8901 (tpp) cc_final: 0.8237 (tpp) REVERT: B 323 MET cc_start: 0.8215 (ttp) cc_final: 0.7890 (ttp) REVERT: B 448 LEU cc_start: 0.9044 (mm) cc_final: 0.8745 (mm) REVERT: D 118 MET cc_start: 0.8366 (tpp) cc_final: 0.7991 (tpp) REVERT: D 214 TYR cc_start: 0.8425 (t80) cc_final: 0.7626 (t80) REVERT: D 276 PHE cc_start: 0.8277 (t80) cc_final: 0.8015 (t80) REVERT: D 371 MET cc_start: 0.8555 (ptp) cc_final: 0.8321 (ptp) REVERT: D 488 ASP cc_start: 0.8382 (m-30) cc_final: 0.8152 (m-30) REVERT: F 71 ILE cc_start: 0.9102 (mt) cc_final: 0.8886 (tt) REVERT: F 198 MET cc_start: 0.8797 (tmm) cc_final: 0.8569 (tmm) REVERT: F 371 TYR cc_start: 0.8435 (m-80) cc_final: 0.8212 (m-80) REVERT: F 373 MET cc_start: 0.8799 (tpp) cc_final: 0.8454 (tpp) REVERT: G 105 ILE cc_start: 0.9262 (mm) cc_final: 0.9004 (mt) REVERT: G 112 MET cc_start: 0.8233 (tpp) cc_final: 0.7971 (tpp) REVERT: H 378 MET cc_start: 0.6022 (tpt) cc_final: 0.5201 (mmm) REVERT: I 17 ARG cc_start: 0.4597 (mtm-85) cc_final: 0.4249 (ptp-170) REVERT: I 84 ARG cc_start: 0.5241 (tpp-160) cc_final: 0.3603 (ttt180) REVERT: I 107 CYS cc_start: 0.7244 (t) cc_final: 0.6795 (t) REVERT: I 109 ASN cc_start: 0.7624 (m-40) cc_final: 0.7398 (m-40) REVERT: I 118 CYS cc_start: 0.6891 (t) cc_final: 0.6487 (p) REVERT: I 121 MET cc_start: 0.2649 (ptp) cc_final: 0.1773 (pmm) REVERT: K 48 TRP cc_start: 0.6842 (t60) cc_final: 0.6526 (t60) REVERT: K 54 LEU cc_start: 0.7876 (pt) cc_final: 0.7241 (tt) REVERT: K 93 ASP cc_start: 0.6499 (p0) cc_final: 0.5752 (p0) REVERT: K 121 TYR cc_start: 0.6240 (m-80) cc_final: 0.5798 (m-80) REVERT: K 134 MET cc_start: 0.5842 (ppp) cc_final: 0.5111 (ppp) REVERT: K 144 ARG cc_start: 0.3730 (mpt180) cc_final: 0.3203 (mmt180) REVERT: K 205 ARG cc_start: 0.1397 (tpm170) cc_final: 0.0950 (tpm170) REVERT: 1 108 LYS cc_start: 0.7798 (mptt) cc_final: 0.7528 (mptt) REVERT: 2 100 TYR cc_start: 0.8513 (t80) cc_final: 0.8223 (t80) REVERT: 2 213 GLU cc_start: 0.8336 (tp30) cc_final: 0.7809 (tm-30) REVERT: 3 202 THR cc_start: 0.9063 (p) cc_final: 0.8857 (p) REVERT: 3 226 MET cc_start: 0.8211 (ppp) cc_final: 0.7589 (ptm) REVERT: 4 249 GLU cc_start: 0.8545 (pp20) cc_final: 0.7845 (pp20) REVERT: 5 182 THR cc_start: 0.8548 (m) cc_final: 0.8336 (p) REVERT: 5 241 PRO cc_start: 0.5398 (Cg_endo) cc_final: 0.5034 (Cg_exo) REVERT: 6 214 PHE cc_start: 0.8934 (t80) cc_final: 0.8621 (t80) REVERT: 6 220 GLU cc_start: 0.7859 (tt0) cc_final: 0.7304 (tp30) REVERT: 6 312 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6284 (tp30) REVERT: 7 149 VAL cc_start: 0.8466 (m) cc_final: 0.8151 (m) REVERT: 7 301 LEU cc_start: 0.8554 (mt) cc_final: 0.8306 (mp) REVERT: 7 308 MET cc_start: 0.4498 (mtt) cc_final: 0.4235 (mtt) REVERT: 8 113 ILE cc_start: 0.8727 (pt) cc_final: 0.8485 (pt) REVERT: 8 123 LEU cc_start: 0.9008 (mm) cc_final: 0.8803 (mt) REVERT: 0 69 ASP cc_start: 0.7701 (t0) cc_final: 0.7470 (t0) REVERT: 0 158 ILE cc_start: 0.9335 (tp) cc_final: 0.8950 (tp) REVERT: 0 198 ASP cc_start: 0.5322 (p0) cc_final: 0.5060 (p0) outliers start: 2 outliers final: 0 residues processed: 736 average time/residue: 0.2387 time to fit residues: 290.1794 Evaluate side-chains 503 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 0.6980 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 0.9990 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 0.0870 chunk 366 optimal weight: 5.9990 chunk 223 optimal weight: 4.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 262 ASN A 294 ASN A 358 GLN B 222 GLN B 296 HIS ** B 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 GLN B 362 ASN D 77 HIS D 125 GLN F 104 GLN G 71 ASN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN H 367 GLN I 32 HIS I 139 GLN J 13 HIS K 91 GLN M 145 ASN ** M 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 86 ASN 5 164 GLN 6 129 ASN 6 381 GLN ** 7 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.136709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.108629 restraints weight = 98926.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.107815 restraints weight = 71148.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.108375 restraints weight = 52275.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.108480 restraints weight = 45869.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.108736 restraints weight = 40789.072| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 41771 Z= 0.144 Angle : 0.856 59.070 56889 Z= 0.382 Chirality : 0.046 0.256 6497 Planarity : 0.006 0.088 7182 Dihedral : 7.788 99.669 5901 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.34 % Favored : 85.53 % Rotamer: Outliers : 1.67 % Allowed : 13.44 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.59 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.73 (0.11), residues: 5280 helix: -1.01 (0.10), residues: 2421 sheet: -2.73 (0.26), residues: 346 loop : -4.09 (0.11), residues: 2513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 6 358 TYR 0.028 0.002 TYR F 516 PHE 0.036 0.002 PHE I 85 TRP 0.031 0.001 TRP J 105 HIS 0.007 0.001 HIS 7 99 Details of bonding type rmsd covalent geometry : bond 0.00309 (41767) covalent geometry : angle 0.74434 (56878) SS BOND : bond 0.00151 ( 1) SS BOND : angle 0.76257 ( 2) hydrogen bonds : bond 0.04483 ( 1619) hydrogen bonds : angle 5.09245 ( 4704) metal coordination : bond 0.02119 ( 3) metal coordination : angle 33.54648 ( 9) *********************** 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 651 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 584 time to evaluate : 1.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 VAL cc_start: 0.7293 (t) cc_final: 0.7032 (t) REVERT: A 133 TRP cc_start: 0.8524 (t60) cc_final: 0.8296 (t60) REVERT: B 320 MET cc_start: 0.8397 (tpp) cc_final: 0.7896 (tpp) REVERT: B 448 LEU cc_start: 0.9022 (mm) cc_final: 0.8682 (mm) REVERT: D 118 MET cc_start: 0.8282 (tpp) cc_final: 0.7705 (tpp) REVERT: D 214 TYR cc_start: 0.8613 (t80) cc_final: 0.7922 (t80) REVERT: F 373 MET cc_start: 0.8678 (tpp) cc_final: 0.8356 (tpp) REVERT: F 768 PHE cc_start: 0.8456 (t80) cc_final: 0.8077 (t80) REVERT: G 43 LEU cc_start: 0.8394 (mp) cc_final: 0.8183 (mt) REVERT: G 105 ILE cc_start: 0.9240 (mm) cc_final: 0.8894 (mt) REVERT: G 112 MET cc_start: 0.8048 (tpp) cc_final: 0.7767 (tpp) REVERT: H 76 MET cc_start: 0.5987 (tpp) cc_final: 0.5741 (tpp) REVERT: H 142 TYR cc_start: 0.6451 (m-10) cc_final: 0.6116 (m-10) REVERT: I 17 ARG cc_start: 0.5483 (mtm-85) cc_final: 0.4869 (ptp-170) REVERT: I 84 ARG cc_start: 0.5672 (tpp-160) cc_final: 0.4114 (ttt180) REVERT: I 118 CYS cc_start: 0.6794 (t) cc_final: 0.6437 (p) REVERT: I 126 GLU cc_start: 0.5210 (mm-30) cc_final: 0.4417 (pp20) REVERT: J 105 TRP cc_start: 0.5087 (p90) cc_final: 0.4153 (p90) REVERT: K 93 ASP cc_start: 0.7899 (p0) cc_final: 0.7304 (p0) REVERT: K 134 MET cc_start: 0.6214 (ppp) cc_final: 0.5619 (ppp) REVERT: K 144 ARG cc_start: 0.4107 (mpt180) cc_final: 0.3576 (mmt180) REVERT: K 205 ARG cc_start: 0.1842 (tpm170) cc_final: 0.0934 (tpt170) REVERT: N 83 ARG cc_start: 0.6654 (tmm-80) cc_final: 0.6417 (tmm160) REVERT: N 199 ARG cc_start: 0.6534 (ttp80) cc_final: 0.4931 (ptt90) REVERT: 2 213 GLU cc_start: 0.8122 (tp30) cc_final: 0.7841 (tm-30) REVERT: 3 226 MET cc_start: 0.7681 (ppp) cc_final: 0.7340 (ptm) REVERT: 4 249 GLU cc_start: 0.8195 (pp20) cc_final: 0.7871 (pp20) REVERT: 5 241 PRO cc_start: 0.5083 (Cg_endo) cc_final: 0.4864 (Cg_exo) REVERT: 7 149 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8108 (m) REVERT: 7 285 TYR cc_start: 0.6964 (m-80) cc_final: 0.6723 (m-80) REVERT: 7 292 PHE cc_start: 0.7503 (t80) cc_final: 0.7267 (t80) REVERT: 7 308 MET cc_start: 0.5383 (mtt) cc_final: 0.5153 (mtt) REVERT: 8 113 ILE cc_start: 0.8602 (pt) cc_final: 0.8354 (pt) REVERT: 0 158 ILE cc_start: 0.9247 (tp) cc_final: 0.9014 (tp) outliers start: 67 outliers final: 36 residues processed: 627 average time/residue: 0.2271 time to fit residues: 239.2020 Evaluate side-chains 534 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 497 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 86 ASN Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 171 VAL Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 265 LEU Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 9 residue 106 TYR Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 114 VAL Chi-restraints excluded: chain 0 residue 197 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 276 optimal weight: 40.0000 chunk 64 optimal weight: 0.0470 chunk 92 optimal weight: 3.9990 chunk 495 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 170 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 313 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN B 317 GLN D 29 ASN D 125 GLN D 287 GLN E 39 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN H 93 GLN ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 HIS ** M 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 HIS N 143 HIS 1 141 ASN 5 206 GLN ** 7 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.131844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.103050 restraints weight = 99682.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.102370 restraints weight = 66181.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.102862 restraints weight = 52828.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.103071 restraints weight = 47521.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.103301 restraints weight = 39668.624| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 41771 Z= 0.229 Angle : 0.890 53.399 56889 Z= 0.407 Chirality : 0.048 0.209 6497 Planarity : 0.006 0.102 7182 Dihedral : 7.967 112.292 5901 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.17 % Allowed : 15.64 % Favored : 84.19 % Rotamer: Outliers : 3.02 % Allowed : 16.68 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.98 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.11), residues: 5280 helix: -0.82 (0.10), residues: 2415 sheet: -2.86 (0.24), residues: 384 loop : -3.96 (0.11), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 5 224 TYR 0.026 0.002 TYR 9 150 PHE 0.033 0.002 PHE 9 105 TRP 0.034 0.002 TRP H 217 HIS 0.012 0.002 HIS F 407 Details of bonding type rmsd covalent geometry : bond 0.00528 (41767) covalent geometry : angle 0.79745 (56878) SS BOND : bond 0.00184 ( 1) SS BOND : angle 0.69184 ( 2) hydrogen bonds : bond 0.04914 ( 1619) hydrogen bonds : angle 5.15833 ( 4704) metal coordination : bond 0.02338 ( 3) metal coordination : angle 31.36377 ( 9) *********************** 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 627 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 506 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8631 (t60) cc_final: 0.8362 (t60) REVERT: A 302 MET cc_start: 0.2574 (tmm) cc_final: 0.2148 (ppp) REVERT: B 265 VAL cc_start: 0.9018 (t) cc_final: 0.8786 (t) REVERT: B 320 MET cc_start: 0.8650 (tpp) cc_final: 0.8421 (tpp) REVERT: B 448 LEU cc_start: 0.8868 (mm) cc_final: 0.8560 (mm) REVERT: D 118 MET cc_start: 0.8317 (tpp) cc_final: 0.7890 (tpp) REVERT: D 214 TYR cc_start: 0.8750 (t80) cc_final: 0.8101 (t80) REVERT: D 271 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7329 (p-80) REVERT: F 174 ASN cc_start: 0.8897 (t0) cc_final: 0.8653 (t0) REVERT: F 373 MET cc_start: 0.8955 (tpp) cc_final: 0.8458 (tpp) REVERT: F 480 THR cc_start: 0.8435 (m) cc_final: 0.8181 (m) REVERT: G 21 LEU cc_start: 0.8256 (tp) cc_final: 0.7981 (mt) REVERT: G 105 ILE cc_start: 0.9249 (mm) cc_final: 0.8861 (mt) REVERT: G 112 MET cc_start: 0.8118 (tpp) cc_final: 0.7865 (tpp) REVERT: H 25 VAL cc_start: 0.6810 (OUTLIER) cc_final: 0.6592 (p) REVERT: H 142 TYR cc_start: 0.6210 (m-10) cc_final: 0.5914 (m-10) REVERT: I 84 ARG cc_start: 0.5588 (tpp-160) cc_final: 0.4138 (ttt180) REVERT: I 126 GLU cc_start: 0.5164 (mm-30) cc_final: 0.4406 (pp20) REVERT: K 28 LEU cc_start: 0.5273 (OUTLIER) cc_final: 0.4659 (mt) REVERT: K 54 LEU cc_start: 0.7875 (pt) cc_final: 0.7375 (tt) REVERT: K 93 ASP cc_start: 0.8071 (p0) cc_final: 0.7255 (p0) REVERT: K 134 MET cc_start: 0.6341 (ppp) cc_final: 0.6081 (ppp) REVERT: K 144 ARG cc_start: 0.3936 (mpt180) cc_final: 0.3422 (mmt180) REVERT: K 205 ARG cc_start: 0.1750 (tpm170) cc_final: 0.0969 (tpt170) REVERT: M 188 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7083 (ttm) REVERT: N 199 ARG cc_start: 0.6133 (ttp80) cc_final: 0.5053 (tmm-80) REVERT: 2 132 MET cc_start: 0.8397 (mmm) cc_final: 0.8067 (mtt) REVERT: 2 213 GLU cc_start: 0.8143 (tp30) cc_final: 0.7819 (tm-30) REVERT: 4 249 GLU cc_start: 0.8382 (pp20) cc_final: 0.7943 (pp20) REVERT: 5 112 ARG cc_start: 0.8686 (tmm-80) cc_final: 0.8385 (tmm-80) REVERT: 5 182 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8422 (p) REVERT: 7 292 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7625 (t80) REVERT: 8 123 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8416 (mm) REVERT: 0 137 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8479 (p) REVERT: 0 158 ILE cc_start: 0.9417 (tp) cc_final: 0.9125 (tp) REVERT: 0 200 TRP cc_start: 0.5773 (p90) cc_final: 0.4131 (t-100) outliers start: 121 outliers final: 76 residues processed: 591 average time/residue: 0.2320 time to fit residues: 229.5570 Evaluate side-chains 554 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 470 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 271 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 307 TYR Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 742 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 377 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 128 CYS Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 203 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 183 VAL Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 2 residue 140 TYR Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 126 SER Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 182 THR Chi-restraints excluded: chain 6 residue 129 ASN Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 171 VAL Chi-restraints excluded: chain 6 residue 200 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 228 LEU Chi-restraints excluded: chain 7 residue 265 LEU Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 7 residue 333 THR Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 129 ILE Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 145 VAL Chi-restraints excluded: chain 0 residue 197 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 412 optimal weight: 1.9990 chunk 361 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 451 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 71 optimal weight: 0.9980 chunk 188 optimal weight: 0.0870 chunk 407 optimal weight: 0.9990 chunk 501 optimal weight: 6.9990 chunk 231 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 GLN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 ASN J 50 ASN N 76 HIS ** 7 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 297 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.136296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.107468 restraints weight = 97990.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.107396 restraints weight = 62793.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.107631 restraints weight = 48339.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.107906 restraints weight = 43265.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.108136 restraints weight = 38807.268| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41771 Z= 0.131 Angle : 0.794 46.713 56889 Z= 0.355 Chirality : 0.044 0.292 6497 Planarity : 0.005 0.093 7182 Dihedral : 7.470 97.367 5901 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.45 % Favored : 86.44 % Rotamer: Outliers : 2.67 % Allowed : 18.73 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.59 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.11), residues: 5280 helix: -0.43 (0.11), residues: 2403 sheet: -2.31 (0.27), residues: 350 loop : -3.76 (0.11), residues: 2527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 7 280 TYR 0.021 0.001 TYR F 487 PHE 0.023 0.001 PHE H 121 TRP 0.033 0.001 TRP H 217 HIS 0.006 0.001 HIS F 407 Details of bonding type rmsd covalent geometry : bond 0.00271 (41767) covalent geometry : angle 0.69643 (56878) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.26918 ( 2) hydrogen bonds : bond 0.03890 ( 1619) hydrogen bonds : angle 4.75898 ( 4704) metal coordination : bond 0.01363 ( 3) metal coordination : angle 30.40149 ( 9) *********************** 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 666 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 559 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8567 (t60) cc_final: 0.8361 (t60) REVERT: A 138 SER cc_start: 0.8829 (t) cc_final: 0.8535 (m) REVERT: A 302 MET cc_start: 0.2716 (tmm) cc_final: 0.2283 (ppp) REVERT: B 253 THR cc_start: 0.9114 (m) cc_final: 0.8708 (p) REVERT: B 265 VAL cc_start: 0.8975 (t) cc_final: 0.8768 (t) REVERT: B 320 MET cc_start: 0.8644 (tpp) cc_final: 0.8363 (tpp) REVERT: B 448 LEU cc_start: 0.8985 (mm) cc_final: 0.8651 (mm) REVERT: F 123 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.7080 (p90) REVERT: F 373 MET cc_start: 0.8711 (tpp) cc_final: 0.8299 (tpp) REVERT: F 768 PHE cc_start: 0.8425 (t80) cc_final: 0.8018 (t80) REVERT: G 21 LEU cc_start: 0.8206 (tp) cc_final: 0.7937 (mt) REVERT: G 105 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8791 (mt) REVERT: G 112 MET cc_start: 0.8069 (tpp) cc_final: 0.7762 (tpp) REVERT: H 15 MET cc_start: 0.6759 (tpp) cc_final: 0.6527 (mmp) REVERT: H 132 PHE cc_start: 0.8266 (m-80) cc_final: 0.7648 (m-10) REVERT: H 142 TYR cc_start: 0.6262 (m-10) cc_final: 0.5964 (m-10) REVERT: I 84 ARG cc_start: 0.5500 (tpp-160) cc_final: 0.4136 (ttt180) REVERT: I 118 CYS cc_start: 0.6774 (t) cc_final: 0.6319 (p) REVERT: J 33 LYS cc_start: 0.7625 (tppt) cc_final: 0.7424 (mmtm) REVERT: J 77 TYR cc_start: 0.2806 (t80) cc_final: 0.2532 (m-80) REVERT: J 115 SER cc_start: 0.7097 (t) cc_final: 0.6695 (p) REVERT: K 28 LEU cc_start: 0.5351 (OUTLIER) cc_final: 0.4727 (mt) REVERT: K 54 LEU cc_start: 0.8113 (pt) cc_final: 0.7729 (tt) REVERT: K 93 ASP cc_start: 0.7944 (p0) cc_final: 0.7128 (p0) REVERT: K 144 ARG cc_start: 0.3902 (mpt180) cc_final: 0.3573 (mmt180) REVERT: K 205 ARG cc_start: 0.1659 (tpm170) cc_final: 0.0912 (tpt170) REVERT: M 188 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6980 (ttm) REVERT: N 199 ARG cc_start: 0.5840 (ttp80) cc_final: 0.5015 (tmm-80) REVERT: 2 213 GLU cc_start: 0.8075 (tp30) cc_final: 0.7730 (tm-30) REVERT: 4 249 GLU cc_start: 0.8192 (pp20) cc_final: 0.7789 (pp20) REVERT: 6 354 MET cc_start: 0.8082 (tpp) cc_final: 0.6991 (tpp) REVERT: 6 385 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.7940 (tt) REVERT: 8 113 ILE cc_start: 0.8423 (pt) cc_final: 0.8201 (pt) REVERT: 0 69 ASP cc_start: 0.6783 (t0) cc_final: 0.6544 (t0) REVERT: 0 158 ILE cc_start: 0.9232 (tp) cc_final: 0.8964 (tp) REVERT: 0 200 TRP cc_start: 0.5664 (p90) cc_final: 0.4096 (t-100) outliers start: 107 outliers final: 57 residues processed: 628 average time/residue: 0.2239 time to fit residues: 237.3584 Evaluate side-chains 556 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 494 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain H residue 369 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 104 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 188 MET Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 4 residue 216 MET Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 202 VAL Chi-restraints excluded: chain 6 residue 148 VAL Chi-restraints excluded: chain 6 residue 171 VAL Chi-restraints excluded: chain 6 residue 200 LEU Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 265 LEU Chi-restraints excluded: chain 8 residue 135 CYS Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 106 TYR Chi-restraints excluded: chain 0 residue 197 MET Chi-restraints excluded: chain 0 residue 214 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 268 optimal weight: 10.0000 chunk 401 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 527 optimal weight: 3.9990 chunk 198 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 311 ASN D 496 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 465 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** H 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 196 ASN N 76 HIS ** 7 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 181 ASN ** 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 = 0.3962 r_free = 0.3962 target = 0.130552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.101023 restraints weight = 99911.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100651 restraints weight = 63483.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100665 restraints weight = 51648.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.100926 restraints weight = 45588.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101132 restraints weight = 40603.529| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 41771 Z= 0.254 Angle : 0.905 47.635 56889 Z= 0.417 Chirality : 0.049 0.239 6497 Planarity : 0.006 0.091 7182 Dihedral : 7.888 109.668 5901 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 16.33 % Favored : 83.50 % Rotamer: Outliers : 3.72 % Allowed : 19.85 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.98 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.11), residues: 5280 helix: -0.54 (0.10), residues: 2413 sheet: -2.71 (0.25), residues: 381 loop : -3.78 (0.11), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 83 TYR 0.029 0.002 TYR 9 150 PHE 0.036 0.002 PHE 9 105 TRP 0.033 0.002 TRP H 217 HIS 0.015 0.002 HIS F 407 Details of bonding type rmsd covalent geometry : bond 0.00585 (41767) covalent geometry : angle 0.82216 (56878) SS BOND : bond 0.00153 ( 1) SS BOND : angle 0.45464 ( 2) hydrogen bonds : bond 0.04905 ( 1619) hydrogen bonds : angle 5.10304 ( 4704) metal coordination : bond 0.03015 ( 3) metal coordination : angle 30.16598 ( 9) *********************** 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 635 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 486 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8711 (t60) cc_final: 0.8405 (t60) REVERT: B 320 MET cc_start: 0.8814 (tpp) cc_final: 0.8580 (tpp) REVERT: B 448 LEU cc_start: 0.8930 (mm) cc_final: 0.8594 (mm) REVERT: D 118 MET cc_start: 0.8587 (tpp) cc_final: 0.8339 (mmt) REVERT: D 371 MET cc_start: 0.7907 (ptp) cc_final: 0.7675 (ptp) REVERT: F 123 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6946 (p90) REVERT: F 373 MET cc_start: 0.9059 (tpp) cc_final: 0.8359 (tpp) REVERT: F 480 THR cc_start: 0.8649 (m) cc_final: 0.8346 (m) REVERT: G 21 LEU cc_start: 0.8347 (tp) cc_final: 0.8032 (mt) REVERT: G 105 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.8875 (mt) REVERT: G 112 MET cc_start: 0.8288 (tpp) cc_final: 0.7130 (tmm) REVERT: H 132 PHE cc_start: 0.8238 (m-80) cc_final: 0.7677 (m-10) REVERT: H 142 TYR cc_start: 0.6237 (m-10) cc_final: 0.5966 (m-10) REVERT: I 84 ARG cc_start: 0.5366 (tpp-160) cc_final: 0.4060 (ttt180) REVERT: J 33 LYS cc_start: 0.7662 (tppt) cc_final: 0.7425 (mmtm) REVERT: J 77 TYR cc_start: 0.2951 (t80) cc_final: 0.2713 (m-80) REVERT: J 106 ARG cc_start: 0.5195 (OUTLIER) cc_final: 0.4044 (ptp90) REVERT: J 115 SER cc_start: 0.7175 (t) cc_final: 0.6779 (p) REVERT: K 28 LEU cc_start: 0.5422 (OUTLIER) cc_final: 0.4804 (mt) REVERT: K 54 LEU cc_start: 0.7907 (pt) cc_final: 0.7604 (tt) REVERT: K 93 ASP cc_start: 0.7848 (p0) cc_final: 0.7239 (p0) REVERT: K 144 ARG cc_start: 0.4136 (mpt180) cc_final: 0.3634 (mmt180) REVERT: K 205 ARG cc_start: 0.1669 (tpm170) cc_final: 0.0976 (tpt170) REVERT: N 189 LEU cc_start: 0.5757 (OUTLIER) cc_final: 0.5465 (mm) REVERT: N 199 ARG cc_start: 0.5853 (ttp80) cc_final: 0.4835 (tmm-80) REVERT: 2 213 GLU cc_start: 0.8280 (tp30) cc_final: 0.7812 (tm-30) REVERT: 4 249 GLU cc_start: 0.8443 (pp20) cc_final: 0.7897 (pp20) REVERT: 6 385 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.7980 (tt) REVERT: 7 292 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7379 (t80) REVERT: 0 158 ILE cc_start: 0.9430 (tp) cc_final: 0.9127 (tp) REVERT: 0 200 TRP cc_start: 0.5670 (p90) cc_final: 0.3952 (t-100) outliers start: 149 outliers final: 99 residues processed: 602 average time/residue: 0.2216 time to fit residues: 226.4111 Evaluate side-chains 570 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 464 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain F residue 735 ILE Chi-restraints excluded: chain F residue 742 VAL Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 182 PHE Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain I residue 71 VAL Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 128 CYS Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 183 VAL Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 3 residue 138 LEU Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 126 SER Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 202 VAL Chi-restraints excluded: chain 6 residue 129 ASN Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 148 VAL Chi-restraints excluded: chain 6 residue 171 VAL Chi-restraints excluded: chain 6 residue 200 LEU Chi-restraints excluded: chain 6 residue 328 LEU Chi-restraints excluded: chain 6 residue 371 THR Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 7 residue 333 THR Chi-restraints excluded: chain 8 residue 135 CYS Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 117 VAL Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 129 ILE Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 145 VAL Chi-restraints excluded: chain 0 residue 197 MET Chi-restraints excluded: chain 0 residue 214 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 523 optimal weight: 1.9990 chunk 468 optimal weight: 0.9980 chunk 505 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 463 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 377 optimal weight: 8.9990 chunk 361 optimal weight: 0.5980 chunk 183 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 311 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.134336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105564 restraints weight = 98720.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.104757 restraints weight = 67151.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.105118 restraints weight = 52258.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.105401 restraints weight = 44248.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.105567 restraints weight = 40099.425| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41771 Z= 0.140 Angle : 0.806 45.473 56889 Z= 0.363 Chirality : 0.045 0.245 6497 Planarity : 0.005 0.092 7182 Dihedral : 7.498 89.922 5901 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.45 % Favored : 86.44 % Rotamer: Outliers : 2.92 % Allowed : 21.75 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.98 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.11), residues: 5280 helix: -0.28 (0.11), residues: 2401 sheet: -2.29 (0.26), residues: 371 loop : -3.63 (0.11), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 280 TYR 0.032 0.001 TYR F 516 PHE 0.025 0.001 PHE K 65 TRP 0.040 0.001 TRP 7 255 HIS 0.008 0.001 HIS F 407 Details of bonding type rmsd covalent geometry : bond 0.00312 (41767) covalent geometry : angle 0.71266 (56878) SS BOND : bond 0.00094 ( 1) SS BOND : angle 0.22758 ( 2) hydrogen bonds : bond 0.04015 ( 1619) hydrogen bonds : angle 4.76118 ( 4704) metal coordination : bond 0.01524 ( 3) metal coordination : angle 29.98682 ( 9) *********************** 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 626 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 509 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8599 (t60) cc_final: 0.8334 (t60) REVERT: A 280 PHE cc_start: 0.6796 (t80) cc_final: 0.6450 (t80) REVERT: B 320 MET cc_start: 0.8693 (tpp) cc_final: 0.8471 (tpp) REVERT: B 448 LEU cc_start: 0.8830 (mm) cc_final: 0.8514 (mm) REVERT: D 196 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.6915 (t70) REVERT: D 271 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.7044 (p-80) REVERT: F 373 MET cc_start: 0.8739 (tpp) cc_final: 0.8291 (tpp) REVERT: G 21 LEU cc_start: 0.8314 (tp) cc_final: 0.8084 (mt) REVERT: G 105 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8896 (mt) REVERT: G 108 VAL cc_start: 0.9223 (t) cc_final: 0.8997 (t) REVERT: G 112 MET cc_start: 0.8119 (tpp) cc_final: 0.7790 (tpp) REVERT: H 132 PHE cc_start: 0.8295 (m-80) cc_final: 0.7722 (m-10) REVERT: H 142 TYR cc_start: 0.6346 (m-10) cc_final: 0.5968 (m-80) REVERT: I 84 ARG cc_start: 0.5130 (tpp-160) cc_final: 0.4019 (ttt180) REVERT: J 77 TYR cc_start: 0.2718 (t80) cc_final: 0.2508 (m-80) REVERT: J 106 ARG cc_start: 0.5244 (OUTLIER) cc_final: 0.4895 (ptp90) REVERT: J 115 SER cc_start: 0.7051 (t) cc_final: 0.6689 (p) REVERT: J 118 MET cc_start: 0.6273 (tpp) cc_final: 0.5977 (tpp) REVERT: K 28 LEU cc_start: 0.5482 (OUTLIER) cc_final: 0.4830 (mt) REVERT: K 54 LEU cc_start: 0.7957 (pt) cc_final: 0.7710 (tt) REVERT: K 93 ASP cc_start: 0.7902 (p0) cc_final: 0.7320 (p0) REVERT: K 144 ARG cc_start: 0.3893 (mpt180) cc_final: 0.3512 (mmt180) REVERT: K 205 ARG cc_start: 0.1710 (tpm170) cc_final: 0.0985 (tpt170) REVERT: N 189 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5469 (mt) REVERT: N 199 ARG cc_start: 0.5609 (ttp80) cc_final: 0.4782 (tmm-80) REVERT: 2 176 ASN cc_start: 0.8553 (p0) cc_final: 0.8113 (m-40) REVERT: 2 213 GLU cc_start: 0.8141 (tp30) cc_final: 0.7752 (tm-30) REVERT: 4 249 GLU cc_start: 0.8211 (pp20) cc_final: 0.7763 (pp20) REVERT: 6 385 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.7994 (tt) REVERT: 7 292 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.7421 (t80) REVERT: 0 69 ASP cc_start: 0.6907 (t0) cc_final: 0.6513 (t0) REVERT: 0 158 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9054 (tp) REVERT: 0 200 TRP cc_start: 0.5490 (p90) cc_final: 0.3972 (t-100) outliers start: 117 outliers final: 80 residues processed: 595 average time/residue: 0.2211 time to fit residues: 222.7626 Evaluate side-chains 569 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 480 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 271 HIS Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain F residue 735 ILE Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 54 ASN Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 182 PHE Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 84 GLU Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 3 residue 138 LEU Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 202 VAL Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 148 VAL Chi-restraints excluded: chain 6 residue 171 VAL Chi-restraints excluded: chain 6 residue 200 LEU Chi-restraints excluded: chain 6 residue 328 LEU Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 208 GLU Chi-restraints excluded: chain 7 residue 265 LEU Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 7 residue 343 VAL Chi-restraints excluded: chain 8 residue 135 CYS Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 8 residue 155 GLU Chi-restraints excluded: chain 8 residue 168 CYS Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 106 TYR Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 117 VAL Chi-restraints excluded: chain 0 residue 97 HIS Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 158 ILE Chi-restraints excluded: chain 0 residue 197 MET Chi-restraints excluded: chain 0 residue 214 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 288 optimal weight: 4.9990 chunk 138 optimal weight: 0.6980 chunk 490 optimal weight: 4.9990 chunk 384 optimal weight: 0.9990 chunk 509 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 293 optimal weight: 7.9990 chunk 235 optimal weight: 20.0000 chunk 187 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 48 HIS H 196 ASN N 76 HIS 5 164 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.134849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.106363 restraints weight = 98910.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.105505 restraints weight = 67282.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.105887 restraints weight = 54035.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.105961 restraints weight = 49485.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.106214 restraints weight = 42313.267| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.003 0.051 41771 Z= 0.138 Angle : 0.797 44.795 56889 Z= 0.358 Chirality : 0.045 0.234 6497 Planarity : 0.005 0.085 7182 Dihedral : 7.131 88.660 5901 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 14.32 % Favored : 85.59 % Rotamer: Outliers : 3.04 % Allowed : 22.07 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.19 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.11), residues: 5280 helix: -0.13 (0.11), residues: 2398 sheet: -2.08 (0.27), residues: 360 loop : -3.60 (0.11), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 199 TYR 0.030 0.001 TYR F 516 PHE 0.038 0.001 PHE K 65 TRP 0.038 0.001 TRP 7 255 HIS 0.008 0.001 HIS F 407 Details of bonding type rmsd covalent geometry : bond 0.00308 (41767) covalent geometry : angle 0.70538 (56878) SS BOND : bond 0.00058 ( 1) SS BOND : angle 0.18319 ( 2) hydrogen bonds : bond 0.03852 ( 1619) hydrogen bonds : angle 4.66549 ( 4704) metal coordination : bond 0.01605 ( 3) metal coordination : angle 29.45596 ( 9) *********************** 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 633 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 511 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8589 (t60) cc_final: 0.8320 (t60) REVERT: A 280 PHE cc_start: 0.6543 (t80) cc_final: 0.6231 (t80) REVERT: A 332 MET cc_start: 0.7997 (ttp) cc_final: 0.7721 (ttp) REVERT: B 47 MET cc_start: 0.8167 (mtt) cc_final: 0.7891 (mtp) REVERT: B 253 THR cc_start: 0.9103 (m) cc_final: 0.8686 (p) REVERT: B 320 MET cc_start: 0.8717 (tpp) cc_final: 0.8462 (tpp) REVERT: B 448 LEU cc_start: 0.8990 (mm) cc_final: 0.8621 (mm) REVERT: D 118 MET cc_start: 0.8529 (mmt) cc_final: 0.7644 (tpp) REVERT: D 196 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.6836 (t70) REVERT: D 271 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7022 (p-80) REVERT: F 371 TYR cc_start: 0.8097 (m-80) cc_final: 0.7781 (m-80) REVERT: F 373 MET cc_start: 0.8618 (tpp) cc_final: 0.8269 (tpp) REVERT: G 21 LEU cc_start: 0.8277 (tp) cc_final: 0.8061 (mt) REVERT: G 66 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.7028 (t80) REVERT: G 105 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8909 (mt) REVERT: G 112 MET cc_start: 0.8103 (tpp) cc_final: 0.7816 (tpp) REVERT: H 76 MET cc_start: 0.6435 (tpt) cc_final: 0.6125 (mmt) REVERT: H 132 PHE cc_start: 0.8410 (m-80) cc_final: 0.7926 (m-10) REVERT: H 142 TYR cc_start: 0.6142 (m-10) cc_final: 0.5743 (m-80) REVERT: H 237 ASP cc_start: 0.8546 (t0) cc_final: 0.8216 (t0) REVERT: I 84 ARG cc_start: 0.5585 (tpp-160) cc_final: 0.4458 (ttt180) REVERT: J 77 TYR cc_start: 0.2844 (t80) cc_final: 0.2554 (m-80) REVERT: J 106 ARG cc_start: 0.5303 (OUTLIER) cc_final: 0.4963 (ptp90) REVERT: J 115 SER cc_start: 0.7089 (t) cc_final: 0.6718 (p) REVERT: K 28 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.4947 (mt) REVERT: K 54 LEU cc_start: 0.7898 (pt) cc_final: 0.7635 (tt) REVERT: K 93 ASP cc_start: 0.7751 (p0) cc_final: 0.7245 (p0) REVERT: K 144 ARG cc_start: 0.3883 (mpt180) cc_final: 0.3517 (mmt180) REVERT: K 205 ARG cc_start: 0.1568 (tpm170) cc_final: 0.0860 (tpt170) REVERT: N 189 LEU cc_start: 0.5638 (OUTLIER) cc_final: 0.5378 (mt) REVERT: N 199 ARG cc_start: 0.5636 (ttp80) cc_final: 0.3609 (ttp80) REVERT: 2 213 GLU cc_start: 0.8122 (tp30) cc_final: 0.7732 (tm-30) REVERT: 4 249 GLU cc_start: 0.8198 (pp20) cc_final: 0.7914 (pt0) REVERT: 6 385 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.7901 (tt) REVERT: 7 232 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6643 (tt0) REVERT: 7 292 PHE cc_start: 0.7569 (OUTLIER) cc_final: 0.7299 (t80) REVERT: 8 113 ILE cc_start: 0.8566 (pt) cc_final: 0.8312 (pt) REVERT: 8 136 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8185 (mm) REVERT: 0 69 ASP cc_start: 0.6893 (t0) cc_final: 0.6474 (t0) REVERT: 0 158 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8988 (tp) REVERT: 0 200 TRP cc_start: 0.5484 (p90) cc_final: 0.3969 (t-100) outliers start: 122 outliers final: 86 residues processed: 604 average time/residue: 0.2241 time to fit residues: 229.6715 Evaluate side-chains 585 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 487 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 271 HIS Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain F residue 735 ILE Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain H residue 182 PHE Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 73 THR Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain M residue 150 LEU Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 3 residue 138 LEU Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 202 VAL Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 148 VAL Chi-restraints excluded: chain 6 residue 171 VAL Chi-restraints excluded: chain 6 residue 200 LEU Chi-restraints excluded: chain 6 residue 328 LEU Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 232 GLU Chi-restraints excluded: chain 7 residue 265 LEU Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 8 residue 136 ILE Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 8 residue 155 GLU Chi-restraints excluded: chain 8 residue 168 CYS Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 117 VAL Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 158 ILE Chi-restraints excluded: chain 0 residue 197 MET Chi-restraints excluded: chain 0 residue 214 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 200 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 359 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 518 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 452 optimal weight: 7.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN F 120 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 GLN H 196 ASN N 76 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.133310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.104602 restraints weight = 98922.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.103645 restraints weight = 68930.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103995 restraints weight = 53593.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.104243 restraints weight = 50363.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.104410 restraints weight = 42607.953| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41771 Z= 0.175 Angle : 0.823 44.568 56889 Z= 0.375 Chirality : 0.046 0.224 6497 Planarity : 0.005 0.087 7182 Dihedral : 7.178 85.723 5901 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.68 % Favored : 85.21 % Rotamer: Outliers : 3.34 % Allowed : 22.32 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.59 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.11), residues: 5280 helix: -0.10 (0.11), residues: 2384 sheet: -2.09 (0.27), residues: 361 loop : -3.56 (0.11), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 80 TYR 0.028 0.002 TYR F 516 PHE 0.049 0.002 PHE I 85 TRP 0.030 0.001 TRP 7 255 HIS 0.009 0.001 HIS F 407 Details of bonding type rmsd covalent geometry : bond 0.00402 (41767) covalent geometry : angle 0.73689 (56878) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.32222 ( 2) hydrogen bonds : bond 0.04139 ( 1619) hydrogen bonds : angle 4.75964 ( 4704) metal coordination : bond 0.02108 ( 3) metal coordination : angle 29.10833 ( 9) *********************** 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 632 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 498 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8622 (t60) cc_final: 0.8345 (t60) REVERT: A 280 PHE cc_start: 0.6586 (t80) cc_final: 0.6285 (t80) REVERT: A 332 MET cc_start: 0.7809 (ttp) cc_final: 0.7522 (ttp) REVERT: B 320 MET cc_start: 0.8722 (tpp) cc_final: 0.8481 (tpp) REVERT: B 448 LEU cc_start: 0.8942 (mm) cc_final: 0.8588 (mm) REVERT: D 193 PRO cc_start: 0.7129 (Cg_exo) cc_final: 0.6844 (Cg_endo) REVERT: D 196 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7054 (t70) REVERT: D 271 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7143 (p-80) REVERT: D 371 MET cc_start: 0.8042 (ptp) cc_final: 0.7763 (ptp) REVERT: F 123 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.7196 (p90) REVERT: F 371 TYR cc_start: 0.8176 (m-80) cc_final: 0.7950 (m-80) REVERT: F 373 MET cc_start: 0.8627 (tpp) cc_final: 0.8248 (tpp) REVERT: G 21 LEU cc_start: 0.8287 (tp) cc_final: 0.8084 (mt) REVERT: G 66 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7541 (t80) REVERT: G 105 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8847 (mt) REVERT: G 108 VAL cc_start: 0.9055 (t) cc_final: 0.8840 (t) REVERT: G 112 MET cc_start: 0.8190 (tpp) cc_final: 0.7951 (tpp) REVERT: H 128 GLN cc_start: 0.4814 (OUTLIER) cc_final: 0.4413 (pm20) REVERT: H 132 PHE cc_start: 0.8382 (m-80) cc_final: 0.7951 (m-10) REVERT: H 142 TYR cc_start: 0.6472 (m-10) cc_final: 0.5974 (m-80) REVERT: H 237 ASP cc_start: 0.8530 (t0) cc_final: 0.8185 (t0) REVERT: I 84 ARG cc_start: 0.5506 (tpp-160) cc_final: 0.4128 (ttt180) REVERT: J 51 TYR cc_start: 0.6848 (t80) cc_final: 0.6093 (t80) REVERT: J 77 TYR cc_start: 0.2976 (t80) cc_final: 0.2748 (m-80) REVERT: J 106 ARG cc_start: 0.5201 (OUTLIER) cc_final: 0.4898 (ptp90) REVERT: J 115 SER cc_start: 0.7112 (t) cc_final: 0.6735 (p) REVERT: K 28 LEU cc_start: 0.5677 (OUTLIER) cc_final: 0.5089 (mt) REVERT: K 93 ASP cc_start: 0.7591 (p0) cc_final: 0.7341 (p0) REVERT: K 144 ARG cc_start: 0.4097 (mpt180) cc_final: 0.3711 (mmt180) REVERT: K 205 ARG cc_start: 0.1814 (tpm170) cc_final: 0.0997 (tpt170) REVERT: M 99 ARG cc_start: 0.6111 (ttt180) cc_final: 0.5753 (ttt180) REVERT: M 125 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6314 (tt) REVERT: N 189 LEU cc_start: 0.5764 (OUTLIER) cc_final: 0.5480 (mt) REVERT: N 199 ARG cc_start: 0.6011 (ttp80) cc_final: 0.5058 (tmm-80) REVERT: 1 163 THR cc_start: 0.6364 (t) cc_final: 0.6138 (p) REVERT: 2 132 MET cc_start: 0.8313 (mtm) cc_final: 0.8044 (ttm) REVERT: 2 213 GLU cc_start: 0.8140 (tp30) cc_final: 0.7733 (tm-30) REVERT: 4 249 GLU cc_start: 0.8286 (pp20) cc_final: 0.8079 (pt0) REVERT: 6 354 MET cc_start: 0.8043 (tpp) cc_final: 0.7042 (tpp) REVERT: 6 385 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.7722 (tt) REVERT: 7 292 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7552 (t80) REVERT: 8 123 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8100 (mm) REVERT: 8 136 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8151 (mm) REVERT: 0 69 ASP cc_start: 0.7066 (t0) cc_final: 0.6672 (t0) REVERT: 0 158 ILE cc_start: 0.9331 (tp) cc_final: 0.9031 (tp) REVERT: 0 200 TRP cc_start: 0.5319 (p90) cc_final: 0.3819 (t-100) outliers start: 134 outliers final: 93 residues processed: 592 average time/residue: 0.2184 time to fit residues: 218.7762 Evaluate side-chains 592 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 485 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 271 HIS Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 356 MET Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 117 TRP Chi-restraints excluded: chain F residue 123 PHE Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain F residue 735 ILE Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain H residue 359 PHE Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain M residue 125 LEU Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 183 VAL Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 1 residue 211 LEU Chi-restraints excluded: chain 3 residue 138 LEU Chi-restraints excluded: chain 4 residue 174 PHE Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 5 residue 202 VAL Chi-restraints excluded: chain 6 residue 171 VAL Chi-restraints excluded: chain 6 residue 200 LEU Chi-restraints excluded: chain 6 residue 328 LEU Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 72 LEU Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 7 residue 343 VAL Chi-restraints excluded: chain 8 residue 123 LEU Chi-restraints excluded: chain 8 residue 135 CYS Chi-restraints excluded: chain 8 residue 136 ILE Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 8 residue 155 GLU Chi-restraints excluded: chain 8 residue 168 CYS Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 117 VAL Chi-restraints excluded: chain 0 residue 129 ILE Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 145 VAL Chi-restraints excluded: chain 0 residue 197 MET Chi-restraints excluded: chain 0 residue 214 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 200 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 435 optimal weight: 0.8980 chunk 365 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 chunk 413 optimal weight: 9.9990 chunk 340 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 204 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 120 ASN F 174 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN H 114 HIS I 58 HIS ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.135805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107051 restraints weight = 98787.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.106547 restraints weight = 64347.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.106802 restraints weight = 50850.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.107052 restraints weight = 43836.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.107214 restraints weight = 39789.505| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 41771 Z= 0.131 Angle : 0.793 44.700 56889 Z= 0.357 Chirality : 0.044 0.220 6497 Planarity : 0.005 0.086 7182 Dihedral : 6.973 82.933 5901 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.67 % Favored : 86.23 % Rotamer: Outliers : 2.72 % Allowed : 23.22 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.19 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.12), residues: 5280 helix: 0.06 (0.11), residues: 2382 sheet: -1.96 (0.28), residues: 361 loop : -3.52 (0.11), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 199 TYR 0.028 0.001 TYR F 516 PHE 0.040 0.001 PHE F 504 TRP 0.047 0.001 TRP 7 255 HIS 0.008 0.001 HIS I 58 Details of bonding type rmsd covalent geometry : bond 0.00291 (41767) covalent geometry : angle 0.70405 (56878) SS BOND : bond 0.00033 ( 1) SS BOND : angle 0.17455 ( 2) hydrogen bonds : bond 0.03706 ( 1619) hydrogen bonds : angle 4.63061 ( 4704) metal coordination : bond 0.01373 ( 3) metal coordination : angle 29.07861 ( 9) *********************** 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 632 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 523 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8610 (t60) cc_final: 0.8378 (t60) REVERT: A 280 PHE cc_start: 0.6296 (t80) cc_final: 0.5965 (t80) REVERT: A 332 MET cc_start: 0.7770 (ttp) cc_final: 0.7522 (ttp) REVERT: B 320 MET cc_start: 0.8705 (tpp) cc_final: 0.8473 (tpp) REVERT: B 448 LEU cc_start: 0.8955 (mm) cc_final: 0.8567 (mm) REVERT: D 118 MET cc_start: 0.8545 (mmt) cc_final: 0.7697 (mpp) REVERT: D 196 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7087 (t70) REVERT: D 271 HIS cc_start: 0.7597 (OUTLIER) cc_final: 0.6980 (p-80) REVERT: F 373 MET cc_start: 0.8528 (tpp) cc_final: 0.8154 (tpp) REVERT: G 66 TYR cc_start: 0.8126 (OUTLIER) cc_final: 0.7747 (t80) REVERT: G 105 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8821 (mt) REVERT: H 28 LEU cc_start: 0.7170 (mm) cc_final: 0.6903 (tp) REVERT: H 132 PHE cc_start: 0.8311 (m-80) cc_final: 0.7893 (m-10) REVERT: H 142 TYR cc_start: 0.6255 (m-10) cc_final: 0.5692 (m-80) REVERT: H 237 ASP cc_start: 0.8527 (t0) cc_final: 0.8182 (t0) REVERT: I 8 PHE cc_start: -0.1435 (OUTLIER) cc_final: -0.1643 (t80) REVERT: I 84 ARG cc_start: 0.5289 (tpp-160) cc_final: 0.3986 (ttt180) REVERT: J 51 TYR cc_start: 0.6794 (t80) cc_final: 0.6307 (t80) REVERT: J 77 TYR cc_start: 0.2651 (t80) cc_final: 0.2392 (m-80) REVERT: J 106 ARG cc_start: 0.5174 (OUTLIER) cc_final: 0.4912 (ptp90) REVERT: K 28 LEU cc_start: 0.5709 (OUTLIER) cc_final: 0.5128 (mt) REVERT: K 93 ASP cc_start: 0.7520 (p0) cc_final: 0.7263 (p0) REVERT: K 144 ARG cc_start: 0.3893 (mpt180) cc_final: 0.3469 (mmt180) REVERT: K 205 ARG cc_start: 0.1710 (tpm170) cc_final: 0.1047 (tpt170) REVERT: N 189 LEU cc_start: 0.5703 (OUTLIER) cc_final: 0.5424 (mt) REVERT: N 199 ARG cc_start: 0.6092 (ttp80) cc_final: 0.4142 (ttp80) REVERT: 2 132 MET cc_start: 0.8105 (mtm) cc_final: 0.7811 (ttm) REVERT: 2 213 GLU cc_start: 0.8064 (tp30) cc_final: 0.7635 (tm-30) REVERT: 4 249 GLU cc_start: 0.8231 (pp20) cc_final: 0.8026 (pt0) REVERT: 6 260 MET cc_start: 0.8044 (tmm) cc_final: 0.7728 (tpt) REVERT: 6 354 MET cc_start: 0.7948 (tpp) cc_final: 0.6960 (tpp) REVERT: 6 385 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.7656 (tt) REVERT: 7 292 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7377 (t80) REVERT: 8 113 ILE cc_start: 0.8533 (pt) cc_final: 0.8272 (pt) REVERT: 8 136 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8014 (mm) REVERT: 0 69 ASP cc_start: 0.6918 (t0) cc_final: 0.6575 (t0) REVERT: 0 158 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.8989 (tp) REVERT: 0 200 TRP cc_start: 0.5463 (p90) cc_final: 0.3967 (t-100) outliers start: 109 outliers final: 79 residues processed: 602 average time/residue: 0.2233 time to fit residues: 228.1817 Evaluate side-chains 588 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 497 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 271 HIS Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 120 ASN Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain F residue 735 ILE Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain H residue 114 HIS Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 182 PHE Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain I residue 8 PHE Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain N residue 88 LEU Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 119 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 181 TYR Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 3 residue 138 LEU Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 148 VAL Chi-restraints excluded: chain 6 residue 200 LEU Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 94 CYS Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 144 ASP Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 292 PHE Chi-restraints excluded: chain 7 residue 343 VAL Chi-restraints excluded: chain 8 residue 136 ILE Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 8 residue 155 GLU Chi-restraints excluded: chain 8 residue 168 CYS Chi-restraints excluded: chain 9 residue 94 ILE Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 9 residue 117 VAL Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 158 ILE Chi-restraints excluded: chain 0 residue 197 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 59 optimal weight: 4.9990 chunk 373 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 392 optimal weight: 8.9990 chunk 455 optimal weight: 5.9990 chunk 374 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 332 optimal weight: 0.2980 chunk 454 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 137 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 ASN E 39 ASN ** G 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN H 114 HIS ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 86 ASN 8 192 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.136814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.106435 restraints weight = 99482.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.107686 restraints weight = 56010.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.108628 restraints weight = 35621.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.108915 restraints weight = 30942.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.108804 restraints weight = 26658.275| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 41771 Z= 0.125 Angle : 0.784 43.211 56889 Z= 0.354 Chirality : 0.044 0.216 6497 Planarity : 0.005 0.086 7182 Dihedral : 6.797 81.843 5901 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.94 % Favored : 86.97 % Rotamer: Outliers : 2.32 % Allowed : 23.82 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.19 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.12), residues: 5280 helix: 0.19 (0.11), residues: 2379 sheet: -1.86 (0.28), residues: 365 loop : -3.45 (0.11), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 80 TYR 0.029 0.001 TYR F 516 PHE 0.044 0.001 PHE F 504 TRP 0.043 0.001 TRP 7 255 HIS 0.010 0.001 HIS H 114 Details of bonding type rmsd covalent geometry : bond 0.00272 (41767) covalent geometry : angle 0.70090 (56878) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.05881 ( 2) hydrogen bonds : bond 0.03503 ( 1619) hydrogen bonds : angle 4.55120 ( 4704) metal coordination : bond 0.01243 ( 3) metal coordination : angle 27.94493 ( 9) ********************** 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 631 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 538 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 TRP cc_start: 0.8664 (t60) cc_final: 0.8448 (t60) REVERT: A 280 PHE cc_start: 0.6327 (t80) cc_final: 0.5998 (t80) REVERT: A 302 MET cc_start: 0.1959 (tmm) cc_final: 0.1737 (ppp) REVERT: B 320 MET cc_start: 0.8789 (tpp) cc_final: 0.8543 (tpp) REVERT: B 448 LEU cc_start: 0.9004 (mm) cc_final: 0.8621 (mm) REVERT: D 118 MET cc_start: 0.8516 (mmt) cc_final: 0.7600 (mpp) REVERT: D 196 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7407 (t70) REVERT: D 234 LEU cc_start: 0.8995 (tp) cc_final: 0.8778 (tp) REVERT: D 271 HIS cc_start: 0.7567 (OUTLIER) cc_final: 0.6930 (p-80) REVERT: D 371 MET cc_start: 0.8088 (ptp) cc_final: 0.7865 (ptp) REVERT: F 373 MET cc_start: 0.8579 (tpp) cc_final: 0.8279 (tpp) REVERT: G 66 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7928 (t80) REVERT: G 105 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8857 (mt) REVERT: H 132 PHE cc_start: 0.8192 (m-80) cc_final: 0.7798 (m-10) REVERT: H 142 TYR cc_start: 0.6389 (m-10) cc_final: 0.6002 (m-80) REVERT: H 237 ASP cc_start: 0.8306 (t0) cc_final: 0.7931 (t0) REVERT: I 84 ARG cc_start: 0.5219 (tpp-160) cc_final: 0.3874 (ttt180) REVERT: J 51 TYR cc_start: 0.6757 (t80) cc_final: 0.6192 (t80) REVERT: J 77 TYR cc_start: 0.2685 (t80) cc_final: 0.2387 (m-80) REVERT: J 106 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4770 (ptp90) REVERT: K 28 LEU cc_start: 0.5746 (OUTLIER) cc_final: 0.5099 (mt) REVERT: K 93 ASP cc_start: 0.7311 (p0) cc_final: 0.6710 (p0) REVERT: K 144 ARG cc_start: 0.3966 (mpt180) cc_final: 0.3628 (mmt180) REVERT: K 205 ARG cc_start: 0.1306 (tpm170) cc_final: 0.0775 (tpt170) REVERT: N 199 ARG cc_start: 0.6230 (ttp80) cc_final: 0.4309 (ttp80) REVERT: 2 132 MET cc_start: 0.7919 (mtm) cc_final: 0.7699 (ttm) REVERT: 2 190 ARG cc_start: 0.7095 (ttp80) cc_final: 0.6322 (ttp80) REVERT: 2 213 GLU cc_start: 0.8064 (tp30) cc_final: 0.7606 (tm-30) REVERT: 4 249 GLU cc_start: 0.8239 (pp20) cc_final: 0.7997 (pt0) REVERT: 5 86 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.7180 (t0) REVERT: 6 260 MET cc_start: 0.7952 (tmm) cc_final: 0.7679 (tpt) REVERT: 6 385 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.7787 (tt) REVERT: 7 216 CYS cc_start: 0.5118 (t) cc_final: 0.4910 (t) REVERT: 8 113 ILE cc_start: 0.8465 (pt) cc_final: 0.8189 (pt) REVERT: 8 136 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7938 (mm) REVERT: 9 157 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6858 (tt0) REVERT: 0 69 ASP cc_start: 0.6852 (t0) cc_final: 0.6481 (t0) REVERT: 0 158 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.9011 (tp) REVERT: 0 200 TRP cc_start: 0.5367 (p90) cc_final: 0.3909 (t-100) outliers start: 93 outliers final: 72 residues processed: 606 average time/residue: 0.2234 time to fit residues: 229.7277 Evaluate side-chains 585 residues out of total 4600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 503 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 271 HIS Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 457 SER Chi-restraints excluded: chain E residue 52 PHE Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 229 PHE Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 407 HIS Chi-restraints excluded: chain F residue 439 THR Chi-restraints excluded: chain F residue 467 TRP Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 671 PHE Chi-restraints excluded: chain F residue 735 ILE Chi-restraints excluded: chain G residue 51 PHE Chi-restraints excluded: chain G residue 66 TYR Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain H residue 114 HIS Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 182 PHE Chi-restraints excluded: chain H residue 326 LEU Chi-restraints excluded: chain I residue 114 CYS Chi-restraints excluded: chain I residue 129 THR Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 133 LEU Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 24 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain 1 residue 101 LEU Chi-restraints excluded: chain 1 residue 117 VAL Chi-restraints excluded: chain 1 residue 156 ILE Chi-restraints excluded: chain 1 residue 171 THR Chi-restraints excluded: chain 1 residue 198 THR Chi-restraints excluded: chain 1 residue 201 VAL Chi-restraints excluded: chain 3 residue 114 ILE Chi-restraints excluded: chain 3 residue 138 LEU Chi-restraints excluded: chain 5 residue 86 ASN Chi-restraints excluded: chain 5 residue 148 THR Chi-restraints excluded: chain 5 residue 168 THR Chi-restraints excluded: chain 6 residue 139 LEU Chi-restraints excluded: chain 6 residue 148 VAL Chi-restraints excluded: chain 6 residue 200 LEU Chi-restraints excluded: chain 6 residue 254 TYR Chi-restraints excluded: chain 6 residue 385 LEU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 116 VAL Chi-restraints excluded: chain 7 residue 149 VAL Chi-restraints excluded: chain 7 residue 173 MET Chi-restraints excluded: chain 7 residue 207 VAL Chi-restraints excluded: chain 7 residue 265 LEU Chi-restraints excluded: chain 7 residue 343 VAL Chi-restraints excluded: chain 8 residue 136 ILE Chi-restraints excluded: chain 8 residue 137 VAL Chi-restraints excluded: chain 8 residue 155 GLU Chi-restraints excluded: chain 9 residue 96 HIS Chi-restraints excluded: chain 9 residue 111 MET Chi-restraints excluded: chain 0 residue 137 VAL Chi-restraints excluded: chain 0 residue 158 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 337 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 410 optimal weight: 0.1980 chunk 479 optimal weight: 4.9990 chunk 345 optimal weight: 8.9990 chunk 319 optimal weight: 10.0000 chunk 458 optimal weight: 0.6980 chunk 428 optimal weight: 0.7980 chunk 267 optimal weight: 40.0000 chunk 108 optimal weight: 0.8980 chunk 301 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN G 8 HIS G 140 ASN I 58 HIS ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 HIS 5 86 ASN 8 184 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.136734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.108555 restraints weight = 99800.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.107738 restraints weight = 65921.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.108082 restraints weight = 53398.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.108377 restraints weight = 44775.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.108520 restraints weight = 41375.311| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41771 Z= 0.128 Angle : 0.796 42.141 56889 Z= 0.357 Chirality : 0.044 0.238 6497 Planarity : 0.005 0.080 7182 Dihedral : 6.690 80.367 5901 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.90 % Favored : 87.01 % Rotamer: Outliers : 2.22 % Allowed : 23.99 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.40 % Cis-general : 0.02 % Twisted Proline : 1.19 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.12), residues: 5280 helix: 0.26 (0.11), residues: 2382 sheet: -1.82 (0.27), residues: 372 loop : -3.44 (0.11), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 80 TYR 0.030 0.001 TYR F 516 PHE 0.046 0.001 PHE F 504 TRP 0.036 0.001 TRP 7 255 HIS 0.010 0.001 HIS I 58 Details of bonding type rmsd covalent geometry : bond 0.00281 (41767) covalent geometry : angle 0.70779 (56878) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.05213 ( 2) hydrogen bonds : bond 0.03499 ( 1619) hydrogen bonds : angle 4.54577 ( 4704) metal coordination : bond 0.01235 ( 3) metal coordination : angle 28.91600 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6905.17 seconds wall clock time: 120 minutes 22.41 seconds (7222.41 seconds total)