Starting phenix.real_space_refine on Wed Aug 27 02:31:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n0f_9314/08_2025/6n0f_9314.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n0f_9314/08_2025/6n0f_9314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n0f_9314/08_2025/6n0f_9314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n0f_9314/08_2025/6n0f_9314.map" model { file = "/net/cci-nas-00/data/ceres_data/6n0f_9314/08_2025/6n0f_9314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n0f_9314/08_2025/6n0f_9314.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 198 5.16 5 C 29148 2.51 5 N 8229 2.21 5 O 8643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46218 Number of models: 1 Model: "" Number of chains: 51 Chain: "A" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "B" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "C" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "D" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "E" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "F" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1520 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Chain: "GA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "ID" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "G" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1484 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 10, 'TRANS': 186} Chain breaks: 1 Chain: "H" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1484 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 10, 'TRANS': 186} Chain breaks: 1 Chain: "I" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "M" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "N" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "O" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "S" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "T" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1488 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Chain: "U" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1489 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 10, 'TRANS': 187} Chain breaks: 1 Time building chain proxies: 11.53, per 1000 atoms: 0.25 Number of scatterers: 46218 At special positions: 0 Unit cell: (154.5, 268.83, 251.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 198 16.00 O 8643 8.00 N 8229 7.00 C 29148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 476.8 nanoseconds 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11424 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 67 sheets defined 41.1% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 15 through 25 Processing helix chain 'A' and resid 47 through 57 removed outlier: 4.032A pdb=" N ASP A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 96 removed outlier: 3.932A pdb=" N VAL A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.521A pdb=" N ILE A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 150 through 161 removed outlier: 3.816A pdb=" N ALA A 158 " --> pdb=" O ALA A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 199 removed outlier: 3.539A pdb=" N ARG A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 46 through 59 removed outlier: 4.436A pdb=" N ARG B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 96 removed outlier: 4.013A pdb=" N VAL B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 4.239A pdb=" N ILE B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 162 removed outlier: 3.752A pdb=" N ALA B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.905A pdb=" N ARG B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 removed outlier: 3.568A pdb=" N THR C 25 " --> pdb=" O PHE C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 81 through 96 removed outlier: 3.521A pdb=" N VAL C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 96 " --> pdb=" O ILE C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 removed outlier: 3.889A pdb=" N GLN C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.879A pdb=" N ALA C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA C 162 " --> pdb=" O ALA C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.748A pdb=" N ARG C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 25 Processing helix chain 'D' and resid 47 through 59 removed outlier: 4.098A pdb=" N VAL D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.513A pdb=" N LEU D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.591A pdb=" N THR D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 150 through 162 removed outlier: 3.718A pdb=" N ALA D 161 " --> pdb=" O GLU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'E' and resid 15 through 25 Processing helix chain 'E' and resid 47 through 59 removed outlier: 3.613A pdb=" N VAL E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 96 removed outlier: 3.580A pdb=" N VAL E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 103 Processing helix chain 'E' and resid 118 through 126 removed outlier: 3.821A pdb=" N ILE E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 150 through 161 removed outlier: 3.804A pdb=" N ALA E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 200 removed outlier: 3.538A pdb=" N ARG E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 25 Processing helix chain 'F' and resid 47 through 59 removed outlier: 4.056A pdb=" N VAL F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 96 removed outlier: 3.645A pdb=" N VAL F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 103 removed outlier: 3.729A pdb=" N GLY F 102 " --> pdb=" O ARG F 99 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG F 103 " --> pdb=" O GLU F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 99 through 103' Processing helix chain 'F' and resid 118 through 126 removed outlier: 4.096A pdb=" N ILE F 124 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 150 through 162 removed outlier: 3.640A pdb=" N ALA F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 161 " --> pdb=" O GLU F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 removed outlier: 3.627A pdb=" N ARG F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'GA' and resid 12 through 27 removed outlier: 3.615A pdb=" N VALGA 24 " --> pdb=" O ALAGA 20 " (cutoff:3.500A) Processing helix chain 'GA' and resid 49 through 65 removed outlier: 4.094A pdb=" N ALAGA 55 " --> pdb=" O ALAGA 51 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLUGA 58 " --> pdb=" O LYSGA 54 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARGGA 62 " --> pdb=" O GLUGA 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLUGA 65 " --> pdb=" O GLNGA 61 " (cutoff:3.500A) Processing helix chain 'GA' and resid 80 through 87 Processing helix chain 'GB' and resid 12 through 27 removed outlier: 3.691A pdb=" N METGB 16 " --> pdb=" O GLYGB 12 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VALGB 24 " --> pdb=" O ALAGB 20 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALAGB 27 " --> pdb=" O METGB 23 " (cutoff:3.500A) Processing helix chain 'GB' and resid 49 through 65 removed outlier: 4.006A pdb=" N ALAGB 55 " --> pdb=" O ALAGB 51 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLUGB 58 " --> pdb=" O LYSGB 54 " (cutoff:3.500A) Processing helix chain 'GB' and resid 80 through 85 removed outlier: 3.934A pdb=" N ASPGB 84 " --> pdb=" O HISGB 80 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALAGB 85 " --> pdb=" O VALGB 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'GB' and resid 80 through 85' Processing helix chain 'GC' and resid 12 through 27 removed outlier: 3.699A pdb=" N METGC 16 " --> pdb=" O GLYGC 12 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VALGC 24 " --> pdb=" O ALAGC 20 " (cutoff:3.500A) Processing helix chain 'GC' and resid 49 through 65 removed outlier: 3.615A pdb=" N ALAGC 55 " --> pdb=" O ALAGC 51 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLUGC 58 " --> pdb=" O LYSGC 54 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALAGC 59 " --> pdb=" O ALAGC 55 " (cutoff:3.500A) Processing helix chain 'GC' and resid 80 through 87 Processing helix chain 'GD' and resid 12 through 27 removed outlier: 3.545A pdb=" N METGD 16 " --> pdb=" O GLYGD 12 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALAGD 27 " --> pdb=" O METGD 23 " (cutoff:3.500A) Processing helix chain 'GD' and resid 49 through 66 removed outlier: 3.853A pdb=" N ALAGD 55 " --> pdb=" O ALAGD 51 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARGGD 62 " --> pdb=" O GLUGD 58 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARGGD 66 " --> pdb=" O ARGGD 62 " (cutoff:3.500A) Processing helix chain 'GD' and resid 80 through 87 removed outlier: 3.794A pdb=" N ASPGD 84 " --> pdb=" O HISGD 80 " (cutoff:3.500A) Processing helix chain 'GE' and resid 12 through 27 removed outlier: 3.867A pdb=" N VALGE 24 " --> pdb=" O ALAGE 20 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYSGE 25 " --> pdb=" O ASPGE 21 " (cutoff:3.500A) Processing helix chain 'GE' and resid 49 through 65 removed outlier: 3.866A pdb=" N GLUGE 58 " --> pdb=" O LYSGE 54 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARGGE 62 " --> pdb=" O GLUGE 58 " (cutoff:3.500A) Processing helix chain 'GE' and resid 80 through 87 removed outlier: 3.564A pdb=" N ASPGE 84 " --> pdb=" O HISGE 80 " (cutoff:3.500A) Processing helix chain 'GF' and resid 12 through 26 Processing helix chain 'GF' and resid 49 through 65 removed outlier: 3.914A pdb=" N ALAGF 55 " --> pdb=" O ALAGF 51 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLUGF 58 " --> pdb=" O LYSGF 54 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARGGF 62 " --> pdb=" O GLUGF 58 " (cutoff:3.500A) Processing helix chain 'GF' and resid 80 through 87 Processing helix chain 'HA' and resid 12 through 25 removed outlier: 3.661A pdb=" N METHA 16 " --> pdb=" O GLYHA 12 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VALHA 24 " --> pdb=" O ALAHA 20 " (cutoff:3.500A) Processing helix chain 'HA' and resid 49 through 65 removed outlier: 4.231A pdb=" N GLUHA 58 " --> pdb=" O LYSHA 54 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLUHA 65 " --> pdb=" O GLNHA 61 " (cutoff:3.500A) Processing helix chain 'HA' and resid 80 through 87 Processing helix chain 'HB' and resid 12 through 27 removed outlier: 3.579A pdb=" N METHB 16 " --> pdb=" O GLYHB 12 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VALHB 24 " --> pdb=" O ALAHB 20 " (cutoff:3.500A) Processing helix chain 'HB' and resid 49 through 68 removed outlier: 3.814A pdb=" N LYSHB 54 " --> pdb=" O VALHB 50 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALAHB 55 " --> pdb=" O ALAHB 51 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ARGHB 62 " --> pdb=" O GLUHB 58 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARGHB 66 " --> pdb=" O ARGHB 62 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VALHB 67 " --> pdb=" O ALAHB 63 " (cutoff:3.500A) Processing helix chain 'HB' and resid 80 through 86 Processing helix chain 'HC' and resid 12 through 27 removed outlier: 3.648A pdb=" N METHC 16 " --> pdb=" O GLYHC 12 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VALHC 24 " --> pdb=" O ALAHC 20 " (cutoff:3.500A) Processing helix chain 'HC' and resid 49 through 65 removed outlier: 3.786A pdb=" N ALAHC 55 " --> pdb=" O ALAHC 51 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLUHC 58 " --> pdb=" O LYSHC 54 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALAHC 59 " --> pdb=" O ALAHC 55 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARGHC 62 " --> pdb=" O GLUHC 58 " (cutoff:3.500A) Processing helix chain 'HC' and resid 80 through 87 Processing helix chain 'HD' and resid 12 through 27 removed outlier: 3.620A pdb=" N METHD 16 " --> pdb=" O GLYHD 12 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VALHD 24 " --> pdb=" O ALAHD 20 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALAHD 27 " --> pdb=" O METHD 23 " (cutoff:3.500A) Processing helix chain 'HD' and resid 49 through 65 removed outlier: 4.139A pdb=" N ALAHD 55 " --> pdb=" O ALAHD 51 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLUHD 58 " --> pdb=" O LYSHD 54 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARGHD 62 " --> pdb=" O GLUHD 58 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALAHD 63 " --> pdb=" O ALAHD 59 " (cutoff:3.500A) Processing helix chain 'HD' and resid 80 through 87 removed outlier: 3.599A pdb=" N ASPHD 84 " --> pdb=" O HISHD 80 " (cutoff:3.500A) Processing helix chain 'HE' and resid 12 through 27 removed outlier: 3.680A pdb=" N ALAHE 27 " --> pdb=" O METHE 23 " (cutoff:3.500A) Processing helix chain 'HE' and resid 49 through 65 removed outlier: 3.852A pdb=" N GLUHE 58 " --> pdb=" O LYSHE 54 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALAHE 59 " --> pdb=" O ALAHE 55 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARGHE 62 " --> pdb=" O GLUHE 58 " (cutoff:3.500A) Processing helix chain 'HE' and resid 80 through 86 Processing helix chain 'HF' and resid 12 through 27 removed outlier: 3.514A pdb=" N VALHF 24 " --> pdb=" O ALAHF 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALAHF 27 " --> pdb=" O METHF 23 " (cutoff:3.500A) Processing helix chain 'HF' and resid 49 through 68 removed outlier: 3.658A pdb=" N ALAHF 55 " --> pdb=" O ALAHF 51 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLUHF 58 " --> pdb=" O LYSHF 54 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARGHF 66 " --> pdb=" O ARGHF 62 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VALHF 67 " --> pdb=" O ALAHF 63 " (cutoff:3.500A) Processing helix chain 'HF' and resid 80 through 87 removed outlier: 3.549A pdb=" N ASPHF 84 " --> pdb=" O HISHF 80 " (cutoff:3.500A) Processing helix chain 'IA' and resid 12 through 27 removed outlier: 3.626A pdb=" N METIA 16 " --> pdb=" O GLYIA 12 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VALIA 24 " --> pdb=" O ALAIA 20 " (cutoff:3.500A) Processing helix chain 'IA' and resid 49 through 65 removed outlier: 3.955A pdb=" N ALAIA 55 " --> pdb=" O ALAIA 51 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARGIA 62 " --> pdb=" O GLUIA 58 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLUIA 65 " --> pdb=" O GLNIA 61 " (cutoff:3.500A) Processing helix chain 'IA' and resid 80 through 87 Processing helix chain 'IB' and resid 12 through 27 removed outlier: 3.568A pdb=" N METIB 16 " --> pdb=" O GLYIB 12 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VALIB 24 " --> pdb=" O ALAIB 20 " (cutoff:3.500A) Processing helix chain 'IB' and resid 49 through 65 removed outlier: 4.045A pdb=" N ALAIB 55 " --> pdb=" O ALAIB 51 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLUIB 58 " --> pdb=" O LYSIB 54 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALAIB 59 " --> pdb=" O ALAIB 55 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARGIB 62 " --> pdb=" O GLUIB 58 " (cutoff:3.500A) Processing helix chain 'IB' and resid 80 through 87 removed outlier: 3.624A pdb=" N ASPIB 84 " --> pdb=" O HISIB 80 " (cutoff:3.500A) Processing helix chain 'IC' and resid 12 through 27 removed outlier: 3.562A pdb=" N METIC 16 " --> pdb=" O GLYIC 12 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VALIC 24 " --> pdb=" O ALAIC 20 " (cutoff:3.500A) Processing helix chain 'IC' and resid 49 through 65 removed outlier: 4.030A pdb=" N GLUIC 58 " --> pdb=" O LYSIC 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALAIC 59 " --> pdb=" O ALAIC 55 " (cutoff:3.500A) Processing helix chain 'IC' and resid 80 through 87 Processing helix chain 'ID' and resid 12 through 27 removed outlier: 3.530A pdb=" N ALAID 27 " --> pdb=" O METID 23 " (cutoff:3.500A) Processing helix chain 'ID' and resid 49 through 65 removed outlier: 3.696A pdb=" N ALAID 55 " --> pdb=" O ALAID 51 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALAID 59 " --> pdb=" O ALAID 55 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARGID 62 " --> pdb=" O GLUID 58 " (cutoff:3.500A) Processing helix chain 'ID' and resid 80 through 86 removed outlier: 3.543A pdb=" N ASPID 84 " --> pdb=" O HISID 80 " (cutoff:3.500A) Processing helix chain 'IE' and resid 12 through 27 removed outlier: 3.538A pdb=" N VALIE 24 " --> pdb=" O ALAIE 20 " (cutoff:3.500A) Processing helix chain 'IE' and resid 49 through 68 removed outlier: 3.942A pdb=" N GLUIE 58 " --> pdb=" O LYSIE 54 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARGIE 62 " --> pdb=" O GLUIE 58 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALAIE 63 " --> pdb=" O ALAIE 59 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARGIE 66 " --> pdb=" O ARGIE 62 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VALIE 67 " --> pdb=" O ALAIE 63 " (cutoff:3.500A) Processing helix chain 'IE' and resid 80 through 87 Processing helix chain 'IF' and resid 12 through 27 Processing helix chain 'IF' and resid 49 through 65 removed outlier: 3.812A pdb=" N ALAIF 55 " --> pdb=" O ALAIF 51 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLUIF 58 " --> pdb=" O LYSIF 54 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARGIF 62 " --> pdb=" O GLUIF 58 " (cutoff:3.500A) Processing helix chain 'IF' and resid 80 through 87 Processing helix chain 'JA' and resid 12 through 27 removed outlier: 3.554A pdb=" N METJA 16 " --> pdb=" O GLYJA 12 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VALJA 24 " --> pdb=" O ALAJA 20 " (cutoff:3.500A) Processing helix chain 'JA' and resid 49 through 59 removed outlier: 3.554A pdb=" N GLUJA 58 " --> pdb=" O LYSJA 54 " (cutoff:3.500A) Processing helix chain 'JA' and resid 80 through 87 Processing helix chain 'JB' and resid 12 through 27 removed outlier: 3.522A pdb=" N METJB 16 " --> pdb=" O GLYJB 12 " (cutoff:3.500A) Processing helix chain 'JB' and resid 49 through 65 removed outlier: 3.813A pdb=" N LYSJB 54 " --> pdb=" O VALJB 50 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALAJB 55 " --> pdb=" O ALAJB 51 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ARGJB 62 " --> pdb=" O GLUJB 58 " (cutoff:3.500A) Processing helix chain 'JB' and resid 80 through 86 Processing helix chain 'JC' and resid 12 through 27 removed outlier: 3.774A pdb=" N METJC 16 " --> pdb=" O GLYJC 12 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VALJC 24 " --> pdb=" O ALAJC 20 " (cutoff:3.500A) Processing helix chain 'JC' and resid 49 through 68 removed outlier: 4.017A pdb=" N ALAJC 55 " --> pdb=" O ALAJC 51 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLUJC 58 " --> pdb=" O LYSJC 54 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALAJC 59 " --> pdb=" O ALAJC 55 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARGJC 62 " --> pdb=" O GLUJC 58 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARGJC 66 " --> pdb=" O ARGJC 62 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VALJC 67 " --> pdb=" O ALAJC 63 " (cutoff:3.500A) Processing helix chain 'JC' and resid 80 through 87 Processing helix chain 'JD' and resid 12 through 27 removed outlier: 3.520A pdb=" N ALAJD 27 " --> pdb=" O METJD 23 " (cutoff:3.500A) Processing helix chain 'JD' and resid 49 through 61 removed outlier: 4.268A pdb=" N ALAJD 55 " --> pdb=" O ALAJD 51 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLUJD 58 " --> pdb=" O LYSJD 54 " (cutoff:3.500A) Processing helix chain 'JD' and resid 64 through 68 removed outlier: 3.587A pdb=" N GLYJD 68 " --> pdb=" O GLUJD 65 " (cutoff:3.500A) Processing helix chain 'JD' and resid 80 through 85 removed outlier: 3.873A pdb=" N ASPJD 84 " --> pdb=" O HISJD 80 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALAJD 85 " --> pdb=" O VALJD 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'JD' and resid 80 through 85' Processing helix chain 'JE' and resid 12 through 27 removed outlier: 3.614A pdb=" N METJE 16 " --> pdb=" O GLYJE 12 " (cutoff:3.500A) Processing helix chain 'JE' and resid 49 through 65 removed outlier: 3.976A pdb=" N GLUJE 58 " --> pdb=" O LYSJE 54 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALAJE 59 " --> pdb=" O ALAJE 55 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLUJE 65 " --> pdb=" O GLNJE 61 " (cutoff:3.500A) Processing helix chain 'JE' and resid 66 through 68 No H-bonds generated for 'chain 'JE' and resid 66 through 68' Processing helix chain 'JE' and resid 80 through 87 removed outlier: 3.550A pdb=" N ASPJE 84 " --> pdb=" O HISJE 80 " (cutoff:3.500A) Processing helix chain 'JF' and resid 12 through 26 removed outlier: 4.037A pdb=" N VALJF 24 " --> pdb=" O ALAJF 20 " (cutoff:3.500A) Processing helix chain 'JF' and resid 49 through 68 removed outlier: 4.197A pdb=" N GLUJF 58 " --> pdb=" O LYSJF 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARGJF 62 " --> pdb=" O GLUJF 58 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARGJF 66 " --> pdb=" O ARGJF 62 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VALJF 67 " --> pdb=" O ALAJF 63 " (cutoff:3.500A) Processing helix chain 'JF' and resid 80 through 87 removed outlier: 3.688A pdb=" N ASPJF 84 " --> pdb=" O HISJF 80 " (cutoff:3.500A) Processing helix chain 'KA' and resid 12 through 27 removed outlier: 3.608A pdb=" N METKA 16 " --> pdb=" O GLYKA 12 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VALKA 24 " --> pdb=" O ALAKA 20 " (cutoff:3.500A) Processing helix chain 'KA' and resid 49 through 64 removed outlier: 3.922A pdb=" N ALAKA 55 " --> pdb=" O ALAKA 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLUKA 58 " --> pdb=" O LYSKA 54 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALAKA 59 " --> pdb=" O ALAKA 55 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARGKA 62 " --> pdb=" O GLUKA 58 " (cutoff:3.500A) Processing helix chain 'KA' and resid 80 through 87 removed outlier: 3.549A pdb=" N ASPKA 84 " --> pdb=" O HISKA 80 " (cutoff:3.500A) Processing helix chain 'KB' and resid 12 through 27 removed outlier: 3.728A pdb=" N METKB 16 " --> pdb=" O GLYKB 12 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VALKB 24 " --> pdb=" O ALAKB 20 " (cutoff:3.500A) Processing helix chain 'KB' and resid 49 through 65 removed outlier: 3.586A pdb=" N ALAKB 59 " --> pdb=" O ALAKB 55 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARGKB 62 " --> pdb=" O GLUKB 58 " (cutoff:3.500A) Processing helix chain 'KB' and resid 80 through 85 removed outlier: 3.957A pdb=" N ASPKB 84 " --> pdb=" O HISKB 80 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALAKB 85 " --> pdb=" O VALKB 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'KB' and resid 80 through 85' Processing helix chain 'KC' and resid 12 through 27 removed outlier: 3.645A pdb=" N METKC 16 " --> pdb=" O GLYKC 12 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VALKC 24 " --> pdb=" O ALAKC 20 " (cutoff:3.500A) Processing helix chain 'KC' and resid 49 through 65 removed outlier: 3.849A pdb=" N GLUKC 58 " --> pdb=" O LYSKC 54 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALAKC 59 " --> pdb=" O ALAKC 55 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLUKC 65 " --> pdb=" O GLNKC 61 " (cutoff:3.500A) Processing helix chain 'KC' and resid 80 through 87 Processing helix chain 'KD' and resid 12 through 27 removed outlier: 3.522A pdb=" N METKD 16 " --> pdb=" O GLYKD 12 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALAKD 27 " --> pdb=" O METKD 23 " (cutoff:3.500A) Processing helix chain 'KD' and resid 49 through 65 removed outlier: 3.597A pdb=" N ALAKD 55 " --> pdb=" O ALAKD 51 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLUKD 58 " --> pdb=" O LYSKD 54 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALAKD 59 " --> pdb=" O ALAKD 55 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARGKD 62 " --> pdb=" O GLUKD 58 " (cutoff:3.500A) Processing helix chain 'KD' and resid 80 through 87 removed outlier: 3.636A pdb=" N ASPKD 84 " --> pdb=" O HISKD 80 " (cutoff:3.500A) Processing helix chain 'KE' and resid 12 through 26 removed outlier: 3.800A pdb=" N VALKE 24 " --> pdb=" O ALAKE 20 " (cutoff:3.500A) Processing helix chain 'KE' and resid 49 through 65 removed outlier: 4.089A pdb=" N GLUKE 58 " --> pdb=" O LYSKE 54 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARGKE 62 " --> pdb=" O GLUKE 58 " (cutoff:3.500A) Processing helix chain 'KE' and resid 80 through 87 Processing helix chain 'KF' and resid 12 through 27 removed outlier: 3.612A pdb=" N METKF 16 " --> pdb=" O GLYKF 12 " (cutoff:3.500A) Processing helix chain 'KF' and resid 49 through 65 removed outlier: 3.917A pdb=" N ALAKF 55 " --> pdb=" O ALAKF 51 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLUKF 58 " --> pdb=" O LYSKF 54 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARGKF 62 " --> pdb=" O GLUKF 58 " (cutoff:3.500A) Processing helix chain 'KF' and resid 80 through 87 Processing helix chain 'LA' and resid 12 through 27 removed outlier: 3.535A pdb=" N METLA 16 " --> pdb=" O GLYLA 12 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VALLA 24 " --> pdb=" O ALALA 20 " (cutoff:3.500A) Processing helix chain 'LA' and resid 49 through 65 removed outlier: 3.911A pdb=" N ARGLA 62 " --> pdb=" O GLULA 58 " (cutoff:3.500A) Processing helix chain 'LA' and resid 80 through 87 Processing helix chain 'LB' and resid 12 through 27 Processing helix chain 'LB' and resid 49 through 65 removed outlier: 3.651A pdb=" N ALALB 55 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLULB 58 " --> pdb=" O LYSLB 54 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARGLB 62 " --> pdb=" O GLULB 58 " (cutoff:3.500A) Processing helix chain 'LB' and resid 80 through 86 removed outlier: 3.542A pdb=" N ASPLB 84 " --> pdb=" O HISLB 80 " (cutoff:3.500A) Processing helix chain 'LC' and resid 12 through 27 removed outlier: 3.587A pdb=" N METLC 16 " --> pdb=" O GLYLC 12 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VALLC 24 " --> pdb=" O ALALC 20 " (cutoff:3.500A) Processing helix chain 'LC' and resid 49 through 65 removed outlier: 3.535A pdb=" N LYSLC 54 " --> pdb=" O VALLC 50 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALALC 55 " --> pdb=" O ALALC 51 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLULC 58 " --> pdb=" O LYSLC 54 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALALC 59 " --> pdb=" O ALALC 55 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARGLC 62 " --> pdb=" O GLULC 58 " (cutoff:3.500A) Processing helix chain 'LC' and resid 80 through 87 Processing helix chain 'LD' and resid 12 through 27 removed outlier: 3.533A pdb=" N METLD 16 " --> pdb=" O GLYLD 12 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VALLD 24 " --> pdb=" O ALALD 20 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALALD 27 " --> pdb=" O METLD 23 " (cutoff:3.500A) Processing helix chain 'LD' and resid 49 through 66 removed outlier: 4.367A pdb=" N ALALD 55 " --> pdb=" O ALALD 51 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLULD 58 " --> pdb=" O LYSLD 54 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARGLD 62 " --> pdb=" O GLULD 58 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARGLD 66 " --> pdb=" O ARGLD 62 " (cutoff:3.500A) Processing helix chain 'LD' and resid 80 through 87 removed outlier: 3.528A pdb=" N ASPLD 84 " --> pdb=" O HISLD 80 " (cutoff:3.500A) Processing helix chain 'LE' and resid 12 through 27 removed outlier: 3.639A pdb=" N METLE 16 " --> pdb=" O GLYLE 12 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALALE 27 " --> pdb=" O METLE 23 " (cutoff:3.500A) Processing helix chain 'LE' and resid 49 through 65 removed outlier: 3.763A pdb=" N GLULE 58 " --> pdb=" O LYSLE 54 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALALE 59 " --> pdb=" O ALALE 55 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARGLE 62 " --> pdb=" O GLULE 58 " (cutoff:3.500A) Processing helix chain 'LE' and resid 80 through 87 removed outlier: 3.518A pdb=" N ASPLE 84 " --> pdb=" O HISLE 80 " (cutoff:3.500A) Processing helix chain 'LF' and resid 12 through 27 removed outlier: 3.805A pdb=" N ALALF 27 " --> pdb=" O METLF 23 " (cutoff:3.500A) Processing helix chain 'LF' and resid 49 through 65 removed outlier: 3.818A pdb=" N ALALF 55 " --> pdb=" O ALALF 51 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLULF 58 " --> pdb=" O LYSLF 54 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLULF 65 " --> pdb=" O GLNLF 61 " (cutoff:3.500A) Processing helix chain 'LF' and resid 80 through 85 removed outlier: 3.505A pdb=" N ASPLF 84 " --> pdb=" O HISLF 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'G' and resid 66 through 82 removed outlier: 3.641A pdb=" N GLY G 82 " --> pdb=" O ARG G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 105 removed outlier: 3.744A pdb=" N LEU G 105 " --> pdb=" O TRP G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 143 removed outlier: 3.876A pdb=" N ALA G 132 " --> pdb=" O THR G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 182 removed outlier: 4.087A pdb=" N GLU G 180 " --> pdb=" O GLU G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 44 removed outlier: 3.695A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 82 removed outlier: 4.377A pdb=" N GLY H 82 " --> pdb=" O ARG H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 143 removed outlier: 3.577A pdb=" N ALA H 143 " --> pdb=" O ALA H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 183 removed outlier: 3.585A pdb=" N GLY H 183 " --> pdb=" O ARG H 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 44 removed outlier: 3.552A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 81 Processing helix chain 'I' and resid 100 through 104 removed outlier: 4.132A pdb=" N ARG I 103 " --> pdb=" O GLN I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 141 Processing helix chain 'I' and resid 167 through 180 Processing helix chain 'M' and resid 30 through 44 removed outlier: 3.608A pdb=" N ALA M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 81 Processing helix chain 'M' and resid 101 through 105 removed outlier: 4.077A pdb=" N LEU M 105 " --> pdb=" O TRP M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 129 through 141 removed outlier: 3.518A pdb=" N LYS M 141 " --> pdb=" O ASP M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 182 removed outlier: 4.055A pdb=" N GLU M 180 " --> pdb=" O GLU M 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 44 Processing helix chain 'N' and resid 66 through 82 removed outlier: 4.545A pdb=" N GLY N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 105 removed outlier: 3.945A pdb=" N LEU N 105 " --> pdb=" O TRP N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 141 Processing helix chain 'N' and resid 167 through 182 Processing helix chain 'N' and resid 196 through 200 removed outlier: 3.748A pdb=" N ARG N 200 " --> pdb=" O ASP N 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 removed outlier: 4.066A pdb=" N PHE O 8 " --> pdb=" O PRO O 5 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP O 9 " --> pdb=" O GLU O 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 5 through 9' Processing helix chain 'O' and resid 29 through 44 removed outlier: 3.667A pdb=" N ALA O 44 " --> pdb=" O ALA O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 82 removed outlier: 3.595A pdb=" N GLY O 82 " --> pdb=" O ARG O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 105 removed outlier: 4.154A pdb=" N LEU O 105 " --> pdb=" O TRP O 102 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 141 removed outlier: 3.775A pdb=" N LYS O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 183 removed outlier: 3.752A pdb=" N GLY O 183 " --> pdb=" O ARG O 179 " (cutoff:3.500A) Processing helix chain 'S' and resid 30 through 44 removed outlier: 3.815A pdb=" N ALA S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 81 Processing helix chain 'S' and resid 101 through 105 removed outlier: 3.827A pdb=" N LEU S 105 " --> pdb=" O TRP S 102 " (cutoff:3.500A) Processing helix chain 'S' and resid 129 through 141 removed outlier: 3.584A pdb=" N LYS S 141 " --> pdb=" O ASP S 137 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 182 removed outlier: 3.928A pdb=" N GLU S 180 " --> pdb=" O GLU S 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 30 through 44 Processing helix chain 'T' and resid 66 through 82 removed outlier: 3.788A pdb=" N GLY T 82 " --> pdb=" O ARG T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 129 through 143 Processing helix chain 'T' and resid 167 through 183 Processing helix chain 'T' and resid 196 through 200 removed outlier: 3.727A pdb=" N ARG T 200 " --> pdb=" O ASP T 197 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 9 removed outlier: 4.322A pdb=" N PHE U 8 " --> pdb=" O PRO U 5 " (cutoff:3.500A) Processing helix chain 'U' and resid 30 through 44 removed outlier: 3.542A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 81 Processing helix chain 'U' and resid 101 through 105 removed outlier: 3.789A pdb=" N LEU U 105 " --> pdb=" O TRP U 102 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 141 removed outlier: 4.003A pdb=" N ALA U 132 " --> pdb=" O THR U 128 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU U 140 " --> pdb=" O ALA U 136 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS U 141 " --> pdb=" O ASP U 137 " (cutoff:3.500A) Processing helix chain 'U' and resid 167 through 183 removed outlier: 3.775A pdb=" N GLY U 183 " --> pdb=" O ARG U 179 " (cutoff:3.500A) Processing helix chain 'U' and resid 196 through 200 removed outlier: 3.642A pdb=" N ARG U 200 " --> pdb=" O ASP U 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 9 removed outlier: 6.352A pdb=" N GLU A 76 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 114 removed outlier: 6.538A pdb=" N GLU A 144 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS A 111 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE A 142 " --> pdb=" O HIS A 111 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE A 113 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 140 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ARG A 177 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL A 169 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TYR A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 11 removed outlier: 4.175A pdb=" N VAL B 65 " --> pdb=" O GLU B 76 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS B 78 " --> pdb=" O PRO B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 113 removed outlier: 6.860A pdb=" N GLU B 144 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS B 111 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE B 142 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE B 113 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 140 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ARG B 177 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N VAL B 169 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 9 removed outlier: 3.798A pdb=" N VAL C 65 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS C 78 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 114 removed outlier: 5.136A pdb=" N VAL C 108 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN C 146 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR C 110 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG C 177 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL C 169 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR C 179 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 11 Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 114 removed outlier: 5.598A pdb=" N VAL D 108 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLN D 146 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR D 110 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN D 112 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D 182 " --> pdb=" O SER D 139 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ARG D 177 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL D 169 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYR D 179 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 11 removed outlier: 4.162A pdb=" N VAL E 65 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N HIS E 78 " --> pdb=" O PRO E 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 107 through 114 removed outlier: 5.364A pdb=" N VAL E 108 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN E 146 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR E 110 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN E 112 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ARG E 177 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL E 169 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR E 179 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 5 through 11 removed outlier: 4.253A pdb=" N VAL F 65 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N HIS F 78 " --> pdb=" O PRO F 63 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 107 through 108 Processing sheet with id=AB4, first strand: chain 'F' and resid 107 through 108 removed outlier: 6.440A pdb=" N ARG F 177 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL F 169 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR F 179 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'GA' and resid 31 through 36 removed outlier: 5.636A pdb=" N LEUGA 31 " --> pdb=" O ARGGA 47 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ARGGA 47 " --> pdb=" O LEUGA 31 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLYGA 33 " --> pdb=" O VALGA 45 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VALGA 45 " --> pdb=" O GLYGA 33 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALAGA 72 " --> pdb=" O GLUGA 9 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARGGA 11 " --> pdb=" O VALGA 70 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VALGA 70 " --> pdb=" O ARGGA 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'GB' and resid 30 through 38 removed outlier: 5.423A pdb=" N LEUGB 31 " --> pdb=" O ARGGB 47 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARGGB 47 " --> pdb=" O LEUGB 31 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLYGB 33 " --> pdb=" O VALGB 45 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYRGB 41 " --> pdb=" O THRGB 37 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HISGB 74 " --> pdb=" O METGB 7 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALAGB 72 " --> pdb=" O GLUGB 9 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARGGB 11 " --> pdb=" O VALGB 70 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VALGB 70 " --> pdb=" O ARGGB 11 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'GC' and resid 31 through 36 removed outlier: 5.975A pdb=" N LEUGC 31 " --> pdb=" O ARGGC 47 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARGGC 47 " --> pdb=" O LEUGC 31 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLYGC 33 " --> pdb=" O VALGC 45 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VALGC 45 " --> pdb=" O GLYGC 33 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALAGC 72 " --> pdb=" O GLUGC 9 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ARGGC 11 " --> pdb=" O VALGC 70 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VALGC 70 " --> pdb=" O ARGGC 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'GD' and resid 31 through 36 removed outlier: 4.210A pdb=" N GLYGD 33 " --> pdb=" O VALGD 45 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VALGD 45 " --> pdb=" O GLYGD 33 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALAGD 72 " --> pdb=" O GLUGD 9 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARGGD 11 " --> pdb=" O VALGD 70 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VALGD 70 " --> pdb=" O ARGGD 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'GE' and resid 31 through 36 removed outlier: 5.869A pdb=" N LEUGE 31 " --> pdb=" O ARGGE 47 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARGGE 47 " --> pdb=" O LEUGE 31 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLYGE 33 " --> pdb=" O VALGE 45 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALAGE 72 " --> pdb=" O GLUGE 9 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARGGE 11 " --> pdb=" O VALGE 70 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VALGE 70 " --> pdb=" O ARGGE 11 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'GF' and resid 31 through 36 removed outlier: 6.499A pdb=" N VALGF 45 " --> pdb=" O ILEGF 32 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N TYRGF 34 " --> pdb=" O THRGF 43 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THRGF 43 " --> pdb=" O TYRGF 34 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LYSGF 36 " --> pdb=" O TYRGF 41 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYRGF 41 " --> pdb=" O LYSGF 36 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARGGF 11 " --> pdb=" O VALGF 70 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VALGF 70 " --> pdb=" O ARGGF 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HA' and resid 30 through 38 removed outlier: 5.415A pdb=" N LEUHA 31 " --> pdb=" O ARGHA 47 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARGHA 47 " --> pdb=" O LEUHA 31 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLYHA 33 " --> pdb=" O VALHA 45 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VALHA 45 " --> pdb=" O GLYHA 33 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYRHA 41 " --> pdb=" O THRHA 37 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALAHA 72 " --> pdb=" O GLUHA 9 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARGHA 11 " --> pdb=" O VALHA 70 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VALHA 70 " --> pdb=" O ARGHA 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'HB' and resid 30 through 36 removed outlier: 5.452A pdb=" N LEUHB 31 " --> pdb=" O ARGHB 47 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARGHB 47 " --> pdb=" O LEUHB 31 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLYHB 33 " --> pdb=" O VALHB 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N METHB 7 " --> pdb=" O HISHB 74 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HISHB 74 " --> pdb=" O METHB 7 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALAHB 72 " --> pdb=" O GLUHB 9 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARGHB 11 " --> pdb=" O VALHB 70 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VALHB 70 " --> pdb=" O ARGHB 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'HC' and resid 31 through 36 removed outlier: 4.446A pdb=" N GLYHC 33 " --> pdb=" O VALHC 45 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VALHC 45 " --> pdb=" O GLYHC 33 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HISHC 74 " --> pdb=" O METHC 7 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALAHC 72 " --> pdb=" O GLUHC 9 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARGHC 11 " --> pdb=" O VALHC 70 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VALHC 70 " --> pdb=" O ARGHC 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'HD' and resid 30 through 38 removed outlier: 7.245A pdb=" N VALHD 45 " --> pdb=" O ILEHD 32 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYRHD 34 " --> pdb=" O THRHD 43 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THRHD 43 " --> pdb=" O TYRHD 34 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LYSHD 36 " --> pdb=" O TYRHD 41 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N TYRHD 41 " --> pdb=" O LYSHD 36 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HISHD 74 " --> pdb=" O METHD 7 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALAHD 72 " --> pdb=" O GLUHD 9 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARGHD 11 " --> pdb=" O VALHD 70 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VALHD 70 " --> pdb=" O ARGHD 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'HE' and resid 30 through 36 removed outlier: 5.522A pdb=" N LEUHE 31 " --> pdb=" O ARGHE 47 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARGHE 47 " --> pdb=" O LEUHE 31 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLYHE 33 " --> pdb=" O VALHE 45 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALAHE 72 " --> pdb=" O GLUHE 9 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARGHE 11 " --> pdb=" O VALHE 70 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VALHE 70 " --> pdb=" O ARGHE 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'HF' and resid 30 through 36 removed outlier: 5.505A pdb=" N LEUHF 31 " --> pdb=" O ARGHF 47 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ARGHF 47 " --> pdb=" O LEUHF 31 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLYHF 33 " --> pdb=" O VALHF 45 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VALHF 45 " --> pdb=" O GLYHF 33 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALAHF 72 " --> pdb=" O GLUHF 9 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARGHF 11 " --> pdb=" O VALHF 70 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VALHF 70 " --> pdb=" O ARGHF 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'IA' and resid 30 through 36 removed outlier: 5.362A pdb=" N LEUIA 31 " --> pdb=" O ARGIA 47 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARGIA 47 " --> pdb=" O LEUIA 31 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLYIA 33 " --> pdb=" O VALIA 45 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALIA 45 " --> pdb=" O GLYIA 33 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALAIA 72 " --> pdb=" O GLUIA 9 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARGIA 11 " --> pdb=" O VALIA 70 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VALIA 70 " --> pdb=" O ARGIA 11 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'IB' and resid 30 through 38 removed outlier: 5.209A pdb=" N LEUIB 31 " --> pdb=" O ARGIB 47 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ARGIB 47 " --> pdb=" O LEUIB 31 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLYIB 33 " --> pdb=" O VALIB 45 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THRIB 37 " --> pdb=" O TYRIB 41 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYRIB 41 " --> pdb=" O THRIB 37 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEUIB 5 " --> pdb=" O VALIB 75 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VALIB 75 " --> pdb=" O LEUIB 5 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N METIB 7 " --> pdb=" O VALIB 73 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VALIB 73 " --> pdb=" O METIB 7 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLUIB 9 " --> pdb=" O VALIB 71 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'IC' and resid 30 through 36 removed outlier: 5.719A pdb=" N LEUIC 31 " --> pdb=" O ARGIC 47 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARGIC 47 " --> pdb=" O LEUIC 31 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLYIC 33 " --> pdb=" O VALIC 45 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VALIC 45 " --> pdb=" O GLYIC 33 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALAIC 72 " --> pdb=" O GLUIC 9 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARGIC 11 " --> pdb=" O VALIC 70 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VALIC 70 " --> pdb=" O ARGIC 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'ID' and resid 30 through 36 removed outlier: 5.634A pdb=" N LEUID 31 " --> pdb=" O ARGID 47 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ARGID 47 " --> pdb=" O LEUID 31 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLYID 33 " --> pdb=" O VALID 45 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VALID 45 " --> pdb=" O GLYID 33 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HISID 74 " --> pdb=" O METID 7 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALAID 72 " --> pdb=" O GLUID 9 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARGID 11 " --> pdb=" O VALID 70 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VALID 70 " --> pdb=" O ARGID 11 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'IE' and resid 30 through 36 removed outlier: 5.532A pdb=" N LEUIE 31 " --> pdb=" O ARGIE 47 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARGIE 47 " --> pdb=" O LEUIE 31 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLYIE 33 " --> pdb=" O VALIE 45 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEUIE 5 " --> pdb=" O VALIE 75 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VALIE 75 " --> pdb=" O LEUIE 5 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N METIE 7 " --> pdb=" O VALIE 73 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VALIE 73 " --> pdb=" O METIE 7 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLUIE 9 " --> pdb=" O VALIE 71 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'IF' and resid 31 through 36 removed outlier: 5.862A pdb=" N LEUIF 31 " --> pdb=" O ARGIF 47 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ARGIF 47 " --> pdb=" O LEUIF 31 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLYIF 33 " --> pdb=" O VALIF 45 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VALIF 45 " --> pdb=" O GLYIF 33 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ARGIF 11 " --> pdb=" O VALIF 70 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VALIF 70 " --> pdb=" O ARGIF 11 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'JA' and resid 30 through 36 removed outlier: 5.407A pdb=" N LEUJA 31 " --> pdb=" O ARGJA 47 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARGJA 47 " --> pdb=" O LEUJA 31 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLYJA 33 " --> pdb=" O VALJA 45 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VALJA 45 " --> pdb=" O GLYJA 33 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEUJA 5 " --> pdb=" O VALJA 75 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VALJA 75 " --> pdb=" O LEUJA 5 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N METJA 7 " --> pdb=" O VALJA 73 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VALJA 73 " --> pdb=" O METJA 7 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLUJA 9 " --> pdb=" O VALJA 71 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'JB' and resid 31 through 36 removed outlier: 5.852A pdb=" N LEUJB 31 " --> pdb=" O ARGJB 47 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARGJB 47 " --> pdb=" O LEUJB 31 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLYJB 33 " --> pdb=" O VALJB 45 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEUJB 5 " --> pdb=" O VALJB 75 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VALJB 75 " --> pdb=" O LEUJB 5 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N METJB 7 " --> pdb=" O VALJB 73 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VALJB 73 " --> pdb=" O METJB 7 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLUJB 9 " --> pdb=" O VALJB 71 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'JC' and resid 31 through 36 removed outlier: 3.968A pdb=" N GLYJC 33 " --> pdb=" O VALJC 45 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HISJC 74 " --> pdb=" O METJC 7 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'JD' and resid 30 through 36 removed outlier: 5.282A pdb=" N LEUJD 31 " --> pdb=" O ARGJD 47 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARGJD 47 " --> pdb=" O LEUJD 31 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLYJD 33 " --> pdb=" O VALJD 45 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VALJD 45 " --> pdb=" O GLYJD 33 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HISJD 74 " --> pdb=" O METJD 7 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALAJD 72 " --> pdb=" O GLUJD 9 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARGJD 11 " --> pdb=" O VALJD 70 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VALJD 70 " --> pdb=" O ARGJD 11 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'JE' and resid 30 through 36 removed outlier: 7.614A pdb=" N VALJE 45 " --> pdb=" O ILEJE 32 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYRJE 34 " --> pdb=" O THRJE 43 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THRJE 43 " --> pdb=" O TYRJE 34 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LYSJE 36 " --> pdb=" O TYRJE 41 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N TYRJE 41 " --> pdb=" O LYSJE 36 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLYJE 48 " --> pdb=" O ALAJE 4 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALAJE 72 " --> pdb=" O GLUJE 9 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARGJE 11 " --> pdb=" O VALJE 70 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VALJE 70 " --> pdb=" O ARGJE 11 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'JF' and resid 30 through 36 removed outlier: 5.544A pdb=" N LEUJF 31 " --> pdb=" O ARGJF 47 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ARGJF 47 " --> pdb=" O LEUJF 31 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLYJF 33 " --> pdb=" O VALJF 45 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ARGJF 11 " --> pdb=" O VALJF 70 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N VALJF 70 " --> pdb=" O ARGJF 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'KA' and resid 31 through 36 removed outlier: 5.860A pdb=" N LEUKA 31 " --> pdb=" O ARGKA 47 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARGKA 47 " --> pdb=" O LEUKA 31 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLYKA 33 " --> pdb=" O VALKA 45 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VALKA 45 " --> pdb=" O GLYKA 33 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEUKA 5 " --> pdb=" O VALKA 75 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VALKA 75 " --> pdb=" O LEUKA 5 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N METKA 7 " --> pdb=" O VALKA 73 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N VALKA 73 " --> pdb=" O METKA 7 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLUKA 9 " --> pdb=" O VALKA 71 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLUKA 69 " --> pdb=" O ARGKA 11 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'KB' and resid 30 through 36 removed outlier: 7.087A pdb=" N VALKB 45 " --> pdb=" O ILEKB 32 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYRKB 34 " --> pdb=" O THRKB 43 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THRKB 43 " --> pdb=" O TYRKB 34 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYSKB 36 " --> pdb=" O TYRKB 41 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYRKB 41 " --> pdb=" O LYSKB 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALAKB 72 " --> pdb=" O GLUKB 9 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ARGKB 11 " --> pdb=" O VALKB 70 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VALKB 70 " --> pdb=" O ARGKB 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'KC' and resid 30 through 36 removed outlier: 5.569A pdb=" N LEUKC 31 " --> pdb=" O ARGKC 47 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARGKC 47 " --> pdb=" O LEUKC 31 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLYKC 33 " --> pdb=" O VALKC 45 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALKC 45 " --> pdb=" O GLYKC 33 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEUKC 5 " --> pdb=" O VALKC 75 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VALKC 75 " --> pdb=" O LEUKC 5 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N METKC 7 " --> pdb=" O VALKC 73 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VALKC 73 " --> pdb=" O METKC 7 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLUKC 9 " --> pdb=" O VALKC 71 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'KD' and resid 30 through 36 removed outlier: 5.651A pdb=" N LEUKD 31 " --> pdb=" O ARGKD 47 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARGKD 47 " --> pdb=" O LEUKD 31 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLYKD 33 " --> pdb=" O VALKD 45 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VALKD 45 " --> pdb=" O GLYKD 33 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HISKD 74 " --> pdb=" O METKD 7 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALAKD 72 " --> pdb=" O GLUKD 9 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARGKD 11 " --> pdb=" O VALKD 70 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VALKD 70 " --> pdb=" O ARGKD 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'KE' and resid 30 through 36 removed outlier: 7.145A pdb=" N VALKE 45 " --> pdb=" O ILEKE 32 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYRKE 34 " --> pdb=" O THRKE 43 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THRKE 43 " --> pdb=" O TYRKE 34 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LYSKE 36 " --> pdb=" O TYRKE 41 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N TYRKE 41 " --> pdb=" O LYSKE 36 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALAKE 72 " --> pdb=" O GLUKE 9 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARGKE 11 " --> pdb=" O VALKE 70 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VALKE 70 " --> pdb=" O ARGKE 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'KF' and resid 31 through 36 removed outlier: 5.755A pdb=" N LEUKF 31 " --> pdb=" O ARGKF 47 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARGKF 47 " --> pdb=" O LEUKF 31 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLYKF 33 " --> pdb=" O VALKF 45 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARGKF 11 " --> pdb=" O VALKF 70 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VALKF 70 " --> pdb=" O ARGKF 11 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LA' and resid 30 through 36 removed outlier: 5.662A pdb=" N LEULA 31 " --> pdb=" O ARGLA 47 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ARGLA 47 " --> pdb=" O LEULA 31 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLYLA 33 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALLA 45 " --> pdb=" O GLYLA 33 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALALA 72 " --> pdb=" O GLULA 9 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARGLA 11 " --> pdb=" O VALLA 70 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VALLA 70 " --> pdb=" O ARGLA 11 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LB' and resid 30 through 36 removed outlier: 5.980A pdb=" N LEULB 31 " --> pdb=" O ARGLB 47 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARGLB 47 " --> pdb=" O LEULB 31 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLYLB 33 " --> pdb=" O VALLB 45 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VALLB 45 " --> pdb=" O GLYLB 33 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLYLB 48 " --> pdb=" O ALALB 4 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEULB 5 " --> pdb=" O VALLB 75 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N VALLB 75 " --> pdb=" O LEULB 5 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N METLB 7 " --> pdb=" O VALLB 73 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VALLB 73 " --> pdb=" O METLB 7 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLULB 9 " --> pdb=" O VALLB 71 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LC' and resid 30 through 36 removed outlier: 5.810A pdb=" N LEULC 31 " --> pdb=" O ARGLC 47 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARGLC 47 " --> pdb=" O LEULC 31 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLYLC 33 " --> pdb=" O VALLC 45 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VALLC 45 " --> pdb=" O GLYLC 33 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LD' and resid 30 through 38 removed outlier: 5.589A pdb=" N LEULD 31 " --> pdb=" O ARGLD 47 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARGLD 47 " --> pdb=" O LEULD 31 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLYLD 33 " --> pdb=" O VALLD 45 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VALLD 45 " --> pdb=" O GLYLD 33 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THRLD 37 " --> pdb=" O TYRLD 41 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N TYRLD 41 " --> pdb=" O THRLD 37 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALALD 72 " --> pdb=" O GLULD 9 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARGLD 11 " --> pdb=" O VALLD 70 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VALLD 70 " --> pdb=" O ARGLD 11 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LE' and resid 30 through 36 removed outlier: 5.531A pdb=" N LEULE 31 " --> pdb=" O ARGLE 47 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARGLE 47 " --> pdb=" O LEULE 31 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLYLE 33 " --> pdb=" O VALLE 45 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VALLE 45 " --> pdb=" O GLYLE 33 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALALE 72 " --> pdb=" O GLULE 9 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARGLE 11 " --> pdb=" O VALLE 70 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VALLE 70 " --> pdb=" O ARGLE 11 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'LF' and resid 30 through 36 removed outlier: 7.553A pdb=" N VALLF 45 " --> pdb=" O ILELF 32 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYRLF 34 " --> pdb=" O THRLF 43 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THRLF 43 " --> pdb=" O TYRLF 34 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYSLF 36 " --> pdb=" O TYRLF 41 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYRLF 41 " --> pdb=" O LYSLF 36 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALALF 72 " --> pdb=" O GLULF 9 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARGLF 11 " --> pdb=" O VALLF 70 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VALLF 70 " --> pdb=" O ARGLF 11 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 47 through 54 removed outlier: 6.443A pdb=" N MET G 62 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER G 51 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU G 60 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LYS G 58 " --> pdb=" O PRO G 53 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 146 through 152 removed outlier: 5.937A pdb=" N LEU G 147 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR G 165 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP G 149 " --> pdb=" O THR G 163 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 47 through 54 removed outlier: 5.236A pdb=" N LEU H 48 " --> pdb=" O ARG H 64 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG H 64 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY H 65 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 146 through 152 removed outlier: 6.727A pdb=" N THR H 163 " --> pdb=" O ARG H 148 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N MET H 150 " --> pdb=" O PHE H 161 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE H 161 " --> pdb=" O MET H 150 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL H 121 " --> pdb=" O CYS H 191 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N CYS H 191 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE H 123 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU H 189 " --> pdb=" O ILE H 123 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU H 125 " --> pdb=" O LEU H 187 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 47 through 54 removed outlier: 6.503A pdb=" N MET I 62 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER I 51 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU I 60 " --> pdb=" O SER I 51 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS I 58 " --> pdb=" O PRO I 53 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY I 65 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 146 through 152 removed outlier: 3.773A pdb=" N VAL I 146 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR I 163 " --> pdb=" O ARG I 148 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET I 150 " --> pdb=" O PHE I 161 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE I 161 " --> pdb=" O MET I 150 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL I 121 " --> pdb=" O CYS I 191 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N CYS I 191 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE I 123 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU I 189 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU I 125 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 48 through 54 Processing sheet with id=AG3, first strand: chain 'M' and resid 146 through 152 removed outlier: 3.665A pdb=" N VAL M 146 " --> pdb=" O THR M 165 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR M 163 " --> pdb=" O ARG M 148 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET M 150 " --> pdb=" O PHE M 161 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE M 161 " --> pdb=" O MET M 150 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL M 121 " --> pdb=" O CYS M 191 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N CYS M 191 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE M 123 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU M 189 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU M 125 " --> pdb=" O LEU M 187 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 47 through 54 removed outlier: 6.519A pdb=" N MET N 62 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER N 51 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU N 60 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS N 58 " --> pdb=" O PRO N 53 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 146 through 152 removed outlier: 6.888A pdb=" N THR N 163 " --> pdb=" O ARG N 148 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N MET N 150 " --> pdb=" O PHE N 161 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE N 161 " --> pdb=" O MET N 150 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL N 121 " --> pdb=" O CYS N 191 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N CYS N 191 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE N 123 " --> pdb=" O LEU N 189 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LEU N 189 " --> pdb=" O ILE N 123 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLU N 125 " --> pdb=" O LEU N 187 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 47 through 54 removed outlier: 5.000A pdb=" N LEU O 48 " --> pdb=" O ARG O 64 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARG O 64 " --> pdb=" O LEU O 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 146 through 152 removed outlier: 6.733A pdb=" N THR O 163 " --> pdb=" O ARG O 148 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET O 150 " --> pdb=" O PHE O 161 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N PHE O 161 " --> pdb=" O MET O 150 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL O 121 " --> pdb=" O ILE O 192 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU O 125 " --> pdb=" O GLU O 188 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU O 188 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 47 through 54 removed outlier: 5.326A pdb=" N LEU S 48 " --> pdb=" O ARG S 64 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG S 64 " --> pdb=" O LEU S 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 146 through 152 removed outlier: 5.871A pdb=" N LEU S 147 " --> pdb=" O THR S 165 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR S 165 " --> pdb=" O LEU S 147 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASP S 149 " --> pdb=" O THR S 163 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL S 121 " --> pdb=" O CYS S 191 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N CYS S 191 " --> pdb=" O VAL S 121 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE S 123 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU S 189 " --> pdb=" O ILE S 123 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLU S 125 " --> pdb=" O LEU S 187 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'T' and resid 47 through 54 removed outlier: 6.686A pdb=" N MET T 62 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER T 51 " --> pdb=" O LEU T 60 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU T 60 " --> pdb=" O SER T 51 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS T 58 " --> pdb=" O PRO T 53 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY T 65 " --> pdb=" O ALA T 21 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'T' and resid 146 through 152 removed outlier: 6.200A pdb=" N LEU T 147 " --> pdb=" O THR T 165 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR T 165 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP T 149 " --> pdb=" O THR T 163 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL T 121 " --> pdb=" O CYS T 191 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N CYS T 191 " --> pdb=" O VAL T 121 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE T 123 " --> pdb=" O LEU T 189 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU T 189 " --> pdb=" O ILE T 123 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU T 125 " --> pdb=" O LEU T 187 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'U' and resid 47 through 54 removed outlier: 5.069A pdb=" N LEU U 48 " --> pdb=" O ARG U 64 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ARG U 64 " --> pdb=" O LEU U 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'U' and resid 146 through 151 removed outlier: 6.819A pdb=" N THR U 163 " --> pdb=" O ARG U 148 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N MET U 150 " --> pdb=" O PHE U 161 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE U 161 " --> pdb=" O MET U 150 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL U 121 " --> pdb=" O CYS U 191 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N CYS U 191 " --> pdb=" O VAL U 121 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE U 123 " --> pdb=" O LEU U 189 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LEU U 189 " --> pdb=" O ILE U 123 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLU U 125 " --> pdb=" O LEU U 187 " (cutoff:3.500A) 2489 hydrogen bonds defined for protein. 7071 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: 12.94 Time building geometry restraints manager: 5.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15640 1.34 - 1.46: 6216 1.46 - 1.57: 24635 1.57 - 1.69: 0 1.69 - 1.81: 369 Bond restraints: 46860 Sorted by residual: bond pdb=" C ALALC 86 " pdb=" N LEULC 87 " ideal model delta sigma weight residual 1.331 1.252 0.079 2.07e-02 2.33e+03 1.46e+01 bond pdb=" CA PRO O 144 " pdb=" CB PRO O 144 " ideal model delta sigma weight residual 1.531 1.512 0.019 6.20e-03 2.60e+04 9.80e+00 bond pdb=" C ALAKB 86 " pdb=" N LEUKB 87 " ideal model delta sigma weight residual 1.331 1.267 0.064 2.07e-02 2.33e+03 9.48e+00 bond pdb=" CG LEUKC 89 " pdb=" CD1 LEUKC 89 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.94e+00 bond pdb=" C PHE A 29 " pdb=" N LEU A 30 " ideal model delta sigma weight residual 1.340 1.230 0.110 5.87e-02 2.90e+02 3.50e+00 ... (remaining 46855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 60394 1.77 - 3.54: 2873 3.54 - 5.31: 302 5.31 - 7.08: 62 7.08 - 8.85: 14 Bond angle restraints: 63645 Sorted by residual: angle pdb=" C GLU A 69 " pdb=" N ARG A 70 " pdb=" CA ARG A 70 " ideal model delta sigma weight residual 120.82 128.36 -7.54 1.50e+00 4.44e-01 2.53e+01 angle pdb=" CA GLYIF 48 " pdb=" C GLYIF 48 " pdb=" N ASPIF 49 " ideal model delta sigma weight residual 115.22 119.43 -4.21 1.15e+00 7.56e-01 1.34e+01 angle pdb=" C ASPKD 49 " pdb=" N VALKD 50 " pdb=" CA VALKD 50 " ideal model delta sigma weight residual 120.46 125.41 -4.95 1.37e+00 5.33e-01 1.31e+01 angle pdb=" C ILE B 114 " pdb=" N ARG B 115 " pdb=" CA ARG B 115 " ideal model delta sigma weight residual 121.56 127.11 -5.55 1.56e+00 4.11e-01 1.26e+01 angle pdb=" N GLYKF 33 " pdb=" CA GLYKF 33 " pdb=" C GLYKF 33 " ideal model delta sigma weight residual 111.56 115.13 -3.57 1.01e+00 9.80e-01 1.25e+01 ... (remaining 63640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 27232 15.18 - 30.36: 917 30.36 - 45.55: 241 45.55 - 60.73: 20 60.73 - 75.91: 12 Dihedral angle restraints: 28422 sinusoidal: 10638 harmonic: 17784 Sorted by residual: dihedral pdb=" CA ASPJF 49 " pdb=" C ASPJF 49 " pdb=" N VALJF 50 " pdb=" CA VALJF 50 " ideal model delta harmonic sigma weight residual -180.00 -148.36 -31.64 0 5.00e+00 4.00e-02 4.00e+01 dihedral pdb=" CA ASPHD 49 " pdb=" C ASPHD 49 " pdb=" N VALHD 50 " pdb=" CA VALHD 50 " ideal model delta harmonic sigma weight residual 180.00 -151.14 -28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASPID 49 " pdb=" C ASPID 49 " pdb=" N VALID 50 " pdb=" CA VALID 50 " ideal model delta harmonic sigma weight residual -180.00 -152.19 -27.81 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 28419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 6055 0.064 - 0.127: 1364 0.127 - 0.191: 178 0.191 - 0.255: 35 0.255 - 0.319: 6 Chirality restraints: 7638 Sorted by residual: chirality pdb=" CB ILE U 122 " pdb=" CA ILE U 122 " pdb=" CG1 ILE U 122 " pdb=" CG2 ILE U 122 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE G 122 " pdb=" CA ILE G 122 " pdb=" CG1 ILE G 122 " pdb=" CG2 ILE G 122 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB ILE N 122 " pdb=" CA ILE N 122 " pdb=" CG1 ILE N 122 " pdb=" CG2 ILE N 122 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 7635 not shown) Planarity restraints: 8340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 122 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.57e+00 pdb=" C THR E 122 " -0.048 2.00e-02 2.50e+03 pdb=" O THR E 122 " 0.018 2.00e-02 2.50e+03 pdb=" N GLN E 123 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 114 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.00e+00 pdb=" C ILE B 114 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE B 114 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG B 115 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG I 52 " 0.039 5.00e-02 4.00e+02 5.82e-02 5.41e+00 pdb=" N PRO I 53 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO I 53 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO I 53 " 0.032 5.00e-02 4.00e+02 ... (remaining 8337 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 8335 2.77 - 3.30: 41257 3.30 - 3.83: 77093 3.83 - 4.37: 87350 4.37 - 4.90: 156250 Nonbonded interactions: 370285 Sorted by model distance: nonbonded pdb=" OE1 GLUKE 9 " pdb=" OG1 THRKE 43 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASP T 149 " pdb=" OG1 THR T 163 " model vdw 2.254 3.040 nonbonded pdb=" OE1 GLUGE 9 " pdb=" OG1 THRGE 43 " model vdw 2.255 3.040 nonbonded pdb=" OG SER O 120 " pdb=" O ILE O 192 " model vdw 2.255 3.040 nonbonded pdb=" OD1 ASP U 149 " pdb=" OG1 THR U 163 " model vdw 2.256 3.040 ... (remaining 370280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 4 through 204) selection = (chain 'B' and resid 4 through 204) selection = (chain 'C' and resid 4 through 204) selection = (chain 'D' and resid 4 through 204) selection = (chain 'E' and resid 4 through 204) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = (chain 'I' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'M' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'N' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'O' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'S' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'T' and (resid 5 through 82 or resid 87 through 205)) selection = (chain 'U' and (resid 5 through 83 or resid 88 through 205)) } ncs_group { reference = chain 'GA' selection = chain 'GB' selection = chain 'GC' selection = chain 'GD' selection = chain 'GE' selection = chain 'GF' selection = chain 'HA' selection = chain 'HB' selection = chain 'HC' selection = chain 'HD' selection = chain 'HE' selection = chain 'HF' selection = chain 'IA' selection = chain 'IB' selection = chain 'IC' selection = chain 'ID' selection = chain 'IE' selection = chain 'IF' selection = chain 'JA' selection = chain 'JB' selection = chain 'JC' selection = chain 'JD' selection = chain 'JE' selection = chain 'JF' selection = chain 'KA' selection = chain 'KB' selection = chain 'KC' selection = chain 'KD' selection = chain 'KE' selection = chain 'KF' selection = chain 'LA' selection = chain 'LB' selection = chain 'LC' selection = chain 'LD' selection = chain 'LE' selection = chain 'LF' } 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: 12.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 1.000 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 45.770 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.290 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 46860 Z= 0.318 Angle : 0.860 8.849 63645 Z= 0.478 Chirality : 0.055 0.319 7638 Planarity : 0.007 0.058 8340 Dihedral : 9.184 75.910 16998 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.31 % Allowed : 3.42 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.98 (0.09), residues: 6183 helix: -3.15 (0.07), residues: 2372 sheet: -1.18 (0.13), residues: 1509 loop : -2.85 (0.11), residues: 2302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGIE 47 TYR 0.033 0.003 TYR F 72 PHE 0.030 0.004 PHE G 162 TRP 0.015 0.003 TRP A 39 HIS 0.010 0.002 HISGB 74 Details of bonding type rmsd covalent geometry : bond 0.00758 (46860) covalent geometry : angle 0.85974 (63645) hydrogen bonds : bond 0.14109 ( 2487) hydrogen bonds : angle 6.34248 ( 7071) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1803 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 1789 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8884 (m) cc_final: 0.8392 (m) REVERT: A 115 ARG cc_start: 0.8450 (mmt180) cc_final: 0.8040 (mmt180) REVERT: A 156 ASN cc_start: 0.8605 (t0) cc_final: 0.8287 (t0) REVERT: A 175 PHE cc_start: 0.7755 (m-80) cc_final: 0.7517 (m-80) REVERT: B 7 THR cc_start: 0.7908 (m) cc_final: 0.7257 (p) REVERT: B 8 TYR cc_start: 0.8420 (t80) cc_final: 0.7842 (t80) REVERT: B 20 THR cc_start: 0.8711 (m) cc_final: 0.8287 (m) REVERT: B 29 PHE cc_start: 0.8700 (m-80) cc_final: 0.8495 (m-80) REVERT: B 67 VAL cc_start: 0.8964 (t) cc_final: 0.8650 (p) REVERT: B 121 GLN cc_start: 0.8536 (tt0) cc_final: 0.8038 (tt0) REVERT: B 128 ASN cc_start: 0.8546 (t0) cc_final: 0.8184 (t0) REVERT: B 163 ASN cc_start: 0.7836 (t0) cc_final: 0.7629 (t0) REVERT: B 188 ASP cc_start: 0.8506 (t0) cc_final: 0.8202 (t70) REVERT: C 128 ASN cc_start: 0.8725 (t0) cc_final: 0.8332 (t0) REVERT: D 8 TYR cc_start: 0.8905 (t80) cc_final: 0.8689 (t80) REVERT: D 27 ARG cc_start: 0.7514 (mmt90) cc_final: 0.7313 (mtp-110) REVERT: D 42 ILE cc_start: 0.9215 (pt) cc_final: 0.8936 (pt) REVERT: D 67 VAL cc_start: 0.9243 (t) cc_final: 0.8859 (m) REVERT: D 72 TYR cc_start: 0.6690 (m-80) cc_final: 0.6311 (m-80) REVERT: D 95 LYS cc_start: 0.8745 (tppt) cc_final: 0.8107 (tppt) REVERT: D 113 ILE cc_start: 0.9369 (mt) cc_final: 0.9067 (pt) REVERT: D 152 VAL cc_start: 0.8998 (m) cc_final: 0.8788 (p) REVERT: E 7 THR cc_start: 0.8707 (m) cc_final: 0.8478 (p) REVERT: E 39 TRP cc_start: 0.7716 (m100) cc_final: 0.6217 (m100) REVERT: E 66 GLN cc_start: 0.9219 (tm130) cc_final: 0.8592 (tm-30) REVERT: E 80 PHE cc_start: 0.9032 (m-80) cc_final: 0.8775 (m-80) REVERT: E 95 LYS cc_start: 0.9251 (tppt) cc_final: 0.8675 (tptp) REVERT: E 109 MET cc_start: 0.8081 (mpm) cc_final: 0.7872 (mpp) REVERT: E 128 ASN cc_start: 0.8534 (t0) cc_final: 0.8142 (t0) REVERT: E 152 VAL cc_start: 0.8607 (m) cc_final: 0.8293 (p) REVERT: F 95 LYS cc_start: 0.9121 (tptp) cc_final: 0.8467 (tptp) REVERT: F 113 ILE cc_start: 0.9193 (mt) cc_final: 0.8932 (pt) REVERT: F 133 MET cc_start: 0.8253 (mtm) cc_final: 0.7960 (mtm) REVERT: F 145 THR cc_start: 0.9541 (p) cc_final: 0.9171 (p) REVERT: GA 16 MET cc_start: 0.9277 (tmm) cc_final: 0.8676 (tmm) REVERT: GA 32 ILE cc_start: 0.8890 (pp) cc_final: 0.8622 (pp) REVERT: GA 43 THR cc_start: 0.9239 (m) cc_final: 0.9028 (p) REVERT: GB 18 GLU cc_start: 0.8947 (tp30) cc_final: 0.8412 (tp30) REVERT: GB 21 ASP cc_start: 0.9042 (t70) cc_final: 0.8508 (t0) REVERT: GB 28 LYS cc_start: 0.8377 (tmmt) cc_final: 0.7569 (mptt) REVERT: GB 73 VAL cc_start: 0.8706 (t) cc_final: 0.7992 (t) REVERT: GB 84 ASP cc_start: 0.8758 (m-30) cc_final: 0.8469 (m-30) REVERT: GC 28 LYS cc_start: 0.8633 (ttpp) cc_final: 0.7906 (mmtt) REVERT: GC 43 THR cc_start: 0.9113 (m) cc_final: 0.8909 (p) REVERT: GC 82 ASN cc_start: 0.8823 (t160) cc_final: 0.8361 (t0) REVERT: GD 62 ARG cc_start: 0.9006 (ttp-110) cc_final: 0.8539 (mtm110) REVERT: GE 32 ILE cc_start: 0.9312 (pp) cc_final: 0.8016 (pp) REVERT: GF 18 GLU cc_start: 0.8822 (tp30) cc_final: 0.8477 (tp30) REVERT: GF 54 LYS cc_start: 0.8564 (tttp) cc_final: 0.8106 (ttpp) REVERT: GF 73 VAL cc_start: 0.9457 (t) cc_final: 0.9247 (m) REVERT: GF 92 THR cc_start: 0.8569 (m) cc_final: 0.8314 (p) REVERT: HA 43 THR cc_start: 0.9273 (m) cc_final: 0.8723 (p) REVERT: HA 61 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8154 (tp40) REVERT: HB 21 ASP cc_start: 0.8534 (t70) cc_final: 0.8282 (t0) REVERT: HB 28 LYS cc_start: 0.8925 (ttpp) cc_final: 0.8567 (ttmm) REVERT: HB 78 ARG cc_start: 0.9078 (ttt90) cc_final: 0.8761 (tpp80) REVERT: HB 92 THR cc_start: 0.8667 (m) cc_final: 0.8246 (p) REVERT: HC 8 ILE cc_start: 0.9032 (mm) cc_final: 0.8763 (tp) REVERT: HC 16 MET cc_start: 0.7994 (tmm) cc_final: 0.7759 (tmm) REVERT: HC 21 ASP cc_start: 0.8819 (t70) cc_final: 0.8447 (t0) REVERT: HC 28 LYS cc_start: 0.7977 (ttpt) cc_final: 0.7540 (mmtt) REVERT: HC 34 TYR cc_start: 0.8429 (p90) cc_final: 0.8217 (p90) REVERT: HD 3 ASP cc_start: 0.8011 (m-30) cc_final: 0.7723 (m-30) REVERT: HD 43 THR cc_start: 0.9593 (m) cc_final: 0.9347 (p) REVERT: HD 78 ARG cc_start: 0.8791 (tmt90) cc_final: 0.7470 (ptp-170) REVERT: HE 16 MET cc_start: 0.8378 (tmm) cc_final: 0.8046 (tmm) REVERT: HE 28 LYS cc_start: 0.9210 (tmmt) cc_final: 0.8903 (tttp) REVERT: HE 30 GLU cc_start: 0.8487 (tt0) cc_final: 0.8150 (tt0) REVERT: HE 43 THR cc_start: 0.9494 (m) cc_final: 0.9228 (p) REVERT: HE 78 ARG cc_start: 0.8248 (tpt170) cc_final: 0.7292 (ptt90) REVERT: HE 84 ASP cc_start: 0.8650 (m-30) cc_final: 0.8329 (p0) REVERT: HF 32 ILE cc_start: 0.9218 (pp) cc_final: 0.8937 (pp) REVERT: HF 43 THR cc_start: 0.8967 (m) cc_final: 0.8519 (p) REVERT: HF 61 GLN cc_start: 0.8975 (tt0) cc_final: 0.8401 (tt0) REVERT: HF 65 GLU cc_start: 0.8737 (mp0) cc_final: 0.8318 (mp0) REVERT: IA 43 THR cc_start: 0.9178 (m) cc_final: 0.8703 (p) REVERT: IB 21 ASP cc_start: 0.8663 (t70) cc_final: 0.8134 (t0) REVERT: IB 78 ARG cc_start: 0.8455 (ttp-170) cc_final: 0.7892 (ttp80) REVERT: IC 5 LEU cc_start: 0.8727 (tp) cc_final: 0.8365 (tp) REVERT: IC 16 MET cc_start: 0.8730 (tmm) cc_final: 0.8479 (tmm) REVERT: IC 35 GLU cc_start: 0.8306 (tp30) cc_final: 0.7999 (tp30) REVERT: IC 43 THR cc_start: 0.9176 (m) cc_final: 0.8894 (p) REVERT: IC 62 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.8114 (mtp-110) REVERT: ID 16 MET cc_start: 0.8886 (tmm) cc_final: 0.8608 (tmm) REVERT: ID 31 LEU cc_start: 0.8957 (tp) cc_final: 0.8756 (tt) REVERT: ID 43 THR cc_start: 0.9492 (m) cc_final: 0.9288 (p) REVERT: IF 9 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8257 (tm-30) REVERT: IF 34 TYR cc_start: 0.8257 (p90) cc_final: 0.8048 (p90) REVERT: IF 80 HIS cc_start: 0.8599 (t-90) cc_final: 0.8398 (t-90) REVERT: JA 16 MET cc_start: 0.9069 (tmm) cc_final: 0.8756 (tmm) REVERT: JB 11 ARG cc_start: 0.8442 (ttt180) cc_final: 0.8180 (ttp-170) REVERT: JB 61 GLN cc_start: 0.9127 (tt0) cc_final: 0.8791 (tt0) REVERT: JC 16 MET cc_start: 0.8107 (tmm) cc_final: 0.7819 (tmm) REVERT: JC 28 LYS cc_start: 0.7883 (tmmt) cc_final: 0.7408 (mmtt) REVERT: JD 23 MET cc_start: 0.8393 (mtm) cc_final: 0.8136 (mtm) REVERT: JD 43 THR cc_start: 0.9376 (m) cc_final: 0.8858 (m) REVERT: JD 62 ARG cc_start: 0.8266 (ttp-110) cc_final: 0.7967 (ptm160) REVERT: JE 16 MET cc_start: 0.8121 (tmm) cc_final: 0.7722 (tmm) REVERT: JE 28 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8350 (ttmm) REVERT: JF 3 ASP cc_start: 0.8473 (m-30) cc_final: 0.8228 (m-30) REVERT: JF 18 GLU cc_start: 0.8158 (tp30) cc_final: 0.7596 (tp30) REVERT: JF 32 ILE cc_start: 0.9139 (pp) cc_final: 0.8567 (pp) REVERT: JF 61 GLN cc_start: 0.8587 (tt0) cc_final: 0.8032 (tt0) REVERT: JF 62 ARG cc_start: 0.8210 (tmm-80) cc_final: 0.7835 (ttm-80) REVERT: KA 3 ASP cc_start: 0.8342 (m-30) cc_final: 0.7857 (m-30) REVERT: KA 9 GLU cc_start: 0.8176 (tp30) cc_final: 0.7625 (tp30) REVERT: KA 16 MET cc_start: 0.9212 (tmm) cc_final: 0.8839 (tmm) REVERT: KA 18 GLU cc_start: 0.8568 (tp30) cc_final: 0.8316 (tp30) REVERT: KA 25 LYS cc_start: 0.8235 (mttt) cc_final: 0.8004 (mmtt) REVERT: KA 30 GLU cc_start: 0.8741 (tt0) cc_final: 0.8207 (tm-30) REVERT: KA 31 LEU cc_start: 0.9400 (tp) cc_final: 0.8995 (tt) REVERT: KA 41 TYR cc_start: 0.8300 (m-10) cc_final: 0.7907 (m-10) REVERT: KA 43 THR cc_start: 0.9193 (m) cc_final: 0.8865 (m) REVERT: KB 21 ASP cc_start: 0.9004 (t70) cc_final: 0.8660 (t0) REVERT: KB 23 MET cc_start: 0.8777 (mtm) cc_final: 0.8498 (mtt) REVERT: KB 28 LYS cc_start: 0.7811 (ttpt) cc_final: 0.7333 (mttt) REVERT: KB 31 LEU cc_start: 0.9126 (tp) cc_final: 0.8903 (tt) REVERT: KB 43 THR cc_start: 0.9193 (m) cc_final: 0.8909 (t) REVERT: KB 78 ARG cc_start: 0.8734 (mtp85) cc_final: 0.7936 (mtm-85) REVERT: KC 28 LYS cc_start: 0.8644 (ttpt) cc_final: 0.8092 (mptt) REVERT: KC 43 THR cc_start: 0.9255 (m) cc_final: 0.8826 (p) REVERT: KD 23 MET cc_start: 0.8687 (mtm) cc_final: 0.8288 (mtp) REVERT: KD 31 LEU cc_start: 0.8866 (tp) cc_final: 0.8419 (tt) REVERT: KD 62 ARG cc_start: 0.8509 (ttp-110) cc_final: 0.8126 (ttp-110) REVERT: KD 78 ARG cc_start: 0.8447 (ttt90) cc_final: 0.7335 (mtm180) REVERT: KE 11 ARG cc_start: 0.8326 (ttt180) cc_final: 0.8103 (ttt90) REVERT: KF 28 LYS cc_start: 0.8183 (ttpp) cc_final: 0.7426 (ptpp) REVERT: KF 41 TYR cc_start: 0.8115 (m-10) cc_final: 0.7830 (m-10) REVERT: KF 92 THR cc_start: 0.8840 (m) cc_final: 0.8587 (p) REVERT: LA 18 GLU cc_start: 0.8399 (tp30) cc_final: 0.7896 (tm-30) REVERT: LA 28 LYS cc_start: 0.8480 (ttpm) cc_final: 0.8265 (ttmm) REVERT: LA 61 GLN cc_start: 0.8912 (tt0) cc_final: 0.8625 (tt0) REVERT: LB 21 ASP cc_start: 0.8791 (t70) cc_final: 0.8573 (t0) REVERT: LB 36 LYS cc_start: 0.7615 (mtmt) cc_final: 0.7392 (mtpt) REVERT: LB 84 ASP cc_start: 0.9240 (m-30) cc_final: 0.8956 (m-30) REVERT: LC 8 ILE cc_start: 0.8624 (mm) cc_final: 0.8115 (tp) REVERT: LC 21 ASP cc_start: 0.8939 (t70) cc_final: 0.8611 (t0) REVERT: LC 66 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7811 (ttp-170) REVERT: LD 16 MET cc_start: 0.8823 (tmm) cc_final: 0.8548 (tmm) REVERT: LD 18 GLU cc_start: 0.8786 (tp30) cc_final: 0.8404 (tp30) REVERT: LD 28 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7947 (tppt) REVERT: LD 30 GLU cc_start: 0.8473 (tt0) cc_final: 0.7968 (tt0) REVERT: LD 62 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7737 (mtp180) REVERT: LE 16 MET cc_start: 0.7975 (tmm) cc_final: 0.7576 (tmm) REVERT: LE 32 ILE cc_start: 0.8705 (pp) cc_final: 0.8484 (pp) REVERT: LF 3 ASP cc_start: 0.7910 (m-30) cc_final: 0.7620 (m-30) REVERT: LF 31 LEU cc_start: 0.8365 (tp) cc_final: 0.7897 (tt) REVERT: G 38 ASP cc_start: 0.7999 (t70) cc_final: 0.7630 (t70) REVERT: G 100 GLN cc_start: 0.8954 (mt0) cc_final: 0.8751 (mt0) REVERT: G 112 ASP cc_start: 0.7037 (p0) cc_final: 0.6364 (m-30) REVERT: H 26 GLU cc_start: 0.7051 (tt0) cc_final: 0.6798 (tt0) REVERT: H 74 MET cc_start: 0.8990 (mmm) cc_final: 0.8501 (mmt) REVERT: H 137 ASP cc_start: 0.8215 (t70) cc_final: 0.7701 (t0) REVERT: I 50 MET cc_start: 0.8533 (ptm) cc_final: 0.8157 (ptt) REVERT: I 62 MET cc_start: 0.9046 (mtt) cc_final: 0.8341 (mtt) REVERT: I 75 ILE cc_start: 0.9121 (tp) cc_final: 0.8877 (pt) REVERT: I 90 ASP cc_start: 0.8155 (t0) cc_final: 0.7731 (t70) REVERT: I 117 ASP cc_start: 0.7383 (p0) cc_final: 0.7143 (p0) REVERT: I 185 ARG cc_start: 0.9123 (mpp80) cc_final: 0.8792 (mtm-85) REVERT: I 187 LEU cc_start: 0.8815 (mt) cc_final: 0.8377 (mp) REVERT: M 19 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8382 (mtt90) REVERT: N 93 GLU cc_start: 0.8287 (tm-30) cc_final: 0.8000 (pt0) REVERT: N 196 VAL cc_start: 0.8963 (t) cc_final: 0.8690 (p) REVERT: O 55 SER cc_start: 0.8577 (m) cc_final: 0.8167 (p) REVERT: O 74 MET cc_start: 0.8805 (mmm) cc_final: 0.8514 (tpp) REVERT: O 90 ASP cc_start: 0.8372 (t0) cc_final: 0.7960 (t0) REVERT: O 118 THR cc_start: 0.8863 (m) cc_final: 0.8340 (p) REVERT: O 119 GLU cc_start: 0.7943 (tt0) cc_final: 0.7681 (tt0) REVERT: O 159 LYS cc_start: 0.9546 (mtmt) cc_final: 0.9128 (mtmm) REVERT: O 176 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8068 (mm-30) REVERT: S 74 MET cc_start: 0.9111 (mmm) cc_final: 0.8800 (mmm) REVERT: S 137 ASP cc_start: 0.8312 (t70) cc_final: 0.7604 (t0) REVERT: S 170 ASP cc_start: 0.8439 (m-30) cc_final: 0.7819 (t0) REVERT: T 71 GLU cc_start: 0.8054 (tp30) cc_final: 0.7806 (tt0) REVERT: T 74 MET cc_start: 0.8758 (mmm) cc_final: 0.8481 (tpp) REVERT: T 90 ASP cc_start: 0.7874 (t0) cc_final: 0.7129 (t70) REVERT: T 96 TYR cc_start: 0.8263 (t80) cc_final: 0.7846 (t80) REVERT: T 106 ASP cc_start: 0.7190 (t0) cc_final: 0.6897 (t0) REVERT: U 75 ILE cc_start: 0.8456 (tp) cc_final: 0.8135 (tp) REVERT: U 100 GLN cc_start: 0.9362 (mt0) cc_final: 0.9125 (mt0) outliers start: 14 outliers final: 4 residues processed: 1800 average time/residue: 0.3075 time to fit residues: 872.5064 Evaluate side-chains 1170 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 1166 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain S residue 124 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 0.6980 chunk 523 optimal weight: 0.5980 chunk 497 optimal weight: 1.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 0.6980 chunk 366 optimal weight: 0.9980 chunk 597 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 78 HIS A 79 HIS ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN B 78 HIS B 79 HIS B 123 GLN B 165 HIS B 168 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS C 123 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS D 123 GLN D 168 ASN E 15 GLN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN F 15 GLN ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 123 GLN ** F 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS GA 82 ASN GB 82 ASN IA 82 ASN IB 82 ASN IE 74 HIS ** IE 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IF 82 ASN JA 82 ASN JB 82 ASN JD 74 HIS JF 82 ASN KB 82 ASN ** KC 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** KF 74 HIS LA 82 ASN LB 82 ASN LE 61 GLN LE 82 ASN LF 80 HIS G 98 HIS S 98 HIS S 100 GLN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.086737 restraints weight = 109744.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088944 restraints weight = 56299.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090420 restraints weight = 33622.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.091412 restraints weight = 22388.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.092103 restraints weight = 16215.416| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46860 Z= 0.143 Angle : 0.621 9.740 63645 Z= 0.326 Chirality : 0.044 0.242 7638 Planarity : 0.005 0.063 8340 Dihedral : 4.901 28.751 6784 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.27 % Allowed : 12.74 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.41 (0.10), residues: 6183 helix: -1.40 (0.10), residues: 2477 sheet: -0.52 (0.13), residues: 1465 loop : -2.42 (0.12), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGHD 47 TYR 0.015 0.001 TYRGB 34 PHE 0.021 0.002 PHE E 10 TRP 0.031 0.002 TRP A 39 HIS 0.006 0.001 HISKD 74 Details of bonding type rmsd covalent geometry : bond 0.00333 (46860) covalent geometry : angle 0.62120 (63645) hydrogen bonds : bond 0.03921 ( 2487) hydrogen bonds : angle 4.76370 ( 7071) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 1329 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.8780 (m) cc_final: 0.8550 (m) REVERT: A 39 TRP cc_start: 0.8611 (m100) cc_final: 0.8267 (m100) REVERT: A 199 ARG cc_start: 0.7693 (ptp90) cc_final: 0.7470 (ptp90) REVERT: B 7 THR cc_start: 0.7959 (m) cc_final: 0.7462 (p) REVERT: B 8 TYR cc_start: 0.8279 (t80) cc_final: 0.7919 (t80) REVERT: B 114 ILE cc_start: 0.8987 (mt) cc_final: 0.8705 (mt) REVERT: B 128 ASN cc_start: 0.8401 (t0) cc_final: 0.8009 (t0) REVERT: B 188 ASP cc_start: 0.8107 (t0) cc_final: 0.7790 (t0) REVERT: C 60 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8606 (ttmt) REVERT: C 128 ASN cc_start: 0.8573 (t0) cc_final: 0.8198 (t0) REVERT: D 67 VAL cc_start: 0.9318 (t) cc_final: 0.9028 (p) REVERT: D 70 ARG cc_start: 0.7678 (ptm160) cc_final: 0.7062 (ttt180) REVERT: D 76 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7354 (tm-30) REVERT: D 103 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7983 (ptt-90) REVERT: D 140 LEU cc_start: 0.9256 (tp) cc_final: 0.9015 (tt) REVERT: E 52 THR cc_start: 0.8894 (m) cc_final: 0.8520 (p) REVERT: E 109 MET cc_start: 0.8048 (mpm) cc_final: 0.7779 (mpm) REVERT: E 128 ASN cc_start: 0.8031 (t0) cc_final: 0.7748 (t0) REVERT: E 145 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.8865 (t) REVERT: F 72 TYR cc_start: 0.8690 (m-80) cc_final: 0.8280 (m-10) REVERT: F 105 LYS cc_start: 0.8794 (tptp) cc_final: 0.8185 (tppt) REVERT: F 175 PHE cc_start: 0.8595 (m-80) cc_final: 0.8362 (m-80) REVERT: F 184 GLU cc_start: 0.7672 (tm-30) cc_final: 0.6921 (tm-30) REVERT: GA 7 MET cc_start: 0.8280 (mtt) cc_final: 0.8051 (mtm) REVERT: GA 10 VAL cc_start: 0.9696 (t) cc_final: 0.9494 (p) REVERT: GA 16 MET cc_start: 0.9108 (tmm) cc_final: 0.8614 (tmm) REVERT: GA 42 VAL cc_start: 0.9234 (OUTLIER) cc_final: 0.8894 (p) REVERT: GA 43 THR cc_start: 0.9128 (m) cc_final: 0.8910 (p) REVERT: GB 21 ASP cc_start: 0.8819 (t70) cc_final: 0.8421 (t0) REVERT: GB 28 LYS cc_start: 0.8460 (tmmt) cc_final: 0.7619 (mptt) REVERT: GB 61 GLN cc_start: 0.8631 (tt0) cc_final: 0.8296 (tt0) REVERT: GC 28 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8040 (mptt) REVERT: GC 43 THR cc_start: 0.9043 (m) cc_final: 0.8804 (p) REVERT: GD 16 MET cc_start: 0.8741 (tmm) cc_final: 0.8371 (tmm) REVERT: GD 62 ARG cc_start: 0.8890 (ttp-110) cc_final: 0.8610 (mtm110) REVERT: GE 32 ILE cc_start: 0.9009 (pp) cc_final: 0.8798 (pp) REVERT: GF 18 GLU cc_start: 0.8790 (tp30) cc_final: 0.8459 (tp30) REVERT: GF 73 VAL cc_start: 0.9452 (t) cc_final: 0.9189 (m) REVERT: GF 92 THR cc_start: 0.8380 (m) cc_final: 0.8172 (p) REVERT: HA 18 GLU cc_start: 0.8387 (tp30) cc_final: 0.8004 (tm-30) REVERT: HA 43 THR cc_start: 0.9157 (m) cc_final: 0.8257 (m) REVERT: HA 54 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8237 (ttmt) REVERT: HA 69 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7280 (tm-30) REVERT: HB 28 LYS cc_start: 0.8826 (ttpp) cc_final: 0.8071 (ttmm) REVERT: HB 92 THR cc_start: 0.8562 (m) cc_final: 0.8148 (p) REVERT: HC 21 ASP cc_start: 0.8662 (t70) cc_final: 0.8338 (t0) REVERT: HC 28 LYS cc_start: 0.7776 (ttpt) cc_final: 0.7537 (mmtm) REVERT: HD 3 ASP cc_start: 0.7994 (m-30) cc_final: 0.7710 (m-30) REVERT: HD 16 MET cc_start: 0.8710 (tmm) cc_final: 0.8491 (tmm) REVERT: HD 78 ARG cc_start: 0.8678 (tmt90) cc_final: 0.7564 (ptp-170) REVERT: HE 16 MET cc_start: 0.8517 (tmm) cc_final: 0.8299 (tmm) REVERT: HE 43 THR cc_start: 0.9395 (m) cc_final: 0.9084 (p) REVERT: HE 78 ARG cc_start: 0.8065 (tpt170) cc_final: 0.7485 (ptt90) REVERT: HF 43 THR cc_start: 0.8757 (m) cc_final: 0.8376 (p) REVERT: HF 61 GLN cc_start: 0.8705 (tt0) cc_final: 0.8306 (tt0) REVERT: HF 62 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7886 (mtm-85) REVERT: IA 41 TYR cc_start: 0.8514 (m-10) cc_final: 0.8139 (m-80) REVERT: IA 43 THR cc_start: 0.8982 (m) cc_final: 0.8686 (p) REVERT: IB 21 ASP cc_start: 0.8394 (t70) cc_final: 0.7819 (t0) REVERT: IC 16 MET cc_start: 0.8552 (tmm) cc_final: 0.8002 (tmm) REVERT: IC 18 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7993 (tm-30) REVERT: IC 62 ARG cc_start: 0.8491 (ttp-110) cc_final: 0.8074 (mtp-110) REVERT: ID 3 ASP cc_start: 0.8153 (m-30) cc_final: 0.7941 (m-30) REVERT: ID 11 ARG cc_start: 0.8625 (mtp180) cc_final: 0.8241 (ttt90) REVERT: ID 16 MET cc_start: 0.8816 (tmm) cc_final: 0.8516 (tmm) REVERT: ID 43 THR cc_start: 0.9481 (m) cc_final: 0.9247 (p) REVERT: ID 61 GLN cc_start: 0.8349 (tm-30) cc_final: 0.8146 (tm-30) REVERT: ID 62 ARG cc_start: 0.8244 (ttp-110) cc_final: 0.7766 (mtm110) REVERT: IF 9 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8390 (tm-30) REVERT: JA 16 MET cc_start: 0.9055 (tmm) cc_final: 0.8795 (tmm) REVERT: JA 30 GLU cc_start: 0.8669 (tp30) cc_final: 0.8413 (tp30) REVERT: JA 58 GLU cc_start: 0.7669 (pp20) cc_final: 0.7374 (pp20) REVERT: JA 65 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7649 (mm-30) REVERT: JB 61 GLN cc_start: 0.9084 (tt0) cc_final: 0.8821 (tt0) REVERT: JC 16 MET cc_start: 0.8257 (tmm) cc_final: 0.7989 (tmm) REVERT: JD 23 MET cc_start: 0.8348 (mtm) cc_final: 0.8083 (mtm) REVERT: JE 16 MET cc_start: 0.8201 (tmm) cc_final: 0.7797 (tmm) REVERT: JE 23 MET cc_start: 0.8088 (mtm) cc_final: 0.7784 (mtm) REVERT: JE 61 GLN cc_start: 0.8880 (tt0) cc_final: 0.8668 (tt0) REVERT: JE 73 VAL cc_start: 0.9300 (t) cc_final: 0.9085 (t) REVERT: JF 18 GLU cc_start: 0.7969 (tp30) cc_final: 0.7540 (tm-30) REVERT: JF 61 GLN cc_start: 0.8565 (tt0) cc_final: 0.7927 (tt0) REVERT: KA 16 MET cc_start: 0.8966 (tmm) cc_final: 0.8177 (tmm) REVERT: KB 21 ASP cc_start: 0.8734 (t70) cc_final: 0.8529 (t0) REVERT: KB 28 LYS cc_start: 0.7706 (ttpt) cc_final: 0.7459 (mttt) REVERT: KB 35 GLU cc_start: 0.7405 (mp0) cc_final: 0.7111 (mp0) REVERT: KC 28 LYS cc_start: 0.8364 (ttpt) cc_final: 0.7983 (mptt) REVERT: KC 43 THR cc_start: 0.9160 (m) cc_final: 0.8745 (p) REVERT: KD 23 MET cc_start: 0.8627 (mtm) cc_final: 0.8085 (mtp) REVERT: KD 62 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.8108 (ttp-110) REVERT: KD 78 ARG cc_start: 0.8312 (ttt90) cc_final: 0.7405 (mtm180) REVERT: KE 43 THR cc_start: 0.8737 (m) cc_final: 0.8375 (p) REVERT: KE 87 LEU cc_start: 0.9106 (mt) cc_final: 0.8819 (mt) REVERT: KF 28 LYS cc_start: 0.8181 (ttpp) cc_final: 0.7602 (ptpp) REVERT: KF 41 TYR cc_start: 0.8379 (m-10) cc_final: 0.8098 (m-10) REVERT: KF 92 THR cc_start: 0.8703 (m) cc_final: 0.8445 (p) REVERT: LA 18 GLU cc_start: 0.8302 (tp30) cc_final: 0.8042 (tm-30) REVERT: LA 32 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7944 (tp) REVERT: LA 61 GLN cc_start: 0.8637 (tt0) cc_final: 0.8071 (tp40) REVERT: LB 21 ASP cc_start: 0.8836 (t70) cc_final: 0.8621 (t0) REVERT: LC 8 ILE cc_start: 0.8555 (mm) cc_final: 0.8241 (tp) REVERT: LC 21 ASP cc_start: 0.8711 (t70) cc_final: 0.8367 (t0) REVERT: LD 17 VAL cc_start: 0.9006 (t) cc_final: 0.8597 (t) REVERT: LD 18 GLU cc_start: 0.8591 (tp30) cc_final: 0.8209 (tp30) REVERT: LD 28 LYS cc_start: 0.8134 (ttpp) cc_final: 0.7876 (tppt) REVERT: LD 62 ARG cc_start: 0.7997 (ttm110) cc_final: 0.7719 (mtp180) REVERT: LE 16 MET cc_start: 0.8141 (tmm) cc_final: 0.7903 (tmm) REVERT: LF 3 ASP cc_start: 0.7578 (m-30) cc_final: 0.7340 (m-30) REVERT: LF 8 ILE cc_start: 0.9027 (mm) cc_final: 0.8681 (mt) REVERT: LF 18 GLU cc_start: 0.7421 (tm-30) cc_final: 0.6977 (tm-30) REVERT: LF 32 ILE cc_start: 0.9238 (pp) cc_final: 0.8981 (tp) REVERT: LF 58 GLU cc_start: 0.7140 (pt0) cc_final: 0.6900 (tm-30) REVERT: LF 78 ARG cc_start: 0.8751 (ttt-90) cc_final: 0.8029 (ttp80) REVERT: G 62 MET cc_start: 0.8954 (mtt) cc_final: 0.8622 (mtt) REVERT: G 92 LEU cc_start: 0.8897 (tp) cc_final: 0.8682 (tt) REVERT: G 202 ARG cc_start: 0.7820 (ptm160) cc_final: 0.6855 (mtp-110) REVERT: H 74 MET cc_start: 0.8923 (mmm) cc_final: 0.8591 (mmm) REVERT: H 118 THR cc_start: 0.8816 (m) cc_final: 0.8546 (p) REVERT: H 137 ASP cc_start: 0.7610 (t70) cc_final: 0.7093 (t0) REVERT: I 55 SER cc_start: 0.8491 (m) cc_final: 0.8022 (p) REVERT: I 60 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8948 (mt) REVERT: I 62 MET cc_start: 0.9040 (mtt) cc_final: 0.8467 (mtt) REVERT: M 96 TYR cc_start: 0.8864 (t80) cc_final: 0.8635 (t80) REVERT: N 26 GLU cc_start: 0.7507 (tt0) cc_final: 0.7264 (tt0) REVERT: N 78 ARG cc_start: 0.8290 (ptp90) cc_final: 0.7728 (mtt180) REVERT: N 196 VAL cc_start: 0.8963 (t) cc_final: 0.8759 (p) REVERT: O 55 SER cc_start: 0.8447 (m) cc_final: 0.8241 (p) REVERT: O 90 ASP cc_start: 0.8193 (t0) cc_final: 0.7689 (t0) REVERT: O 92 LEU cc_start: 0.8932 (tp) cc_final: 0.8555 (tt) REVERT: O 118 THR cc_start: 0.9086 (m) cc_final: 0.8638 (p) REVERT: O 159 LYS cc_start: 0.9566 (mtmt) cc_final: 0.9121 (mtmm) REVERT: O 176 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7768 (mm-30) REVERT: S 74 MET cc_start: 0.9024 (mmm) cc_final: 0.8786 (mmm) REVERT: S 137 ASP cc_start: 0.8138 (t70) cc_final: 0.7260 (t0) REVERT: T 90 ASP cc_start: 0.7852 (t0) cc_final: 0.7040 (t70) REVERT: U 90 ASP cc_start: 0.7038 (m-30) cc_final: 0.6617 (m-30) REVERT: U 187 LEU cc_start: 0.8352 (mt) cc_final: 0.7906 (tp) outliers start: 149 outliers final: 77 residues processed: 1423 average time/residue: 0.2612 time to fit residues: 599.6962 Evaluate side-chains 1208 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1125 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 103 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GB residue 43 THR Chi-restraints excluded: chain GC residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 17 VAL Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HB residue 10 VAL Chi-restraints excluded: chain HB residue 71 VAL Chi-restraints excluded: chain HC residue 17 VAL Chi-restraints excluded: chain HE residue 31 LEU Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 75 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain ID residue 69 GLU Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain JE residue 8 ILE Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 30 GLU Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 84 ASP Chi-restraints excluded: chain LF residue 81 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain O residue 63 MET Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 152 LEU Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 46 SER Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 67 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 291 optimal weight: 5.9990 chunk 438 optimal weight: 1.9990 chunk 414 optimal weight: 0.0980 chunk 440 optimal weight: 0.8980 chunk 276 optimal weight: 0.4980 chunk 82 optimal weight: 5.9990 chunk 371 optimal weight: 1.9990 chunk 599 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 168 ASN ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 ASN F 165 HIS HD 80 HIS ** IE 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IF 74 HIS IF 82 ASN JB 82 ASN ** KB 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** KE 82 ASN LE 61 GLN LE 82 ASN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 100 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.092911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.083253 restraints weight = 112554.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.085388 restraints weight = 58572.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086819 restraints weight = 35614.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.087802 restraints weight = 24064.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.088477 restraints weight = 17650.323| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 46860 Z= 0.184 Angle : 0.631 9.823 63645 Z= 0.327 Chirality : 0.044 0.202 7638 Planarity : 0.004 0.051 8340 Dihedral : 4.642 32.120 6784 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.19 % Allowed : 14.96 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.11), residues: 6183 helix: -0.67 (0.10), residues: 2477 sheet: -0.20 (0.13), residues: 1450 loop : -2.15 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGJB 62 TYR 0.017 0.002 TYRGB 34 PHE 0.023 0.002 PHE C 10 TRP 0.016 0.002 TRP E 39 HIS 0.012 0.001 HISKD 74 Details of bonding type rmsd covalent geometry : bond 0.00431 (46860) covalent geometry : angle 0.63052 (63645) hydrogen bonds : bond 0.03755 ( 2487) hydrogen bonds : angle 4.60307 ( 7071) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1368 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 1177 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 ARG cc_start: 0.8251 (mmt180) cc_final: 0.7998 (mmt180) REVERT: A 157 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7641 (mm-30) REVERT: A 199 ARG cc_start: 0.7781 (ptp90) cc_final: 0.7403 (ptp90) REVERT: B 24 LYS cc_start: 0.7750 (tttt) cc_final: 0.7541 (tttt) REVERT: B 128 ASN cc_start: 0.8381 (t0) cc_final: 0.8108 (t0) REVERT: B 188 ASP cc_start: 0.8184 (t0) cc_final: 0.7836 (t0) REVERT: C 128 ASN cc_start: 0.8561 (t0) cc_final: 0.8170 (t0) REVERT: C 187 ILE cc_start: 0.9171 (tp) cc_final: 0.8919 (tp) REVERT: D 140 LEU cc_start: 0.9325 (tp) cc_final: 0.9050 (tt) REVERT: E 52 THR cc_start: 0.8913 (m) cc_final: 0.8589 (p) REVERT: E 128 ASN cc_start: 0.8101 (t0) cc_final: 0.7811 (t0) REVERT: F 72 TYR cc_start: 0.8825 (m-80) cc_final: 0.8420 (m-10) REVERT: F 175 PHE cc_start: 0.8623 (m-80) cc_final: 0.8326 (m-80) REVERT: F 188 ASP cc_start: 0.7774 (m-30) cc_final: 0.7427 (m-30) REVERT: GA 10 VAL cc_start: 0.9737 (t) cc_final: 0.9523 (p) REVERT: GA 16 MET cc_start: 0.9107 (tmm) cc_final: 0.8606 (tmm) REVERT: GA 34 TYR cc_start: 0.8578 (p90) cc_final: 0.8338 (p90) REVERT: GA 42 VAL cc_start: 0.9196 (OUTLIER) cc_final: 0.8906 (p) REVERT: GA 43 THR cc_start: 0.9215 (m) cc_final: 0.8939 (p) REVERT: GB 7 MET cc_start: 0.8970 (ptp) cc_final: 0.8671 (ptp) REVERT: GB 21 ASP cc_start: 0.8973 (t70) cc_final: 0.8524 (t0) REVERT: GB 28 LYS cc_start: 0.8401 (tmmt) cc_final: 0.7666 (mttt) REVERT: GB 61 GLN cc_start: 0.8658 (tt0) cc_final: 0.8340 (tt0) REVERT: GC 28 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8008 (mptt) REVERT: GC 43 THR cc_start: 0.9069 (m) cc_final: 0.8785 (p) REVERT: GD 16 MET cc_start: 0.8711 (tmm) cc_final: 0.8427 (tmm) REVERT: GD 36 LYS cc_start: 0.8521 (ptmt) cc_final: 0.8218 (ptpp) REVERT: GD 62 ARG cc_start: 0.8863 (ttp-110) cc_final: 0.8560 (mtm110) REVERT: GE 32 ILE cc_start: 0.9080 (pp) cc_final: 0.8877 (pp) REVERT: GF 11 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.7742 (ttm110) REVERT: GF 18 GLU cc_start: 0.8838 (tp30) cc_final: 0.8457 (tp30) REVERT: GF 92 THR cc_start: 0.8438 (m) cc_final: 0.8198 (p) REVERT: HA 18 GLU cc_start: 0.8509 (tp30) cc_final: 0.8089 (tm-30) REVERT: HA 43 THR cc_start: 0.8985 (m) cc_final: 0.8590 (p) REVERT: HB 65 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7111 (mt-10) REVERT: HB 92 THR cc_start: 0.8580 (m) cc_final: 0.8131 (p) REVERT: HC 7 MET cc_start: 0.8333 (OUTLIER) cc_final: 0.8039 (mtp) REVERT: HC 21 ASP cc_start: 0.8613 (t70) cc_final: 0.8253 (t0) REVERT: HC 28 LYS cc_start: 0.7827 (ttpt) cc_final: 0.7564 (mmtt) REVERT: HD 3 ASP cc_start: 0.7900 (m-30) cc_final: 0.7601 (m-30) REVERT: HD 78 ARG cc_start: 0.8760 (tmt90) cc_final: 0.7639 (ptp-170) REVERT: HE 16 MET cc_start: 0.8314 (tmm) cc_final: 0.8079 (tmm) REVERT: HE 43 THR cc_start: 0.9354 (m) cc_final: 0.9098 (t) REVERT: HE 78 ARG cc_start: 0.8076 (tpt170) cc_final: 0.7648 (ptt90) REVERT: HF 43 THR cc_start: 0.8710 (m) cc_final: 0.8342 (p) REVERT: HF 61 GLN cc_start: 0.8821 (tt0) cc_final: 0.8257 (tt0) REVERT: HF 62 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7874 (mtm-85) REVERT: HF 65 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8308 (mp0) REVERT: IA 42 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8854 (p) REVERT: IA 43 THR cc_start: 0.9096 (m) cc_final: 0.8771 (p) REVERT: IB 21 ASP cc_start: 0.8388 (t70) cc_final: 0.7839 (t0) REVERT: IC 16 MET cc_start: 0.8619 (tmm) cc_final: 0.8374 (tmm) REVERT: IC 18 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8067 (tm-30) REVERT: ID 11 ARG cc_start: 0.8647 (mtp180) cc_final: 0.8017 (ttt90) REVERT: ID 16 MET cc_start: 0.8945 (tmm) cc_final: 0.8480 (tmm) REVERT: ID 43 THR cc_start: 0.9524 (m) cc_final: 0.9250 (p) REVERT: ID 61 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8193 (tm-30) REVERT: ID 62 ARG cc_start: 0.8203 (ttp-110) cc_final: 0.7818 (mtm110) REVERT: IE 32 ILE cc_start: 0.9191 (pp) cc_final: 0.8965 (pp) REVERT: IF 9 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8402 (tm-30) REVERT: JA 16 MET cc_start: 0.8608 (tmm) cc_final: 0.8206 (tmm) REVERT: JA 23 MET cc_start: 0.8626 (mtp) cc_final: 0.8416 (mtm) REVERT: JA 65 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7774 (mm-30) REVERT: JB 58 GLU cc_start: 0.7824 (tt0) cc_final: 0.7475 (tt0) REVERT: JB 84 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8470 (m-30) REVERT: JC 16 MET cc_start: 0.8284 (tmm) cc_final: 0.7982 (tmm) REVERT: JE 16 MET cc_start: 0.8294 (tmm) cc_final: 0.7960 (tmm) REVERT: JE 43 THR cc_start: 0.9292 (m) cc_final: 0.9070 (m) REVERT: JE 65 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: JF 18 GLU cc_start: 0.8030 (tp30) cc_final: 0.7607 (tm-30) REVERT: JF 61 GLN cc_start: 0.8541 (tt0) cc_final: 0.8260 (tt0) REVERT: KA 16 MET cc_start: 0.8993 (tmm) cc_final: 0.8293 (tmm) REVERT: KB 21 ASP cc_start: 0.8691 (t70) cc_final: 0.8349 (t0) REVERT: KB 35 GLU cc_start: 0.7377 (mp0) cc_final: 0.6982 (mp0) REVERT: KC 28 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7995 (mptt) REVERT: KC 43 THR cc_start: 0.9205 (m) cc_final: 0.8754 (p) REVERT: KD 21 ASP cc_start: 0.8666 (t70) cc_final: 0.8459 (t0) REVERT: KD 23 MET cc_start: 0.8661 (mtm) cc_final: 0.8168 (mtp) REVERT: KD 78 ARG cc_start: 0.8328 (ttt90) cc_final: 0.7411 (mtm180) REVERT: KE 11 ARG cc_start: 0.8503 (ttt90) cc_final: 0.8070 (ttt90) REVERT: KE 43 THR cc_start: 0.8569 (m) cc_final: 0.8263 (p) REVERT: KF 28 LYS cc_start: 0.8163 (ttpp) cc_final: 0.7579 (ptpp) REVERT: KF 41 TYR cc_start: 0.8256 (m-10) cc_final: 0.7862 (m-10) REVERT: KF 92 THR cc_start: 0.8799 (m) cc_final: 0.8536 (p) REVERT: LA 18 GLU cc_start: 0.8381 (tp30) cc_final: 0.8088 (tm-30) REVERT: LA 32 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7839 (pp) REVERT: LA 61 GLN cc_start: 0.8526 (tt0) cc_final: 0.8053 (tp40) REVERT: LC 8 ILE cc_start: 0.8660 (mm) cc_final: 0.8339 (tp) REVERT: LC 21 ASP cc_start: 0.8725 (t70) cc_final: 0.8427 (t0) REVERT: LD 18 GLU cc_start: 0.8656 (tp30) cc_final: 0.8304 (tp30) REVERT: LD 28 LYS cc_start: 0.8189 (ttpp) cc_final: 0.7911 (tppt) REVERT: LF 3 ASP cc_start: 0.7561 (m-30) cc_final: 0.7351 (m-30) REVERT: LF 58 GLU cc_start: 0.7264 (pt0) cc_final: 0.6929 (tm-30) REVERT: LF 78 ARG cc_start: 0.8787 (ttt-90) cc_final: 0.8069 (ttp80) REVERT: G 62 MET cc_start: 0.8959 (mtt) cc_final: 0.8574 (mtt) REVERT: G 92 LEU cc_start: 0.8991 (tp) cc_final: 0.8770 (tt) REVERT: H 74 MET cc_start: 0.8961 (mmm) cc_final: 0.8719 (mmm) REVERT: H 118 THR cc_start: 0.8819 (m) cc_final: 0.8502 (p) REVERT: H 137 ASP cc_start: 0.7623 (t70) cc_final: 0.7145 (t0) REVERT: I 50 MET cc_start: 0.8702 (ptt) cc_final: 0.8177 (ptt) REVERT: I 55 SER cc_start: 0.8547 (m) cc_final: 0.8084 (p) REVERT: M 62 MET cc_start: 0.8426 (mtt) cc_final: 0.8135 (mtp) REVERT: M 96 TYR cc_start: 0.8877 (t80) cc_final: 0.8577 (t80) REVERT: N 74 MET cc_start: 0.8634 (tpp) cc_final: 0.7828 (tpp) REVERT: O 90 ASP cc_start: 0.8155 (t0) cc_final: 0.7691 (t0) REVERT: O 118 THR cc_start: 0.9085 (m) cc_final: 0.8620 (p) REVERT: O 137 ASP cc_start: 0.8088 (t70) cc_final: 0.7724 (t70) REVERT: O 159 LYS cc_start: 0.9511 (mtmt) cc_final: 0.9290 (mtmm) REVERT: S 74 MET cc_start: 0.9060 (mmm) cc_final: 0.8821 (mmm) REVERT: S 137 ASP cc_start: 0.8147 (t70) cc_final: 0.7296 (t0) REVERT: U 58 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7557 (ptmt) REVERT: U 187 LEU cc_start: 0.8381 (mt) cc_final: 0.7923 (tp) outliers start: 191 outliers final: 117 residues processed: 1283 average time/residue: 0.2909 time to fit residues: 600.1437 Evaluate side-chains 1205 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 1080 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 72 TYR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain GA residue 17 VAL Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 71 VAL Chi-restraints excluded: chain HC residue 7 MET Chi-restraints excluded: chain HC residue 17 VAL Chi-restraints excluded: chain HC residue 70 VAL Chi-restraints excluded: chain HE residue 70 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HE residue 76 ILE Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 65 GLU Chi-restraints excluded: chain HF residue 78 ARG Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 9 GLU Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 75 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain JA residue 43 THR Chi-restraints excluded: chain JB residue 84 ASP Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 65 GLU Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KE residue 34 TYR Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LA residue 84 ASP Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LC residue 69 GLU Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LF residue 31 LEU Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 124 VAL Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 46 SER Chi-restraints excluded: chain T residue 126 THR Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 7 ARG Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 67 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 608 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 356 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 469 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 614 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 549 optimal weight: 2.9990 chunk 503 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 123 GLN B 168 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN F 130 GLN ** GC 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** HE 82 ASN IF 82 ASN JB 82 ASN KE 82 ASN LE 61 GLN LE 82 ASN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.082255 restraints weight = 113075.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.084393 restraints weight = 59217.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.085836 restraints weight = 36182.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086821 restraints weight = 24649.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087510 restraints weight = 18154.153| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 46860 Z= 0.195 Angle : 0.635 9.620 63645 Z= 0.329 Chirality : 0.045 0.195 7638 Planarity : 0.004 0.053 8340 Dihedral : 4.545 34.874 6784 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.58 % Allowed : 16.51 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.11), residues: 6183 helix: -0.45 (0.10), residues: 2516 sheet: -0.08 (0.13), residues: 1445 loop : -2.06 (0.13), residues: 2222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGJB 62 TYR 0.017 0.002 TYR C 8 PHE 0.022 0.002 PHE E 10 TRP 0.042 0.002 TRP A 39 HIS 0.008 0.001 HISGC 74 Details of bonding type rmsd covalent geometry : bond 0.00459 (46860) covalent geometry : angle 0.63482 (63645) hydrogen bonds : bond 0.03671 ( 2487) hydrogen bonds : angle 4.53606 ( 7071) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 1123 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.8472 (m100) cc_final: 0.8103 (m100) REVERT: A 115 ARG cc_start: 0.8294 (mmt180) cc_final: 0.8073 (mmt180) REVERT: A 157 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7719 (mm-30) REVERT: A 199 ARG cc_start: 0.7735 (ptp90) cc_final: 0.7355 (ptp90) REVERT: B 128 ASN cc_start: 0.8493 (t0) cc_final: 0.8143 (t0) REVERT: B 188 ASP cc_start: 0.8234 (t0) cc_final: 0.7873 (t0) REVERT: C 128 ASN cc_start: 0.8568 (t0) cc_final: 0.8141 (t0) REVERT: D 76 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7514 (tm-30) REVERT: D 120 TYR cc_start: 0.8231 (m-80) cc_final: 0.8012 (m-80) REVERT: E 50 ARG cc_start: 0.8416 (ttm110) cc_final: 0.8041 (ttm110) REVERT: E 109 MET cc_start: 0.7978 (mpm) cc_final: 0.7749 (mpm) REVERT: E 128 ASN cc_start: 0.8085 (t0) cc_final: 0.7789 (t0) REVERT: F 72 TYR cc_start: 0.8886 (m-80) cc_final: 0.8594 (m-10) REVERT: F 115 ARG cc_start: 0.7435 (mpt-90) cc_final: 0.6894 (mpt-90) REVERT: GA 16 MET cc_start: 0.9104 (tmm) cc_final: 0.8628 (tmm) REVERT: GA 42 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8943 (p) REVERT: GA 43 THR cc_start: 0.9216 (m) cc_final: 0.8993 (p) REVERT: GB 7 MET cc_start: 0.8919 (ptp) cc_final: 0.8367 (ptp) REVERT: GB 21 ASP cc_start: 0.8979 (t70) cc_final: 0.8613 (t0) REVERT: GB 28 LYS cc_start: 0.8427 (tmmt) cc_final: 0.7656 (mttt) REVERT: GB 61 GLN cc_start: 0.8634 (tt0) cc_final: 0.8380 (tt0) REVERT: GC 28 LYS cc_start: 0.8530 (ttpp) cc_final: 0.7984 (mptt) REVERT: GC 43 THR cc_start: 0.9085 (m) cc_final: 0.8802 (p) REVERT: GD 36 LYS cc_start: 0.8545 (ptmt) cc_final: 0.8254 (ptpp) REVERT: GD 62 ARG cc_start: 0.8854 (ttp-110) cc_final: 0.8520 (mtm110) REVERT: GF 11 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8111 (ttm110) REVERT: GF 18 GLU cc_start: 0.8887 (tp30) cc_final: 0.8511 (tp30) REVERT: GF 92 THR cc_start: 0.8488 (m) cc_final: 0.8249 (p) REVERT: HA 9 GLU cc_start: 0.8105 (tp30) cc_final: 0.7788 (tp30) REVERT: HA 18 GLU cc_start: 0.8574 (tp30) cc_final: 0.8073 (tm-30) REVERT: HA 43 THR cc_start: 0.8983 (m) cc_final: 0.8426 (m) REVERT: HA 69 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7329 (tm-30) REVERT: HB 16 MET cc_start: 0.9020 (tmm) cc_final: 0.8436 (tmm) REVERT: HB 92 THR cc_start: 0.8627 (m) cc_final: 0.8175 (p) REVERT: HC 7 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7933 (mtp) REVERT: HC 21 ASP cc_start: 0.8597 (t70) cc_final: 0.8293 (t0) REVERT: HC 28 LYS cc_start: 0.7864 (ttpt) cc_final: 0.7534 (mmtt) REVERT: HD 3 ASP cc_start: 0.7949 (m-30) cc_final: 0.7610 (m-30) REVERT: HD 78 ARG cc_start: 0.8716 (tmt90) cc_final: 0.7662 (ptp-170) REVERT: HE 10 VAL cc_start: 0.9200 (t) cc_final: 0.8927 (m) REVERT: HE 43 THR cc_start: 0.9336 (m) cc_final: 0.9124 (t) REVERT: HE 78 ARG cc_start: 0.8077 (tpt170) cc_final: 0.7599 (ptt180) REVERT: HF 43 THR cc_start: 0.8703 (m) cc_final: 0.8332 (p) REVERT: HF 61 GLN cc_start: 0.8709 (tt0) cc_final: 0.8116 (tt0) REVERT: HF 62 ARG cc_start: 0.8318 (mtm-85) cc_final: 0.7945 (mtm-85) REVERT: HF 65 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: IA 42 VAL cc_start: 0.9179 (OUTLIER) cc_final: 0.8872 (p) REVERT: IA 43 THR cc_start: 0.9122 (m) cc_final: 0.8794 (p) REVERT: IB 21 ASP cc_start: 0.8373 (t70) cc_final: 0.7837 (t0) REVERT: IB 58 GLU cc_start: 0.7036 (pt0) cc_final: 0.6833 (pt0) REVERT: IC 16 MET cc_start: 0.8709 (tmm) cc_final: 0.8412 (tmm) REVERT: IC 18 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8059 (tm-30) REVERT: ID 11 ARG cc_start: 0.8589 (mtp180) cc_final: 0.8063 (ttt90) REVERT: ID 16 MET cc_start: 0.8936 (tmm) cc_final: 0.8644 (tmm) REVERT: ID 43 THR cc_start: 0.9522 (m) cc_final: 0.9282 (p) REVERT: ID 61 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8183 (tm-30) REVERT: ID 62 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.7731 (mtm110) REVERT: IE 32 ILE cc_start: 0.9213 (pp) cc_final: 0.9004 (pp) REVERT: IF 9 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8425 (tm-30) REVERT: JA 16 MET cc_start: 0.8100 (tmm) cc_final: 0.7516 (tmm) REVERT: JA 65 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7907 (mm-30) REVERT: JD 18 GLU cc_start: 0.8553 (tp30) cc_final: 0.8216 (tp30) REVERT: JD 62 ARG cc_start: 0.8455 (mtp-110) cc_final: 0.8252 (ptm160) REVERT: JE 16 MET cc_start: 0.8335 (tmm) cc_final: 0.7962 (tmm) REVERT: JE 23 MET cc_start: 0.8178 (mtm) cc_final: 0.7873 (mtm) REVERT: JE 43 THR cc_start: 0.9285 (m) cc_final: 0.9037 (m) REVERT: JE 65 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: JF 18 GLU cc_start: 0.8097 (tp30) cc_final: 0.7733 (tm-30) REVERT: KA 16 MET cc_start: 0.9037 (tmm) cc_final: 0.8436 (tmm) REVERT: KB 21 ASP cc_start: 0.8642 (t70) cc_final: 0.8350 (t0) REVERT: KC 28 LYS cc_start: 0.8408 (ttpt) cc_final: 0.8025 (mptt) REVERT: KC 43 THR cc_start: 0.9177 (m) cc_final: 0.8796 (p) REVERT: KD 21 ASP cc_start: 0.8718 (t70) cc_final: 0.8501 (t0) REVERT: KD 23 MET cc_start: 0.8633 (mtm) cc_final: 0.8151 (mtp) REVERT: KD 78 ARG cc_start: 0.8359 (ttt90) cc_final: 0.7506 (mtm180) REVERT: KE 43 THR cc_start: 0.8516 (m) cc_final: 0.8248 (p) REVERT: KF 28 LYS cc_start: 0.8225 (ttpp) cc_final: 0.7653 (ptpp) REVERT: KF 92 THR cc_start: 0.8857 (m) cc_final: 0.8575 (p) REVERT: LA 18 GLU cc_start: 0.8424 (tp30) cc_final: 0.8077 (tm-30) REVERT: LA 32 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7870 (pp) REVERT: LA 61 GLN cc_start: 0.8482 (tt0) cc_final: 0.7974 (tp40) REVERT: LC 8 ILE cc_start: 0.8684 (mm) cc_final: 0.8341 (tp) REVERT: LC 21 ASP cc_start: 0.8692 (t70) cc_final: 0.8398 (t0) REVERT: LD 18 GLU cc_start: 0.8753 (tp30) cc_final: 0.8465 (tp30) REVERT: LD 21 ASP cc_start: 0.8668 (m-30) cc_final: 0.8428 (m-30) REVERT: LD 28 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7960 (tppt) REVERT: LF 3 ASP cc_start: 0.7555 (m-30) cc_final: 0.7339 (m-30) REVERT: LF 58 GLU cc_start: 0.7343 (pt0) cc_final: 0.6931 (tm-30) REVERT: G 62 MET cc_start: 0.8984 (mtt) cc_final: 0.8645 (mtt) REVERT: H 74 MET cc_start: 0.9014 (mmm) cc_final: 0.8790 (mmm) REVERT: H 118 THR cc_start: 0.8862 (m) cc_final: 0.8525 (p) REVERT: H 137 ASP cc_start: 0.7594 (t70) cc_final: 0.7092 (t0) REVERT: I 74 MET cc_start: 0.9084 (tpp) cc_final: 0.8017 (mpp) REVERT: M 62 MET cc_start: 0.8481 (mtt) cc_final: 0.8210 (mtp) REVERT: M 96 TYR cc_start: 0.8852 (t80) cc_final: 0.8596 (t80) REVERT: O 90 ASP cc_start: 0.8046 (t0) cc_final: 0.7587 (t0) REVERT: O 118 THR cc_start: 0.8936 (m) cc_final: 0.8427 (p) REVERT: O 137 ASP cc_start: 0.8162 (t70) cc_final: 0.7571 (t0) REVERT: S 137 ASP cc_start: 0.8202 (t70) cc_final: 0.7344 (t0) REVERT: S 170 ASP cc_start: 0.8069 (t70) cc_final: 0.7795 (t0) REVERT: U 58 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7621 (ptmt) REVERT: U 187 LEU cc_start: 0.8389 (mt) cc_final: 0.7897 (tp) outliers start: 209 outliers final: 138 residues processed: 1244 average time/residue: 0.2633 time to fit residues: 529.8914 Evaluate side-chains 1203 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 1058 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain GA residue 17 VAL Chi-restraints excluded: chain GA residue 42 VAL Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 65 GLU Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 71 VAL Chi-restraints excluded: chain HC residue 7 MET Chi-restraints excluded: chain HC residue 70 VAL Chi-restraints excluded: chain HE residue 8 ILE Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HE residue 76 ILE Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 58 GLU Chi-restraints excluded: chain HF residue 65 GLU Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 78 ARG Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 75 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain ID residue 69 GLU Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 42 VAL Chi-restraints excluded: chain JE residue 65 GLU Chi-restraints excluded: chain JE residue 73 VAL Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KD residue 50 VAL Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LC residue 23 MET Chi-restraints excluded: chain LC residue 69 GLU Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 58 GLU Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain H residue 170 ASP Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 171 VAL Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain O residue 134 ASP Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 46 SER Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 126 THR Chi-restraints excluded: chain T residue 128 THR Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 67 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 25 optimal weight: 0.9980 chunk 358 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 367 optimal weight: 2.9990 chunk 449 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 526 optimal weight: 2.9990 chunk 458 optimal weight: 2.9990 chunk 426 optimal weight: 0.6980 chunk 379 optimal weight: 3.9990 chunk 316 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 HIS GB 82 ASN ** GC 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 82 ASN KE 82 ASN LE 61 GLN LE 82 ASN G 98 HIS ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.093204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.083534 restraints weight = 112677.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.085668 restraints weight = 58750.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.087091 restraints weight = 35819.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.088092 restraints weight = 24227.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.088785 restraints weight = 17869.361| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 46860 Z= 0.157 Angle : 0.624 13.575 63645 Z= 0.319 Chirality : 0.044 0.216 7638 Planarity : 0.004 0.075 8340 Dihedral : 4.386 35.520 6783 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.36 % Allowed : 17.68 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.11), residues: 6183 helix: -0.23 (0.10), residues: 2516 sheet: -0.12 (0.13), residues: 1481 loop : -1.86 (0.14), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 103 TYR 0.021 0.001 TYR C 8 PHE 0.024 0.002 PHE C 10 TRP 0.018 0.001 TRP A 39 HIS 0.008 0.001 HISKF 74 Details of bonding type rmsd covalent geometry : bond 0.00374 (46860) covalent geometry : angle 0.62374 (63645) hydrogen bonds : bond 0.03444 ( 2487) hydrogen bonds : angle 4.41968 ( 7071) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 1129 time to evaluate : 1.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TRP cc_start: 0.8466 (m100) cc_final: 0.8124 (m100) REVERT: A 128 ASN cc_start: 0.8652 (t0) cc_final: 0.8447 (t0) REVERT: A 199 ARG cc_start: 0.7730 (ptp90) cc_final: 0.7334 (ptp90) REVERT: B 8 TYR cc_start: 0.8402 (t80) cc_final: 0.8140 (t80) REVERT: B 128 ASN cc_start: 0.8449 (t0) cc_final: 0.8112 (t0) REVERT: B 188 ASP cc_start: 0.8234 (t0) cc_final: 0.7841 (t0) REVERT: C 128 ASN cc_start: 0.8593 (t0) cc_final: 0.8141 (t0) REVERT: C 132 MET cc_start: 0.8118 (ttm) cc_final: 0.7760 (ttm) REVERT: C 187 ILE cc_start: 0.9136 (tp) cc_final: 0.8862 (tp) REVERT: D 76 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7550 (tm-30) REVERT: E 109 MET cc_start: 0.7964 (mpm) cc_final: 0.7676 (mpm) REVERT: E 128 ASN cc_start: 0.8013 (t0) cc_final: 0.7695 (t0) REVERT: F 72 TYR cc_start: 0.8877 (m-80) cc_final: 0.8597 (m-80) REVERT: F 115 ARG cc_start: 0.7361 (mpt-90) cc_final: 0.7144 (mmt90) REVERT: F 133 MET cc_start: 0.8014 (mtm) cc_final: 0.7723 (mtp) REVERT: GA 11 ARG cc_start: 0.8757 (ttm-80) cc_final: 0.8481 (ttt90) REVERT: GA 16 MET cc_start: 0.9079 (tmm) cc_final: 0.8653 (tmm) REVERT: GA 34 TYR cc_start: 0.8515 (p90) cc_final: 0.8264 (p90) REVERT: GB 7 MET cc_start: 0.8843 (ptp) cc_final: 0.8326 (ptp) REVERT: GB 21 ASP cc_start: 0.8927 (t70) cc_final: 0.8580 (t0) REVERT: GB 28 LYS cc_start: 0.8443 (tmmt) cc_final: 0.7586 (mttt) REVERT: GC 28 LYS cc_start: 0.8538 (ttpp) cc_final: 0.7965 (mptt) REVERT: GC 43 THR cc_start: 0.9112 (m) cc_final: 0.8838 (p) REVERT: GD 36 LYS cc_start: 0.8549 (ptmt) cc_final: 0.8298 (ptpp) REVERT: GD 62 ARG cc_start: 0.8849 (ttp-110) cc_final: 0.8532 (mtm110) REVERT: GF 18 GLU cc_start: 0.8919 (tp30) cc_final: 0.8545 (tp30) REVERT: GF 92 THR cc_start: 0.8445 (m) cc_final: 0.8201 (p) REVERT: HA 9 GLU cc_start: 0.8090 (tp30) cc_final: 0.7813 (tp30) REVERT: HA 18 GLU cc_start: 0.8551 (tp30) cc_final: 0.8064 (tm-30) REVERT: HA 43 THR cc_start: 0.9030 (m) cc_final: 0.8300 (m) REVERT: HA 69 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7295 (tm-30) REVERT: HB 92 THR cc_start: 0.8636 (m) cc_final: 0.8165 (p) REVERT: HC 21 ASP cc_start: 0.8621 (t70) cc_final: 0.8241 (t0) REVERT: HC 28 LYS cc_start: 0.7850 (ttpt) cc_final: 0.7505 (mmtt) REVERT: HD 3 ASP cc_start: 0.7941 (m-30) cc_final: 0.7638 (m-30) REVERT: HD 32 ILE cc_start: 0.9540 (pp) cc_final: 0.9245 (tp) REVERT: HD 78 ARG cc_start: 0.8617 (tmt90) cc_final: 0.7571 (ptp-170) REVERT: HE 10 VAL cc_start: 0.9185 (t) cc_final: 0.8950 (m) REVERT: HE 43 THR cc_start: 0.9274 (m) cc_final: 0.8993 (t) REVERT: HE 78 ARG cc_start: 0.8131 (tpt170) cc_final: 0.7634 (ptt180) REVERT: HF 43 THR cc_start: 0.8651 (m) cc_final: 0.8326 (p) REVERT: HF 61 GLN cc_start: 0.8694 (tt0) cc_final: 0.8171 (tt0) REVERT: HF 62 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7801 (mtm-85) REVERT: IA 43 THR cc_start: 0.9088 (m) cc_final: 0.8746 (p) REVERT: IB 21 ASP cc_start: 0.8333 (t70) cc_final: 0.7826 (t0) REVERT: IC 16 MET cc_start: 0.8699 (tmm) cc_final: 0.8430 (tmm) REVERT: IC 18 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7835 (tm-30) REVERT: ID 43 THR cc_start: 0.9529 (m) cc_final: 0.9263 (p) REVERT: IF 9 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8524 (tm-30) REVERT: IF 32 ILE cc_start: 0.8790 (pp) cc_final: 0.8492 (tp) REVERT: JA 16 MET cc_start: 0.8135 (tmm) cc_final: 0.7602 (tmm) REVERT: JA 65 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7979 (mm-30) REVERT: JD 18 GLU cc_start: 0.8512 (tp30) cc_final: 0.8209 (tp30) REVERT: JD 23 MET cc_start: 0.8403 (mtm) cc_final: 0.8192 (mtm) REVERT: JD 69 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6773 (mm-30) REVERT: JE 16 MET cc_start: 0.8289 (tmm) cc_final: 0.8026 (tmm) REVERT: JE 43 THR cc_start: 0.9265 (m) cc_final: 0.8994 (m) REVERT: JE 65 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: JF 18 GLU cc_start: 0.8140 (tp30) cc_final: 0.7932 (tm-30) REVERT: JF 65 GLU cc_start: 0.8476 (mp0) cc_final: 0.8166 (mp0) REVERT: JF 84 ASP cc_start: 0.7982 (t70) cc_final: 0.7760 (t70) REVERT: KA 16 MET cc_start: 0.8954 (tmm) cc_final: 0.8454 (tmm) REVERT: KB 21 ASP cc_start: 0.8605 (t70) cc_final: 0.8274 (t0) REVERT: KB 23 MET cc_start: 0.8349 (mtm) cc_final: 0.8039 (mtm) REVERT: KC 28 LYS cc_start: 0.8422 (ttpt) cc_final: 0.7949 (mptt) REVERT: KC 43 THR cc_start: 0.9217 (m) cc_final: 0.8691 (p) REVERT: KD 23 MET cc_start: 0.8568 (mtm) cc_final: 0.8093 (mtp) REVERT: KD 78 ARG cc_start: 0.8329 (ttt90) cc_final: 0.7537 (mtm180) REVERT: KE 47 ARG cc_start: 0.8890 (mmm160) cc_final: 0.8665 (mmt90) REVERT: KF 28 LYS cc_start: 0.8281 (ttpp) cc_final: 0.7679 (ptpp) REVERT: KF 92 THR cc_start: 0.8849 (m) cc_final: 0.8614 (p) REVERT: LA 18 GLU cc_start: 0.8354 (tp30) cc_final: 0.7993 (tm-30) REVERT: LA 32 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7843 (pp) REVERT: LA 61 GLN cc_start: 0.8445 (tt0) cc_final: 0.7941 (tp40) REVERT: LC 8 ILE cc_start: 0.8652 (mm) cc_final: 0.8349 (tp) REVERT: LC 21 ASP cc_start: 0.8631 (t70) cc_final: 0.8356 (t0) REVERT: LD 18 GLU cc_start: 0.8740 (tp30) cc_final: 0.8454 (tp30) REVERT: LD 21 ASP cc_start: 0.8723 (m-30) cc_final: 0.8464 (m-30) REVERT: LD 28 LYS cc_start: 0.8184 (ttpp) cc_final: 0.7946 (tppt) REVERT: LF 3 ASP cc_start: 0.7573 (m-30) cc_final: 0.7328 (m-30) REVERT: LF 58 GLU cc_start: 0.7300 (pt0) cc_final: 0.6966 (tm-30) REVERT: G 63 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: H 74 MET cc_start: 0.9044 (mmm) cc_final: 0.8815 (mmm) REVERT: H 118 THR cc_start: 0.8865 (m) cc_final: 0.8555 (p) REVERT: H 137 ASP cc_start: 0.7386 (t70) cc_final: 0.6909 (t0) REVERT: I 74 MET cc_start: 0.9115 (tpp) cc_final: 0.8770 (mmm) REVERT: M 62 MET cc_start: 0.8464 (mtt) cc_final: 0.8238 (mtp) REVERT: M 96 TYR cc_start: 0.8827 (t80) cc_final: 0.8560 (t80) REVERT: M 156 ILE cc_start: 0.8673 (pt) cc_final: 0.8453 (tp) REVERT: N 130 CYS cc_start: 0.8616 (m) cc_final: 0.8098 (m) REVERT: O 90 ASP cc_start: 0.7968 (t0) cc_final: 0.7635 (t0) REVERT: O 118 THR cc_start: 0.8877 (m) cc_final: 0.8370 (p) REVERT: O 137 ASP cc_start: 0.8086 (t70) cc_final: 0.7437 (t0) REVERT: S 137 ASP cc_start: 0.8198 (t70) cc_final: 0.7342 (t0) REVERT: S 170 ASP cc_start: 0.8012 (t70) cc_final: 0.7728 (t0) REVERT: U 9 ASP cc_start: 0.8470 (p0) cc_final: 0.8226 (p0) REVERT: U 58 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7698 (ptmt) REVERT: U 64 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8311 (ptm-80) REVERT: U 90 ASP cc_start: 0.7476 (m-30) cc_final: 0.7237 (m-30) outliers start: 199 outliers final: 136 residues processed: 1245 average time/residue: 0.2797 time to fit residues: 562.6678 Evaluate side-chains 1195 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1054 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GB residue 43 THR Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 71 VAL Chi-restraints excluded: chain HE residue 70 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 75 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain JA residue 10 VAL Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 65 GLU Chi-restraints excluded: chain JE residue 73 VAL Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain KA residue 30 GLU Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 5 LEU Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LC residue 23 MET Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 46 SER Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 126 THR Chi-restraints excluded: chain T residue 128 THR Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 64 ARG Chi-restraints excluded: chain U residue 67 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 16 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 263 optimal weight: 0.9990 chunk 547 optimal weight: 0.8980 chunk 271 optimal weight: 0.6980 chunk 415 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 452 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** GC 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HC 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JB 82 ASN LE 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.093432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.083703 restraints weight = 112729.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.085854 restraints weight = 58938.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.087296 restraints weight = 35963.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.088302 restraints weight = 24406.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.088992 restraints weight = 17867.865| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 46860 Z= 0.157 Angle : 0.619 9.957 63645 Z= 0.318 Chirality : 0.044 0.192 7638 Planarity : 0.004 0.053 8340 Dihedral : 4.334 38.804 6783 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.25 % Allowed : 18.62 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.11), residues: 6183 helix: -0.06 (0.11), residues: 2508 sheet: -0.07 (0.13), residues: 1481 loop : -1.78 (0.14), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGHA 66 TYR 0.021 0.001 TYR C 8 PHE 0.023 0.002 PHE C 10 TRP 0.014 0.001 TRP A 39 HIS 0.008 0.001 HISKF 74 Details of bonding type rmsd covalent geometry : bond 0.00372 (46860) covalent geometry : angle 0.61905 (63645) hydrogen bonds : bond 0.03384 ( 2487) hydrogen bonds : angle 4.37654 ( 7071) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 1092 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7936 (ttpt) cc_final: 0.7500 (ttpt) REVERT: A 39 TRP cc_start: 0.8392 (m100) cc_final: 0.8151 (m100) REVERT: A 128 ASN cc_start: 0.8687 (t0) cc_final: 0.8443 (t0) REVERT: A 199 ARG cc_start: 0.7715 (ptp90) cc_final: 0.7332 (ptp90) REVERT: B 8 TYR cc_start: 0.8441 (t80) cc_final: 0.8198 (t80) REVERT: B 128 ASN cc_start: 0.8499 (t0) cc_final: 0.8138 (t0) REVERT: B 188 ASP cc_start: 0.8229 (t0) cc_final: 0.7832 (t0) REVERT: C 128 ASN cc_start: 0.8599 (t0) cc_final: 0.8199 (t0) REVERT: C 187 ILE cc_start: 0.9143 (tp) cc_final: 0.8881 (tp) REVERT: E 50 ARG cc_start: 0.8446 (ttm110) cc_final: 0.8121 (ttm110) REVERT: E 109 MET cc_start: 0.8089 (mpm) cc_final: 0.7772 (mpm) REVERT: E 128 ASN cc_start: 0.7995 (t0) cc_final: 0.7740 (t0) REVERT: F 72 TYR cc_start: 0.8866 (m-80) cc_final: 0.8627 (m-80) REVERT: F 96 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8485 (mm) REVERT: F 133 MET cc_start: 0.8007 (mtm) cc_final: 0.7764 (mtp) REVERT: GB 7 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8558 (mtm) REVERT: GB 21 ASP cc_start: 0.8948 (t70) cc_final: 0.8624 (t0) REVERT: GB 28 LYS cc_start: 0.8461 (tmmt) cc_final: 0.7553 (mttt) REVERT: GB 61 GLN cc_start: 0.8713 (tt0) cc_final: 0.8308 (tt0) REVERT: GC 28 LYS cc_start: 0.8512 (ttpp) cc_final: 0.7942 (mptt) REVERT: GC 43 THR cc_start: 0.9040 (m) cc_final: 0.8770 (p) REVERT: GD 62 ARG cc_start: 0.8886 (ttp-110) cc_final: 0.8543 (mtm110) REVERT: GF 18 GLU cc_start: 0.8924 (tp30) cc_final: 0.8537 (tp30) REVERT: GF 92 THR cc_start: 0.8434 (m) cc_final: 0.8216 (p) REVERT: HA 9 GLU cc_start: 0.8096 (tp30) cc_final: 0.7856 (tp30) REVERT: HA 18 GLU cc_start: 0.8579 (tp30) cc_final: 0.8101 (tm-30) REVERT: HA 43 THR cc_start: 0.8963 (m) cc_final: 0.8254 (m) REVERT: HB 16 MET cc_start: 0.9091 (tmm) cc_final: 0.8858 (tmm) REVERT: HB 92 THR cc_start: 0.8641 (m) cc_final: 0.8183 (p) REVERT: HC 21 ASP cc_start: 0.8523 (t70) cc_final: 0.8226 (t0) REVERT: HC 28 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7494 (mmtt) REVERT: HD 3 ASP cc_start: 0.7939 (m-30) cc_final: 0.7670 (m-30) REVERT: HD 32 ILE cc_start: 0.9528 (pp) cc_final: 0.9248 (tp) REVERT: HE 21 ASP cc_start: 0.7691 (t70) cc_final: 0.7436 (t70) REVERT: HE 43 THR cc_start: 0.9193 (m) cc_final: 0.8896 (t) REVERT: HE 78 ARG cc_start: 0.8082 (tpt170) cc_final: 0.7690 (ptt180) REVERT: HF 43 THR cc_start: 0.8599 (m) cc_final: 0.8278 (p) REVERT: HF 62 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7858 (mtm-85) REVERT: HF 78 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8378 (ptm160) REVERT: IA 42 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8891 (p) REVERT: IA 43 THR cc_start: 0.9100 (m) cc_final: 0.8751 (p) REVERT: IB 21 ASP cc_start: 0.8335 (t70) cc_final: 0.7859 (t0) REVERT: IB 23 MET cc_start: 0.8462 (mtm) cc_final: 0.8108 (mtp) REVERT: IC 18 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7937 (tm-30) REVERT: ID 43 THR cc_start: 0.9516 (m) cc_final: 0.9241 (p) REVERT: IF 9 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8519 (tm-30) REVERT: IF 32 ILE cc_start: 0.8813 (pp) cc_final: 0.8550 (tp) REVERT: JA 11 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7936 (ttp80) REVERT: JA 16 MET cc_start: 0.8111 (tmm) cc_final: 0.7593 (tmm) REVERT: JA 65 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7878 (mm-30) REVERT: JD 18 GLU cc_start: 0.8502 (tp30) cc_final: 0.8192 (tp30) REVERT: JE 16 MET cc_start: 0.8293 (tmm) cc_final: 0.8046 (tmm) REVERT: JE 23 MET cc_start: 0.8054 (mtm) cc_final: 0.7792 (mtm) REVERT: JE 65 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7552 (pm20) REVERT: JF 18 GLU cc_start: 0.8209 (tp30) cc_final: 0.7937 (tm-30) REVERT: JF 65 GLU cc_start: 0.8525 (mp0) cc_final: 0.8232 (mp0) REVERT: JF 84 ASP cc_start: 0.7989 (t70) cc_final: 0.7785 (t70) REVERT: KA 16 MET cc_start: 0.8992 (tmm) cc_final: 0.8501 (tmm) REVERT: KB 21 ASP cc_start: 0.8507 (t70) cc_final: 0.8168 (t0) REVERT: KC 28 LYS cc_start: 0.8424 (ttpt) cc_final: 0.7950 (mptt) REVERT: KC 35 GLU cc_start: 0.7807 (mp0) cc_final: 0.7579 (mp0) REVERT: KC 43 THR cc_start: 0.9110 (m) cc_final: 0.8761 (p) REVERT: KD 23 MET cc_start: 0.8563 (mtm) cc_final: 0.8114 (mtp) REVERT: KD 78 ARG cc_start: 0.8332 (ttt90) cc_final: 0.7538 (mtm180) REVERT: KE 8 ILE cc_start: 0.8905 (mt) cc_final: 0.8564 (tt) REVERT: KE 47 ARG cc_start: 0.8805 (mmm160) cc_final: 0.8492 (mmt90) REVERT: KF 28 LYS cc_start: 0.8291 (ttpp) cc_final: 0.7742 (ptpp) REVERT: KF 92 THR cc_start: 0.8856 (m) cc_final: 0.8649 (p) REVERT: LA 61 GLN cc_start: 0.8516 (tt0) cc_final: 0.8044 (tp40) REVERT: LC 8 ILE cc_start: 0.8657 (mm) cc_final: 0.8347 (tp) REVERT: LC 21 ASP cc_start: 0.8581 (t70) cc_final: 0.8273 (t0) REVERT: LD 18 GLU cc_start: 0.8653 (tp30) cc_final: 0.8359 (tp30) REVERT: LD 21 ASP cc_start: 0.8745 (m-30) cc_final: 0.8542 (m-30) REVERT: LF 3 ASP cc_start: 0.7529 (m-30) cc_final: 0.7275 (m-30) REVERT: LF 58 GLU cc_start: 0.7273 (pt0) cc_final: 0.7033 (tm-30) REVERT: H 74 MET cc_start: 0.8974 (mmm) cc_final: 0.8722 (mmm) REVERT: H 90 ASP cc_start: 0.8118 (t0) cc_final: 0.7842 (t0) REVERT: H 118 THR cc_start: 0.8857 (m) cc_final: 0.8539 (p) REVERT: H 137 ASP cc_start: 0.7386 (t70) cc_final: 0.6894 (t0) REVERT: I 74 MET cc_start: 0.9156 (tpp) cc_final: 0.8822 (mmm) REVERT: M 62 MET cc_start: 0.8500 (mtt) cc_final: 0.8288 (mtp) REVERT: M 156 ILE cc_start: 0.8688 (pt) cc_final: 0.8470 (tp) REVERT: N 24 VAL cc_start: 0.8958 (t) cc_final: 0.8521 (p) REVERT: N 130 CYS cc_start: 0.8604 (m) cc_final: 0.7997 (m) REVERT: O 90 ASP cc_start: 0.7917 (t0) cc_final: 0.7606 (t0) REVERT: O 92 LEU cc_start: 0.8506 (tt) cc_final: 0.8253 (tp) REVERT: O 118 THR cc_start: 0.8856 (m) cc_final: 0.8334 (p) REVERT: O 137 ASP cc_start: 0.8026 (t70) cc_final: 0.7473 (t0) REVERT: S 117 ASP cc_start: 0.7946 (p0) cc_final: 0.7594 (p0) REVERT: S 137 ASP cc_start: 0.8178 (t70) cc_final: 0.7389 (t0) REVERT: S 170 ASP cc_start: 0.7929 (t70) cc_final: 0.7677 (t0) REVERT: T 60 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8709 (mt) REVERT: U 9 ASP cc_start: 0.8420 (p0) cc_final: 0.8172 (p0) REVERT: U 58 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7724 (ptmt) outliers start: 194 outliers final: 149 residues processed: 1215 average time/residue: 0.2212 time to fit residues: 437.5322 Evaluate side-chains 1193 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1037 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 202 SER Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GB residue 7 MET Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HB residue 71 VAL Chi-restraints excluded: chain HC residue 70 VAL Chi-restraints excluded: chain HD residue 8 ILE Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 70 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 78 ARG Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 75 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain JA residue 10 VAL Chi-restraints excluded: chain JB residue 71 VAL Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JD residue 89 LEU Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 65 GLU Chi-restraints excluded: chain JE residue 73 VAL Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 5 LEU Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KC residue 50 VAL Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KE residue 7 MET Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LA residue 84 ASP Chi-restraints excluded: chain LB residue 7 MET Chi-restraints excluded: chain LC residue 17 VAL Chi-restraints excluded: chain LC residue 23 MET Chi-restraints excluded: chain LC residue 69 GLU Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 125 GLU Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 121 VAL Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 186 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 46 SER Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain T residue 60 LEU Chi-restraints excluded: chain T residue 126 THR Chi-restraints excluded: chain T residue 128 THR Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 156 ILE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 121 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 394 optimal weight: 1.9990 chunk 593 optimal weight: 2.9990 chunk 384 optimal weight: 0.0970 chunk 301 optimal weight: 3.9990 chunk 474 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 329 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 482 optimal weight: 7.9990 chunk 576 optimal weight: 0.2980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 ASN E 156 ASN ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JB 82 ASN KE 82 ASN LB 74 HIS LE 82 ASN G 98 HIS ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.094650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.085021 restraints weight = 112237.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.087188 restraints weight = 58231.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.088636 restraints weight = 35249.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.089631 restraints weight = 23754.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.090309 restraints weight = 17361.651| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 46860 Z= 0.132 Angle : 0.622 12.698 63645 Z= 0.317 Chirality : 0.044 0.238 7638 Planarity : 0.004 0.144 8340 Dihedral : 4.231 37.406 6783 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.99 % Allowed : 19.54 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.11), residues: 6183 helix: 0.17 (0.11), residues: 2468 sheet: -0.03 (0.13), residues: 1488 loop : -1.71 (0.14), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARGHA 66 TYR 0.022 0.001 TYR C 8 PHE 0.025 0.002 PHE E 10 TRP 0.026 0.001 TRP F 39 HIS 0.017 0.001 HISLB 74 Details of bonding type rmsd covalent geometry : bond 0.00315 (46860) covalent geometry : angle 0.62211 (63645) hydrogen bonds : bond 0.03230 ( 2487) hydrogen bonds : angle 4.29656 ( 7071) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 1109 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7533 (ttpt) REVERT: A 128 ASN cc_start: 0.8610 (t0) cc_final: 0.8316 (t0) REVERT: B 128 ASN cc_start: 0.8517 (t0) cc_final: 0.8128 (t0) REVERT: B 188 ASP cc_start: 0.8203 (t0) cc_final: 0.7787 (t0) REVERT: C 128 ASN cc_start: 0.8609 (t0) cc_final: 0.8151 (t0) REVERT: C 132 MET cc_start: 0.8119 (ttm) cc_final: 0.7906 (ttm) REVERT: C 187 ILE cc_start: 0.9106 (tp) cc_final: 0.8831 (tp) REVERT: D 76 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 163 ASN cc_start: 0.7935 (p0) cc_final: 0.7713 (p0) REVERT: E 50 ARG cc_start: 0.8493 (ttm110) cc_final: 0.8193 (ttm110) REVERT: E 77 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8772 (m) REVERT: E 109 MET cc_start: 0.8120 (mpm) cc_final: 0.7834 (mpm) REVERT: E 115 ARG cc_start: 0.7912 (mmt180) cc_final: 0.7152 (mmt-90) REVERT: E 128 ASN cc_start: 0.7981 (t0) cc_final: 0.7709 (t0) REVERT: F 39 TRP cc_start: 0.7593 (m100) cc_final: 0.7244 (m100) REVERT: F 72 TYR cc_start: 0.8869 (m-80) cc_final: 0.8543 (m-80) REVERT: F 96 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8529 (mm) REVERT: F 115 ARG cc_start: 0.7331 (mpt-90) cc_final: 0.6926 (mmt90) REVERT: F 133 MET cc_start: 0.8039 (mtm) cc_final: 0.7806 (mtp) REVERT: GA 16 MET cc_start: 0.8993 (tmm) cc_final: 0.8632 (tmm) REVERT: GA 18 GLU cc_start: 0.8616 (tp30) cc_final: 0.8277 (tp30) REVERT: GB 7 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8571 (mtm) REVERT: GB 21 ASP cc_start: 0.9014 (t70) cc_final: 0.8627 (t0) REVERT: GB 28 LYS cc_start: 0.8416 (tmmt) cc_final: 0.7539 (mttt) REVERT: GB 61 GLN cc_start: 0.8729 (tt0) cc_final: 0.8296 (tt0) REVERT: GC 28 LYS cc_start: 0.8529 (ttpp) cc_final: 0.7950 (mptt) REVERT: GC 43 THR cc_start: 0.9024 (m) cc_final: 0.8757 (p) REVERT: GD 62 ARG cc_start: 0.8879 (ttp-110) cc_final: 0.8556 (mtm110) REVERT: GD 78 ARG cc_start: 0.8198 (tmt90) cc_final: 0.7457 (mtm180) REVERT: GE 16 MET cc_start: 0.8877 (tmm) cc_final: 0.8556 (tmm) REVERT: GF 18 GLU cc_start: 0.8858 (tp30) cc_final: 0.8495 (tp30) REVERT: GF 92 THR cc_start: 0.8490 (m) cc_final: 0.8265 (p) REVERT: HA 9 GLU cc_start: 0.7960 (tp30) cc_final: 0.7730 (tp30) REVERT: HA 18 GLU cc_start: 0.8586 (tp30) cc_final: 0.8082 (tm-30) REVERT: HA 43 THR cc_start: 0.8940 (m) cc_final: 0.8392 (m) REVERT: HB 92 THR cc_start: 0.8633 (m) cc_final: 0.8163 (p) REVERT: HC 21 ASP cc_start: 0.8521 (t70) cc_final: 0.8179 (t0) REVERT: HC 28 LYS cc_start: 0.7789 (ttpt) cc_final: 0.7554 (mmtt) REVERT: HD 3 ASP cc_start: 0.7826 (m-30) cc_final: 0.7507 (m-30) REVERT: HD 78 ARG cc_start: 0.8631 (tmt90) cc_final: 0.7627 (ptp-170) REVERT: HE 10 VAL cc_start: 0.9098 (t) cc_final: 0.8856 (m) REVERT: HE 21 ASP cc_start: 0.7657 (t70) cc_final: 0.7388 (t70) REVERT: HE 43 THR cc_start: 0.9148 (m) cc_final: 0.8935 (t) REVERT: HE 78 ARG cc_start: 0.8085 (tpt170) cc_final: 0.7749 (ptt90) REVERT: HF 43 THR cc_start: 0.8593 (m) cc_final: 0.8261 (p) REVERT: HF 62 ARG cc_start: 0.8014 (mtm-85) cc_final: 0.7806 (mtm-85) REVERT: HF 78 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8402 (ptm160) REVERT: IA 42 VAL cc_start: 0.9198 (OUTLIER) cc_final: 0.8886 (p) REVERT: IA 43 THR cc_start: 0.9090 (m) cc_final: 0.8704 (p) REVERT: IB 21 ASP cc_start: 0.8349 (t70) cc_final: 0.7871 (t0) REVERT: IB 23 MET cc_start: 0.8473 (mtm) cc_final: 0.8050 (mtp) REVERT: IC 18 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7840 (tm-30) REVERT: ID 11 ARG cc_start: 0.8529 (mtp180) cc_final: 0.8190 (ttt90) REVERT: ID 16 MET cc_start: 0.8846 (tmm) cc_final: 0.8634 (tmm) REVERT: ID 25 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8612 (mttp) REVERT: ID 43 THR cc_start: 0.9508 (m) cc_final: 0.9225 (p) REVERT: IF 9 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8574 (tm-30) REVERT: IF 16 MET cc_start: 0.8866 (tmm) cc_final: 0.8623 (tmm) REVERT: IF 32 ILE cc_start: 0.8760 (pp) cc_final: 0.8472 (tp) REVERT: JA 16 MET cc_start: 0.8138 (tmm) cc_final: 0.7594 (tmm) REVERT: JA 65 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7893 (mm-30) REVERT: JB 61 GLN cc_start: 0.8681 (tt0) cc_final: 0.8218 (mt0) REVERT: JD 18 GLU cc_start: 0.8478 (tp30) cc_final: 0.8186 (tp30) REVERT: JD 80 HIS cc_start: 0.7915 (t-90) cc_final: 0.7637 (t-170) REVERT: JE 16 MET cc_start: 0.8176 (tmm) cc_final: 0.7847 (tmm) REVERT: JE 23 MET cc_start: 0.7988 (mtm) cc_final: 0.7637 (mtm) REVERT: JE 65 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: JF 18 GLU cc_start: 0.8022 (tp30) cc_final: 0.7812 (tm-30) REVERT: JF 65 GLU cc_start: 0.8475 (mp0) cc_final: 0.8130 (mp0) REVERT: KA 16 MET cc_start: 0.8964 (tmm) cc_final: 0.8475 (tmm) REVERT: KB 21 ASP cc_start: 0.8500 (t70) cc_final: 0.8153 (t0) REVERT: KC 7 MET cc_start: 0.7361 (mtm) cc_final: 0.7143 (mtm) REVERT: KC 28 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7899 (mptt) REVERT: KC 35 GLU cc_start: 0.7806 (mp0) cc_final: 0.7523 (mp0) REVERT: KC 43 THR cc_start: 0.9068 (m) cc_final: 0.8706 (p) REVERT: KD 23 MET cc_start: 0.8485 (mtm) cc_final: 0.8058 (mtp) REVERT: KD 78 ARG cc_start: 0.8311 (ttt90) cc_final: 0.7545 (mtm180) REVERT: KE 47 ARG cc_start: 0.8669 (mmm160) cc_final: 0.8215 (mmt90) REVERT: KF 28 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7722 (ptpp) REVERT: LA 32 ILE cc_start: 0.8126 (OUTLIER) cc_final: 0.7744 (pp) REVERT: LA 61 GLN cc_start: 0.8484 (tt0) cc_final: 0.8015 (tp40) REVERT: LC 21 ASP cc_start: 0.8482 (t70) cc_final: 0.8183 (t0) REVERT: LD 18 GLU cc_start: 0.8606 (tp30) cc_final: 0.8274 (tp30) REVERT: LF 78 ARG cc_start: 0.8737 (ttt-90) cc_final: 0.8013 (ttp80) REVERT: G 63 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7961 (mtm) REVERT: H 74 MET cc_start: 0.8961 (mmm) cc_final: 0.8696 (mmm) REVERT: H 90 ASP cc_start: 0.8209 (t0) cc_final: 0.7998 (t0) REVERT: H 118 THR cc_start: 0.8835 (m) cc_final: 0.8506 (p) REVERT: H 137 ASP cc_start: 0.7278 (t70) cc_final: 0.6810 (t0) REVERT: I 74 MET cc_start: 0.9149 (tpp) cc_final: 0.8858 (mmm) REVERT: M 152 LEU cc_start: 0.8422 (tp) cc_final: 0.8196 (tp) REVERT: M 156 ILE cc_start: 0.8663 (pt) cc_final: 0.8456 (tp) REVERT: N 24 VAL cc_start: 0.8942 (t) cc_final: 0.8476 (p) REVERT: N 130 CYS cc_start: 0.8527 (m) cc_final: 0.7888 (m) REVERT: O 90 ASP cc_start: 0.7853 (t0) cc_final: 0.7510 (t0) REVERT: O 118 THR cc_start: 0.8857 (m) cc_final: 0.8327 (p) REVERT: O 137 ASP cc_start: 0.8039 (t70) cc_final: 0.7433 (t0) REVERT: S 137 ASP cc_start: 0.8171 (t70) cc_final: 0.7388 (t0) REVERT: S 170 ASP cc_start: 0.7906 (t70) cc_final: 0.7671 (t0) REVERT: U 50 MET cc_start: 0.8467 (ppp) cc_final: 0.8200 (ptm) REVERT: U 58 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7738 (ptmt) REVERT: U 90 ASP cc_start: 0.7517 (m-30) cc_final: 0.7297 (m-30) outliers start: 182 outliers final: 132 residues processed: 1213 average time/residue: 0.2434 time to fit residues: 475.7675 Evaluate side-chains 1184 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 1043 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GB residue 7 MET Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 65 GLU Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HA residue 84 ASP Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HC residue 70 VAL Chi-restraints excluded: chain HD residue 8 ILE Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 70 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 78 ARG Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain JA residue 10 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 65 GLU Chi-restraints excluded: chain JE residue 73 VAL Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain JF residue 8 ILE Chi-restraints excluded: chain KA residue 42 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 5 LEU Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KC residue 50 VAL Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KE residue 7 MET Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LA residue 84 ASP Chi-restraints excluded: chain LB residue 7 MET Chi-restraints excluded: chain LB residue 31 LEU Chi-restraints excluded: chain LC residue 23 MET Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 142 THR Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 46 SER Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 156 ILE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 60 LEU Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain U residue 156 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 537 optimal weight: 4.9990 chunk 261 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 355 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 136 optimal weight: 0.0030 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IF 82 ASN JB 82 ASN ** JD 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LE 82 ASN ** T 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085295 restraints weight = 112592.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.087462 restraints weight = 58632.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088907 restraints weight = 35651.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.089899 restraints weight = 24111.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.090594 restraints weight = 17586.456| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 46860 Z= 0.135 Angle : 0.630 12.761 63645 Z= 0.321 Chirality : 0.044 0.268 7638 Planarity : 0.004 0.094 8340 Dihedral : 4.220 36.747 6783 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.79 % Allowed : 20.66 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.11), residues: 6183 helix: 0.25 (0.11), residues: 2472 sheet: -0.04 (0.13), residues: 1514 loop : -1.62 (0.14), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARGHA 66 TYR 0.026 0.001 TYR D 8 PHE 0.026 0.002 PHE D 10 TRP 0.062 0.002 TRP A 39 HIS 0.007 0.001 HISKF 74 Details of bonding type rmsd covalent geometry : bond 0.00324 (46860) covalent geometry : angle 0.62979 (63645) hydrogen bonds : bond 0.03230 ( 2487) hydrogen bonds : angle 4.29212 ( 7071) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 1082 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8001 (ttpt) cc_final: 0.7490 (ttpt) REVERT: A 39 TRP cc_start: 0.8363 (m100) cc_final: 0.8076 (m100) REVERT: A 75 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8428 (pp) REVERT: A 128 ASN cc_start: 0.8585 (t0) cc_final: 0.8325 (t0) REVERT: B 8 TYR cc_start: 0.8333 (t80) cc_final: 0.8069 (t80) REVERT: B 114 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8694 (mt) REVERT: B 128 ASN cc_start: 0.8498 (t0) cc_final: 0.8088 (t0) REVERT: B 188 ASP cc_start: 0.8194 (t0) cc_final: 0.7772 (t0) REVERT: C 128 ASN cc_start: 0.8626 (t0) cc_final: 0.8185 (t0) REVERT: C 187 ILE cc_start: 0.9116 (tp) cc_final: 0.8820 (tp) REVERT: D 76 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7436 (tm-30) REVERT: D 163 ASN cc_start: 0.7907 (p0) cc_final: 0.7683 (p0) REVERT: E 50 ARG cc_start: 0.8491 (ttm110) cc_final: 0.8214 (ttm110) REVERT: E 77 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8775 (m) REVERT: E 109 MET cc_start: 0.8141 (mpm) cc_final: 0.7881 (mpm) REVERT: E 128 ASN cc_start: 0.7869 (t0) cc_final: 0.7547 (t0) REVERT: F 39 TRP cc_start: 0.7557 (m100) cc_final: 0.6856 (m100) REVERT: F 72 TYR cc_start: 0.8847 (m-80) cc_final: 0.8512 (m-80) REVERT: F 96 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8496 (mm) REVERT: F 133 MET cc_start: 0.8026 (mtm) cc_final: 0.7774 (mtp) REVERT: GA 16 MET cc_start: 0.8964 (tmm) cc_final: 0.8568 (tmm) REVERT: GA 18 GLU cc_start: 0.8585 (tp30) cc_final: 0.8337 (tp30) REVERT: GB 7 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8494 (mtm) REVERT: GB 21 ASP cc_start: 0.8954 (t70) cc_final: 0.8577 (t0) REVERT: GB 28 LYS cc_start: 0.8396 (tmmt) cc_final: 0.7528 (mttt) REVERT: GB 61 GLN cc_start: 0.8696 (tt0) cc_final: 0.8301 (tt0) REVERT: GC 28 LYS cc_start: 0.8533 (ttpp) cc_final: 0.7952 (mptt) REVERT: GC 43 THR cc_start: 0.8985 (m) cc_final: 0.8732 (p) REVERT: GD 13 PHE cc_start: 0.8647 (t80) cc_final: 0.8443 (t80) REVERT: GD 62 ARG cc_start: 0.8861 (ttp-110) cc_final: 0.8532 (mtm110) REVERT: GD 78 ARG cc_start: 0.8206 (tmt90) cc_final: 0.7468 (mtm180) REVERT: GE 16 MET cc_start: 0.8783 (tmm) cc_final: 0.8422 (tmm) REVERT: GF 18 GLU cc_start: 0.8816 (tp30) cc_final: 0.8504 (tp30) REVERT: GF 92 THR cc_start: 0.8557 (m) cc_final: 0.8345 (p) REVERT: HA 9 GLU cc_start: 0.7893 (tp30) cc_final: 0.7601 (tp30) REVERT: HA 18 GLU cc_start: 0.8583 (tp30) cc_final: 0.8085 (tm-30) REVERT: HA 43 THR cc_start: 0.8933 (m) cc_final: 0.8483 (m) REVERT: HB 92 THR cc_start: 0.8635 (m) cc_final: 0.8172 (p) REVERT: HC 9 GLU cc_start: 0.7914 (tp30) cc_final: 0.7341 (tp30) REVERT: HC 21 ASP cc_start: 0.8485 (t70) cc_final: 0.8170 (t0) REVERT: HC 28 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7549 (mmtt) REVERT: HD 3 ASP cc_start: 0.7774 (m-30) cc_final: 0.7498 (m-30) REVERT: HD 78 ARG cc_start: 0.8613 (tmt90) cc_final: 0.7636 (ptp-170) REVERT: HE 21 ASP cc_start: 0.7639 (t70) cc_final: 0.7390 (t70) REVERT: HE 43 THR cc_start: 0.9121 (m) cc_final: 0.8866 (t) REVERT: HE 78 ARG cc_start: 0.8056 (tpt170) cc_final: 0.7759 (ptt90) REVERT: HF 43 THR cc_start: 0.8612 (m) cc_final: 0.8280 (p) REVERT: HF 62 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7746 (mtm-85) REVERT: IA 42 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8931 (p) REVERT: IA 43 THR cc_start: 0.9045 (m) cc_final: 0.8680 (p) REVERT: IB 21 ASP cc_start: 0.8348 (t70) cc_final: 0.7877 (t0) REVERT: IB 23 MET cc_start: 0.8437 (mtm) cc_final: 0.8021 (mtp) REVERT: IC 5 LEU cc_start: 0.8827 (tp) cc_final: 0.8396 (tp) REVERT: ID 11 ARG cc_start: 0.8508 (mtp180) cc_final: 0.8100 (ttt90) REVERT: ID 16 MET cc_start: 0.8838 (tmm) cc_final: 0.8618 (tmm) REVERT: ID 43 THR cc_start: 0.9497 (m) cc_final: 0.9207 (p) REVERT: IF 9 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8562 (tm-30) REVERT: IF 32 ILE cc_start: 0.8749 (pp) cc_final: 0.8446 (tp) REVERT: JA 16 MET cc_start: 0.8172 (tmm) cc_final: 0.7614 (tmm) REVERT: JA 65 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7899 (mm-30) REVERT: JB 61 GLN cc_start: 0.8701 (tt0) cc_final: 0.8395 (mt0) REVERT: JD 18 GLU cc_start: 0.8470 (tp30) cc_final: 0.8176 (tp30) REVERT: JD 69 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6612 (mm-30) REVERT: JD 80 HIS cc_start: 0.7965 (t-90) cc_final: 0.7727 (t-170) REVERT: JE 16 MET cc_start: 0.8176 (tmm) cc_final: 0.7834 (tmm) REVERT: JE 23 MET cc_start: 0.7881 (mtm) cc_final: 0.7562 (mtm) REVERT: JE 65 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: JF 65 GLU cc_start: 0.8542 (mp0) cc_final: 0.8341 (mp0) REVERT: KA 16 MET cc_start: 0.8890 (tmm) cc_final: 0.8551 (tmm) REVERT: KB 21 ASP cc_start: 0.8471 (t70) cc_final: 0.8112 (t0) REVERT: KC 28 LYS cc_start: 0.8342 (ttpt) cc_final: 0.7898 (mptt) REVERT: KC 35 GLU cc_start: 0.7796 (mp0) cc_final: 0.7557 (mp0) REVERT: KC 43 THR cc_start: 0.9064 (m) cc_final: 0.8718 (p) REVERT: KD 23 MET cc_start: 0.8434 (mtm) cc_final: 0.8070 (mtp) REVERT: KD 78 ARG cc_start: 0.8318 (ttt90) cc_final: 0.7564 (mtm180) REVERT: KF 28 LYS cc_start: 0.8268 (ttpp) cc_final: 0.7793 (ptpp) REVERT: LA 32 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7736 (pp) REVERT: LA 61 GLN cc_start: 0.8438 (tt0) cc_final: 0.8016 (tp40) REVERT: LC 21 ASP cc_start: 0.8467 (t70) cc_final: 0.8176 (t0) REVERT: LD 18 GLU cc_start: 0.8612 (tp30) cc_final: 0.8257 (tp30) REVERT: LF 58 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7032 (tt0) REVERT: LF 78 ARG cc_start: 0.8683 (ttt-90) cc_final: 0.7955 (ttp80) REVERT: H 74 MET cc_start: 0.8951 (mmm) cc_final: 0.8670 (mmm) REVERT: H 90 ASP cc_start: 0.8239 (t0) cc_final: 0.7989 (t0) REVERT: H 137 ASP cc_start: 0.7251 (t70) cc_final: 0.6918 (t0) REVERT: H 188 GLU cc_start: 0.6686 (tt0) cc_final: 0.6094 (tt0) REVERT: I 74 MET cc_start: 0.9188 (tpp) cc_final: 0.8885 (mmm) REVERT: M 152 LEU cc_start: 0.8567 (tp) cc_final: 0.8263 (tp) REVERT: M 156 ILE cc_start: 0.8645 (pt) cc_final: 0.8425 (tp) REVERT: N 24 VAL cc_start: 0.8948 (t) cc_final: 0.8496 (p) REVERT: N 130 CYS cc_start: 0.8487 (m) cc_final: 0.7880 (m) REVERT: O 26 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7144 (pt0) REVERT: O 36 VAL cc_start: 0.9072 (t) cc_final: 0.8792 (p) REVERT: O 90 ASP cc_start: 0.8071 (t0) cc_final: 0.7566 (t0) REVERT: O 118 THR cc_start: 0.8861 (m) cc_final: 0.8313 (p) REVERT: O 137 ASP cc_start: 0.8063 (t70) cc_final: 0.7621 (t70) REVERT: S 26 GLU cc_start: 0.7595 (tt0) cc_final: 0.7243 (tt0) REVERT: S 49 LEU cc_start: 0.8975 (tp) cc_final: 0.8747 (tp) REVERT: S 170 ASP cc_start: 0.7965 (t70) cc_final: 0.7729 (t0) REVERT: U 50 MET cc_start: 0.8411 (ppp) cc_final: 0.8196 (ptm) REVERT: U 58 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7707 (ptmt) REVERT: U 90 ASP cc_start: 0.7653 (m-30) cc_final: 0.7333 (m-30) REVERT: U 91 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7506 (tt0) outliers start: 173 outliers final: 133 residues processed: 1178 average time/residue: 0.1881 time to fit residues: 362.5472 Evaluate side-chains 1191 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 1047 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain GA residue 75 VAL Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GB residue 7 MET Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 65 GLU Chi-restraints excluded: chain GE residue 76 ILE Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HC residue 70 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 70 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain HF residue 92 THR Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IB residue 61 GLN Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain IF residue 89 LEU Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 65 GLU Chi-restraints excluded: chain JE residue 73 VAL Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain KA residue 42 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KC residue 50 VAL Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KE residue 7 MET Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LA residue 84 ASP Chi-restraints excluded: chain LB residue 7 MET Chi-restraints excluded: chain LB residue 31 LEU Chi-restraints excluded: chain LC residue 23 MET Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LF residue 7 MET Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain T residue 126 THR Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 156 ILE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 91 GLU Chi-restraints excluded: chain U residue 121 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 170 optimal weight: 0.7980 chunk 476 optimal weight: 0.5980 chunk 507 optimal weight: 1.9990 chunk 544 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 606 optimal weight: 0.5980 chunk 335 optimal weight: 0.0000 chunk 491 optimal weight: 2.9990 chunk 424 optimal weight: 0.1980 chunk 230 optimal weight: 0.6980 chunk 410 optimal weight: 1.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 123 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LE 82 ASN I 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086751 restraints weight = 111987.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088920 restraints weight = 58252.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.090347 restraints weight = 35286.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091298 restraints weight = 23907.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.091990 restraints weight = 17651.284| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 46860 Z= 0.123 Angle : 0.635 12.491 63645 Z= 0.322 Chirality : 0.044 0.206 7638 Planarity : 0.004 0.077 8340 Dihedral : 4.172 35.525 6783 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.44 % Allowed : 21.16 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.11), residues: 6183 helix: 0.34 (0.11), residues: 2467 sheet: 0.04 (0.13), residues: 1504 loop : -1.57 (0.14), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGHA 66 TYR 0.030 0.001 TYR D 8 PHE 0.024 0.002 PHE D 10 TRP 0.042 0.001 TRP A 39 HIS 0.006 0.001 HISKF 74 Details of bonding type rmsd covalent geometry : bond 0.00295 (46860) covalent geometry : angle 0.63518 (63645) hydrogen bonds : bond 0.03122 ( 2487) hydrogen bonds : angle 4.26989 ( 7071) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1271 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1114 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7475 (ttpt) REVERT: A 75 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8367 (pp) REVERT: A 168 ASN cc_start: 0.8959 (t0) cc_final: 0.8632 (t0) REVERT: B 8 TYR cc_start: 0.8271 (t80) cc_final: 0.8024 (t80) REVERT: B 99 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7141 (mtp-110) REVERT: B 128 ASN cc_start: 0.8486 (t0) cc_final: 0.8043 (t0) REVERT: B 188 ASP cc_start: 0.8163 (t0) cc_final: 0.7756 (t0) REVERT: C 39 TRP cc_start: 0.7516 (m100) cc_final: 0.7109 (m100) REVERT: C 50 ARG cc_start: 0.7461 (tpm170) cc_final: 0.7228 (tpm170) REVERT: C 123 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7665 (mm110) REVERT: C 128 ASN cc_start: 0.8590 (t0) cc_final: 0.8139 (t0) REVERT: C 187 ILE cc_start: 0.9075 (tp) cc_final: 0.8775 (tp) REVERT: D 70 ARG cc_start: 0.7238 (ptm160) cc_final: 0.6890 (ttm-80) REVERT: D 76 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7370 (tm-30) REVERT: D 163 ASN cc_start: 0.7899 (p0) cc_final: 0.7657 (p0) REVERT: E 50 ARG cc_start: 0.8510 (ttm110) cc_final: 0.8307 (ttm110) REVERT: E 77 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8757 (m) REVERT: E 109 MET cc_start: 0.8142 (mpm) cc_final: 0.7855 (mpm) REVERT: E 128 ASN cc_start: 0.7781 (t0) cc_final: 0.7433 (t0) REVERT: F 72 TYR cc_start: 0.8876 (m-80) cc_final: 0.8617 (m-80) REVERT: F 96 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8466 (mm) REVERT: F 133 MET cc_start: 0.8043 (mtm) cc_final: 0.7773 (mtp) REVERT: GA 16 MET cc_start: 0.9000 (tmm) cc_final: 0.8610 (tmm) REVERT: GA 34 TYR cc_start: 0.8374 (p90) cc_final: 0.8067 (p90) REVERT: GB 21 ASP cc_start: 0.8936 (t70) cc_final: 0.8524 (t0) REVERT: GB 28 LYS cc_start: 0.8421 (tmmt) cc_final: 0.7590 (mttt) REVERT: GB 61 GLN cc_start: 0.8704 (tt0) cc_final: 0.8293 (tt0) REVERT: GC 28 LYS cc_start: 0.8477 (ttpp) cc_final: 0.7956 (mptt) REVERT: GC 43 THR cc_start: 0.9005 (m) cc_final: 0.8742 (p) REVERT: GD 13 PHE cc_start: 0.8647 (t80) cc_final: 0.8435 (t80) REVERT: GD 62 ARG cc_start: 0.8844 (ttp-110) cc_final: 0.8536 (mtm110) REVERT: GD 78 ARG cc_start: 0.8196 (tmt90) cc_final: 0.7463 (mtm180) REVERT: GE 16 MET cc_start: 0.8790 (tmm) cc_final: 0.8467 (tmm) REVERT: GF 18 GLU cc_start: 0.8738 (tp30) cc_final: 0.8469 (tp30) REVERT: HA 9 GLU cc_start: 0.7980 (tp30) cc_final: 0.7699 (tp30) REVERT: HA 18 GLU cc_start: 0.8559 (tp30) cc_final: 0.8096 (tm-30) REVERT: HA 43 THR cc_start: 0.8867 (m) cc_final: 0.8257 (m) REVERT: HB 92 THR cc_start: 0.8629 (m) cc_final: 0.8145 (p) REVERT: HC 21 ASP cc_start: 0.8487 (t70) cc_final: 0.8158 (t0) REVERT: HC 28 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7547 (mmtm) REVERT: HC 65 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7925 (mm-30) REVERT: HD 3 ASP cc_start: 0.7835 (m-30) cc_final: 0.7558 (m-30) REVERT: HD 78 ARG cc_start: 0.8486 (tmt90) cc_final: 0.7560 (ptp-170) REVERT: HE 21 ASP cc_start: 0.7597 (t70) cc_final: 0.7379 (t70) REVERT: HE 43 THR cc_start: 0.9090 (m) cc_final: 0.8856 (t) REVERT: HE 78 ARG cc_start: 0.8040 (tpt170) cc_final: 0.7759 (ptt90) REVERT: HF 43 THR cc_start: 0.8570 (m) cc_final: 0.8269 (p) REVERT: IA 42 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8997 (p) REVERT: IA 43 THR cc_start: 0.8976 (m) cc_final: 0.8664 (p) REVERT: IB 21 ASP cc_start: 0.8352 (t70) cc_final: 0.7916 (t0) REVERT: IB 23 MET cc_start: 0.8382 (mtm) cc_final: 0.7994 (mtp) REVERT: IC 5 LEU cc_start: 0.8868 (tp) cc_final: 0.8437 (tp) REVERT: ID 11 ARG cc_start: 0.8504 (mtp180) cc_final: 0.8105 (ttt90) REVERT: ID 16 MET cc_start: 0.8836 (tmm) cc_final: 0.8598 (tmm) REVERT: ID 25 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8831 (mttp) REVERT: ID 43 THR cc_start: 0.9481 (m) cc_final: 0.9191 (p) REVERT: IF 9 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8542 (tm-30) REVERT: IF 32 ILE cc_start: 0.8688 (pp) cc_final: 0.8348 (tp) REVERT: JA 16 MET cc_start: 0.8207 (tmm) cc_final: 0.7734 (tmm) REVERT: JA 32 ILE cc_start: 0.8293 (pp) cc_final: 0.7963 (pp) REVERT: JA 65 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7962 (mm-30) REVERT: JB 61 GLN cc_start: 0.8648 (tt0) cc_final: 0.8385 (mt0) REVERT: JD 18 GLU cc_start: 0.8355 (tp30) cc_final: 0.8062 (tp30) REVERT: JD 69 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6610 (mm-30) REVERT: JE 16 MET cc_start: 0.8147 (tmm) cc_final: 0.7843 (tmm) REVERT: JE 23 MET cc_start: 0.7827 (mtm) cc_final: 0.7499 (mtm) REVERT: JE 65 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: JF 65 GLU cc_start: 0.8534 (mp0) cc_final: 0.8318 (mp0) REVERT: KA 16 MET cc_start: 0.8923 (tmm) cc_final: 0.8601 (tmm) REVERT: KA 43 THR cc_start: 0.9031 (p) cc_final: 0.8804 (p) REVERT: KB 21 ASP cc_start: 0.8416 (t70) cc_final: 0.8102 (t0) REVERT: KB 23 MET cc_start: 0.8298 (mtm) cc_final: 0.8079 (mtm) REVERT: KC 28 LYS cc_start: 0.8308 (ttpt) cc_final: 0.7886 (mptt) REVERT: KC 43 THR cc_start: 0.8967 (m) cc_final: 0.8598 (p) REVERT: KD 23 MET cc_start: 0.8317 (mtm) cc_final: 0.8051 (mtp) REVERT: KD 25 LYS cc_start: 0.8490 (mttm) cc_final: 0.8256 (mttm) REVERT: KD 78 ARG cc_start: 0.8317 (ttt90) cc_final: 0.7568 (mtm180) REVERT: KE 11 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.8254 (ttm-80) REVERT: KF 28 LYS cc_start: 0.8247 (ttpp) cc_final: 0.7814 (ptpp) REVERT: KF 80 HIS cc_start: 0.7627 (t-90) cc_final: 0.7259 (t-90) REVERT: LA 32 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7673 (pp) REVERT: LA 61 GLN cc_start: 0.8411 (tt0) cc_final: 0.8026 (tp40) REVERT: LC 21 ASP cc_start: 0.8413 (t70) cc_final: 0.8139 (t0) REVERT: LD 18 GLU cc_start: 0.8580 (tp30) cc_final: 0.8269 (tp30) REVERT: LE 16 MET cc_start: 0.8004 (tmm) cc_final: 0.7733 (tmm) REVERT: LE 23 MET cc_start: 0.8440 (mtm) cc_final: 0.8195 (mtm) REVERT: LE 43 THR cc_start: 0.9123 (m) cc_final: 0.8758 (p) REVERT: LF 58 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7024 (tt0) REVERT: LF 78 ARG cc_start: 0.8671 (ttt-90) cc_final: 0.7972 (ttp80) REVERT: G 58 LYS cc_start: 0.8082 (mtmm) cc_final: 0.7774 (ptpt) REVERT: H 74 MET cc_start: 0.8985 (mmm) cc_final: 0.8648 (mmt) REVERT: H 90 ASP cc_start: 0.8195 (t0) cc_final: 0.7960 (t0) REVERT: I 74 MET cc_start: 0.9175 (tpp) cc_final: 0.8901 (mmm) REVERT: M 119 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6532 (tm-30) REVERT: M 152 LEU cc_start: 0.8631 (tp) cc_final: 0.8333 (tp) REVERT: M 156 ILE cc_start: 0.8611 (pt) cc_final: 0.8411 (tp) REVERT: M 180 GLU cc_start: 0.8595 (pp20) cc_final: 0.8326 (pp20) REVERT: N 24 VAL cc_start: 0.9040 (t) cc_final: 0.8555 (p) REVERT: N 130 CYS cc_start: 0.8454 (m) cc_final: 0.7806 (m) REVERT: O 26 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7170 (pt0) REVERT: O 36 VAL cc_start: 0.9043 (t) cc_final: 0.8799 (p) REVERT: O 90 ASP cc_start: 0.7968 (t0) cc_final: 0.7454 (t0) REVERT: O 118 THR cc_start: 0.8837 (m) cc_final: 0.8156 (p) REVERT: O 137 ASP cc_start: 0.7992 (t70) cc_final: 0.7567 (t70) REVERT: S 26 GLU cc_start: 0.7566 (tt0) cc_final: 0.7202 (tt0) REVERT: S 106 ASP cc_start: 0.8135 (t0) cc_final: 0.7783 (m-30) REVERT: S 170 ASP cc_start: 0.7936 (t70) cc_final: 0.7692 (t0) REVERT: U 58 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7756 (ptmt) REVERT: U 90 ASP cc_start: 0.7529 (m-30) cc_final: 0.7305 (m-30) outliers start: 157 outliers final: 122 residues processed: 1202 average time/residue: 0.1912 time to fit residues: 374.3880 Evaluate side-chains 1161 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 1031 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain GE residue 65 GLU Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 70 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 50 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain JC residue 23 MET Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 65 GLU Chi-restraints excluded: chain JE residue 73 VAL Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain KA residue 42 VAL Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KC residue 7 MET Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KE residue 7 MET Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LA residue 84 ASP Chi-restraints excluded: chain LB residue 7 MET Chi-restraints excluded: chain LC residue 23 MET Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LF residue 7 MET Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 29 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 58 LYS Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 156 ILE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 308 optimal weight: 0.6980 chunk 462 optimal weight: 2.9990 chunk 576 optimal weight: 0.0030 chunk 404 optimal weight: 0.7980 chunk 301 optimal weight: 3.9990 chunk 510 optimal weight: 0.8980 chunk 417 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 505 optimal weight: 0.2980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JB 82 ASN ** KA 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LE 61 GLN LE 82 ASN T 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.086742 restraints weight = 112731.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.088903 restraints weight = 58429.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.090364 restraints weight = 35391.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.091355 restraints weight = 23785.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092046 restraints weight = 17258.443| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 46860 Z= 0.133 Angle : 0.652 12.342 63645 Z= 0.331 Chirality : 0.044 0.228 7638 Planarity : 0.004 0.070 8340 Dihedral : 4.179 36.052 6782 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.14 % Allowed : 22.02 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.11), residues: 6183 helix: 0.29 (0.11), residues: 2501 sheet: 0.03 (0.13), residues: 1506 loop : -1.76 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGHA 66 TYR 0.031 0.001 TYR D 8 PHE 0.024 0.002 PHE D 10 TRP 0.085 0.002 TRP A 39 HIS 0.008 0.001 HISKA 80 Details of bonding type rmsd covalent geometry : bond 0.00320 (46860) covalent geometry : angle 0.65160 (63645) hydrogen bonds : bond 0.03191 ( 2487) hydrogen bonds : angle 4.28277 ( 7071) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12366 Ramachandran restraints generated. 6183 Oldfield, 0 Emsley, 6183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1066 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASN cc_start: 0.8952 (t0) cc_final: 0.8632 (t0) REVERT: B 8 TYR cc_start: 0.8296 (t80) cc_final: 0.8050 (t80) REVERT: B 128 ASN cc_start: 0.8463 (t0) cc_final: 0.8012 (t0) REVERT: B 188 ASP cc_start: 0.8134 (t0) cc_final: 0.7761 (t0) REVERT: C 7 THR cc_start: 0.8048 (OUTLIER) cc_final: 0.7705 (t) REVERT: C 39 TRP cc_start: 0.7523 (m100) cc_final: 0.7064 (m100) REVERT: C 50 ARG cc_start: 0.7494 (tpm170) cc_final: 0.7273 (tpm170) REVERT: C 128 ASN cc_start: 0.8586 (t0) cc_final: 0.8140 (t0) REVERT: D 48 ILE cc_start: 0.9194 (tp) cc_final: 0.8922 (tp) REVERT: D 163 ASN cc_start: 0.7852 (p0) cc_final: 0.7636 (p0) REVERT: E 77 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8805 (m) REVERT: E 109 MET cc_start: 0.8099 (mpm) cc_final: 0.7857 (mpm) REVERT: E 115 ARG cc_start: 0.7737 (mmt-90) cc_final: 0.7343 (mmt180) REVERT: E 128 ASN cc_start: 0.7746 (t0) cc_final: 0.7463 (t0) REVERT: F 72 TYR cc_start: 0.8894 (m-80) cc_final: 0.8589 (m-80) REVERT: F 96 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8458 (mm) REVERT: F 133 MET cc_start: 0.8058 (mtm) cc_final: 0.7770 (mtp) REVERT: GA 16 MET cc_start: 0.8921 (tmm) cc_final: 0.8575 (tmm) REVERT: GA 34 TYR cc_start: 0.8350 (p90) cc_final: 0.8097 (p90) REVERT: GB 21 ASP cc_start: 0.8920 (t70) cc_final: 0.8498 (t0) REVERT: GB 28 LYS cc_start: 0.8417 (tmmt) cc_final: 0.7598 (mttt) REVERT: GB 61 GLN cc_start: 0.8690 (tt0) cc_final: 0.8270 (tt0) REVERT: GC 28 LYS cc_start: 0.8480 (ttpp) cc_final: 0.7963 (mptt) REVERT: GC 43 THR cc_start: 0.9044 (m) cc_final: 0.8742 (p) REVERT: GD 13 PHE cc_start: 0.8647 (t80) cc_final: 0.8423 (t80) REVERT: GD 62 ARG cc_start: 0.8819 (ttp-110) cc_final: 0.8513 (mtm110) REVERT: GD 78 ARG cc_start: 0.8210 (tmt90) cc_final: 0.7458 (mtm180) REVERT: GE 16 MET cc_start: 0.8799 (tmm) cc_final: 0.8477 (tmm) REVERT: GF 18 GLU cc_start: 0.8768 (tp30) cc_final: 0.8462 (tp30) REVERT: HA 9 GLU cc_start: 0.7901 (tp30) cc_final: 0.7695 (tp30) REVERT: HA 18 GLU cc_start: 0.8558 (tp30) cc_final: 0.8016 (tm-30) REVERT: HA 43 THR cc_start: 0.8982 (m) cc_final: 0.8279 (m) REVERT: HA 58 GLU cc_start: 0.7988 (pm20) cc_final: 0.7490 (pm20) REVERT: HB 61 GLN cc_start: 0.8653 (tt0) cc_final: 0.7989 (tt0) REVERT: HB 92 THR cc_start: 0.8615 (m) cc_final: 0.8123 (p) REVERT: HC 9 GLU cc_start: 0.7921 (tp30) cc_final: 0.7215 (tp30) REVERT: HC 21 ASP cc_start: 0.8483 (t70) cc_final: 0.8146 (t0) REVERT: HC 28 LYS cc_start: 0.7885 (ttpt) cc_final: 0.7543 (mmtm) REVERT: HD 3 ASP cc_start: 0.7803 (m-30) cc_final: 0.7532 (m-30) REVERT: HD 78 ARG cc_start: 0.8490 (tmt90) cc_final: 0.7581 (ptp-170) REVERT: HE 21 ASP cc_start: 0.7655 (t70) cc_final: 0.7431 (t70) REVERT: HE 43 THR cc_start: 0.9092 (m) cc_final: 0.8857 (t) REVERT: HE 78 ARG cc_start: 0.8039 (tpt170) cc_final: 0.7753 (ptt90) REVERT: HF 43 THR cc_start: 0.8576 (m) cc_final: 0.8268 (p) REVERT: IA 42 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8968 (p) REVERT: IA 43 THR cc_start: 0.9112 (m) cc_final: 0.8664 (p) REVERT: IB 21 ASP cc_start: 0.8369 (t70) cc_final: 0.7918 (t0) REVERT: IB 23 MET cc_start: 0.8377 (mtm) cc_final: 0.7988 (mtp) REVERT: IC 5 LEU cc_start: 0.8899 (tp) cc_final: 0.8502 (tp) REVERT: ID 11 ARG cc_start: 0.8515 (mtp180) cc_final: 0.8019 (ttt90) REVERT: ID 16 MET cc_start: 0.8860 (tmm) cc_final: 0.8627 (tmm) REVERT: ID 25 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8838 (mttp) REVERT: ID 43 THR cc_start: 0.9490 (m) cc_final: 0.9214 (p) REVERT: ID 62 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7980 (mtm110) REVERT: IF 9 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8587 (tm-30) REVERT: IF 32 ILE cc_start: 0.8704 (pp) cc_final: 0.8386 (tp) REVERT: JA 16 MET cc_start: 0.8225 (tmm) cc_final: 0.7743 (tmm) REVERT: JA 32 ILE cc_start: 0.8212 (pp) cc_final: 0.7866 (pp) REVERT: JA 65 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7972 (mm-30) REVERT: JB 61 GLN cc_start: 0.8681 (tt0) cc_final: 0.8473 (mt0) REVERT: JD 18 GLU cc_start: 0.8335 (tp30) cc_final: 0.8014 (tp30) REVERT: JE 16 MET cc_start: 0.8176 (tmm) cc_final: 0.7838 (tmm) REVERT: JE 23 MET cc_start: 0.7807 (mtm) cc_final: 0.7442 (mtm) REVERT: JE 65 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7537 (pm20) REVERT: JF 62 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.7632 (ttp80) REVERT: JF 65 GLU cc_start: 0.8537 (mp0) cc_final: 0.8253 (mp0) REVERT: KA 16 MET cc_start: 0.8919 (tmm) cc_final: 0.8554 (tmm) REVERT: KB 21 ASP cc_start: 0.8398 (t70) cc_final: 0.8081 (t0) REVERT: KB 23 MET cc_start: 0.8340 (mtm) cc_final: 0.8101 (mtm) REVERT: KC 28 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7844 (mptt) REVERT: KC 43 THR cc_start: 0.8969 (m) cc_final: 0.8659 (p) REVERT: KD 23 MET cc_start: 0.8303 (mtm) cc_final: 0.8021 (mtp) REVERT: KD 25 LYS cc_start: 0.8469 (mttm) cc_final: 0.8204 (mttm) REVERT: KD 78 ARG cc_start: 0.8308 (ttt90) cc_final: 0.7570 (mtm180) REVERT: KE 11 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8046 (ttt90) REVERT: KF 28 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7798 (ptpp) REVERT: LA 32 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7676 (pp) REVERT: LA 61 GLN cc_start: 0.8432 (tt0) cc_final: 0.8018 (tp40) REVERT: LC 5 LEU cc_start: 0.9352 (tp) cc_final: 0.9055 (tp) REVERT: LC 21 ASP cc_start: 0.8436 (t70) cc_final: 0.8152 (t0) REVERT: LE 43 THR cc_start: 0.9119 (m) cc_final: 0.8756 (p) REVERT: LE 65 GLU cc_start: 0.7857 (pt0) cc_final: 0.7506 (pm20) REVERT: LF 58 GLU cc_start: 0.7516 (tm-30) cc_final: 0.6973 (tt0) REVERT: LF 78 ARG cc_start: 0.8663 (ttt-90) cc_final: 0.7963 (ttp80) REVERT: H 74 MET cc_start: 0.9016 (mmm) cc_final: 0.8657 (mmt) REVERT: H 90 ASP cc_start: 0.8265 (t0) cc_final: 0.7971 (t0) REVERT: H 137 ASP cc_start: 0.7683 (t70) cc_final: 0.7333 (t0) REVERT: I 74 MET cc_start: 0.9200 (tpp) cc_final: 0.8942 (mmm) REVERT: M 119 GLU cc_start: 0.7057 (tm-30) cc_final: 0.6717 (tm-30) REVERT: M 152 LEU cc_start: 0.8667 (tp) cc_final: 0.8366 (tp) REVERT: N 24 VAL cc_start: 0.8989 (t) cc_final: 0.8553 (p) REVERT: N 130 CYS cc_start: 0.8416 (m) cc_final: 0.7782 (m) REVERT: O 26 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7187 (pt0) REVERT: O 90 ASP cc_start: 0.7976 (t0) cc_final: 0.7500 (t0) REVERT: O 118 THR cc_start: 0.8594 (m) cc_final: 0.8064 (p) REVERT: O 137 ASP cc_start: 0.8028 (t70) cc_final: 0.7576 (t70) REVERT: S 50 MET cc_start: 0.8402 (ttp) cc_final: 0.7848 (ptm) REVERT: S 106 ASP cc_start: 0.8139 (t0) cc_final: 0.7798 (m-30) REVERT: S 170 ASP cc_start: 0.7935 (t70) cc_final: 0.7691 (t0) REVERT: U 58 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7761 (ptmt) REVERT: U 90 ASP cc_start: 0.7629 (m-30) cc_final: 0.7317 (m-30) outliers start: 143 outliers final: 120 residues processed: 1154 average time/residue: 0.1800 time to fit residues: 340.4804 Evaluate side-chains 1157 residues out of total 4560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 1029 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 111 HIS Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 111 HIS Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain GA residue 92 THR Chi-restraints excluded: chain GC residue 73 VAL Chi-restraints excluded: chain GD residue 17 VAL Chi-restraints excluded: chain GD residue 50 VAL Chi-restraints excluded: chain HA residue 42 VAL Chi-restraints excluded: chain HB residue 17 VAL Chi-restraints excluded: chain HD residue 50 VAL Chi-restraints excluded: chain HE residue 73 VAL Chi-restraints excluded: chain HE residue 75 VAL Chi-restraints excluded: chain HF residue 8 ILE Chi-restraints excluded: chain HF residue 31 LEU Chi-restraints excluded: chain HF residue 37 THR Chi-restraints excluded: chain HF residue 61 GLN Chi-restraints excluded: chain HF residue 71 VAL Chi-restraints excluded: chain IA residue 42 VAL Chi-restraints excluded: chain IA residue 50 VAL Chi-restraints excluded: chain IB residue 17 VAL Chi-restraints excluded: chain IC residue 50 VAL Chi-restraints excluded: chain IC residue 89 LEU Chi-restraints excluded: chain IE residue 36 LYS Chi-restraints excluded: chain IE residue 50 VAL Chi-restraints excluded: chain IF residue 42 VAL Chi-restraints excluded: chain IF residue 61 GLN Chi-restraints excluded: chain JB residue 82 ASN Chi-restraints excluded: chain JC residue 23 MET Chi-restraints excluded: chain JC residue 50 VAL Chi-restraints excluded: chain JD residue 50 VAL Chi-restraints excluded: chain JD residue 74 HIS Chi-restraints excluded: chain JE residue 7 MET Chi-restraints excluded: chain JE residue 21 ASP Chi-restraints excluded: chain JE residue 65 GLU Chi-restraints excluded: chain JE residue 73 VAL Chi-restraints excluded: chain JE residue 75 VAL Chi-restraints excluded: chain JF residue 58 GLU Chi-restraints excluded: chain KA residue 75 VAL Chi-restraints excluded: chain KB residue 17 VAL Chi-restraints excluded: chain KC residue 50 VAL Chi-restraints excluded: chain KC residue 65 GLU Chi-restraints excluded: chain KE residue 30 GLU Chi-restraints excluded: chain KF residue 5 LEU Chi-restraints excluded: chain KF residue 82 ASN Chi-restraints excluded: chain LA residue 32 ILE Chi-restraints excluded: chain LA residue 84 ASP Chi-restraints excluded: chain LB residue 7 MET Chi-restraints excluded: chain LC residue 23 MET Chi-restraints excluded: chain LD residue 50 VAL Chi-restraints excluded: chain LD residue 89 LEU Chi-restraints excluded: chain LF residue 7 MET Chi-restraints excluded: chain LF residue 92 THR Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 121 VAL Chi-restraints excluded: chain G residue 123 ILE Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 154 ILE Chi-restraints excluded: chain I residue 18 ASP Chi-restraints excluded: chain I residue 56 SER Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 80 ILE Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 189 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain M residue 46 SER Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 126 THR Chi-restraints excluded: chain M residue 196 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 154 ILE Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain O residue 26 GLU Chi-restraints excluded: chain O residue 38 ASP Chi-restraints excluded: chain O residue 50 MET Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain S residue 24 VAL Chi-restraints excluded: chain S residue 34 ILE Chi-restraints excluded: chain S residue 93 GLU Chi-restraints excluded: chain S residue 128 THR Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 50 MET Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain T residue 156 ILE Chi-restraints excluded: chain T residue 163 THR Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain T residue 199 LEU Chi-restraints excluded: chain U residue 58 LYS Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain U residue 121 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 615 random chunks: chunk 365 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 340 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 376 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 237 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 610 optimal weight: 0.0070 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN B 123 GLN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 HIS ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN ** F 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IB 74 HIS JB 82 ASN KF 61 GLN LE 61 GLN LE 82 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.096126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.086667 restraints weight = 112041.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088818 restraints weight = 58154.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.090264 restraints weight = 35098.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.091242 restraints weight = 23545.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.091920 restraints weight = 17126.184| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 46860 Z= 0.138 Angle : 0.662 12.144 63645 Z= 0.337 Chirality : 0.045 0.234 7638 Planarity : 0.004 0.068 8340 Dihedral : 4.171 36.218 6781 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.03 % Allowed : 22.74 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.11), residues: 6183 helix: 0.32 (0.11), residues: 2491 sheet: -0.02 (0.13), residues: 1516 loop : -1.70 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGHA 66 TYR 0.026 0.001 TYR C 8 PHE 0.026 0.002 PHE D 10 TRP 0.107 0.002 TRP A 39 HIS 0.010 0.001 HISIB 74 Details of bonding type rmsd covalent geometry : bond 0.00333 (46860) covalent geometry : angle 0.66150 (63645) hydrogen bonds : bond 0.03215 ( 2487) hydrogen bonds : angle 4.28823 ( 7071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9387.34 seconds wall clock time: 161 minutes 21.74 seconds (9681.74 seconds total)