Starting phenix.real_space_refine on Fri Mar 6 21:30:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7znj_14803/03_2026/7znj_14803.cif Found real_map, /net/cci-nas-00/data/ceres_data/7znj_14803/03_2026/7znj_14803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7znj_14803/03_2026/7znj_14803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7znj_14803/03_2026/7znj_14803.map" model { file = "/net/cci-nas-00/data/ceres_data/7znj_14803/03_2026/7znj_14803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7znj_14803/03_2026/7znj_14803.cif" } resolution = 2.4 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= 0.003 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 6 5.21 5 S 156 5.16 5 C 22086 2.51 5 N 5994 2.21 5 O 6798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 163 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35088 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "B" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "C" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "D" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "a" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "b" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "c" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "d" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "e" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "F" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "G" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "I" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "f" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "g" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "h" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "i" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "j" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "K" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "L" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "M" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "N" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "O" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "k" Number of atoms: 3071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3071 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 369} Chain: "l" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1196 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain: "m" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 731 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain: "n" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 701 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "o" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 117 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pyr': 6} Link IDs: {'rna3p': 5} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.68, per 1000 atoms: 0.22 Number of scatterers: 35088 At special positions: 0 Unit cell: (176.715, 166.32, 117.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 156 16.00 P 48 15.00 Mg 6 11.99 O 6798 8.00 N 5994 7.00 C 22086 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: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7884 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 42 sheets defined 40.1% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 39 through 43 removed outlier: 3.826A pdb=" N THR A 42 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.507A pdb=" N TYR A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 74 removed outlier: 3.940A pdb=" N ILE A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LYS A 70 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 99 removed outlier: 3.628A pdb=" N PHE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.521A pdb=" N ASP A 149 " --> pdb=" O ASN A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 197 through 207 removed outlier: 4.181A pdb=" N TYR A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 removed outlier: 3.557A pdb=" N MET A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 263 through 271 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 312 through 325 Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.617A pdb=" N TYR A 361 " --> pdb=" O ASN A 357 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'B' and resid 53 through 68 removed outlier: 3.505A pdb=" N MET B 57 " --> pdb=" O HIS B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 72 Processing helix chain 'B' and resid 106 through 112 removed outlier: 3.751A pdb=" N VAL B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 142 removed outlier: 3.519A pdb=" N GLN B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 94 removed outlier: 3.586A pdb=" N LYS C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 155 through 167 removed outlier: 3.670A pdb=" N ALA D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) Processing helix chain 'a' and resid 39 through 43 removed outlier: 3.576A pdb=" N THR a 42 " --> pdb=" O THR a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 57 Processing helix chain 'a' and resid 64 through 74 removed outlier: 3.989A pdb=" N ILE a 69 " --> pdb=" O GLN a 65 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS a 70 " --> pdb=" O GLN a 66 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN a 71 " --> pdb=" O ARG a 67 " (cutoff:3.500A) Processing helix chain 'a' and resid 87 through 99 removed outlier: 3.604A pdb=" N PHE a 92 " --> pdb=" O LYS a 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU a 97 " --> pdb=" O SER a 93 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS a 99 " --> pdb=" O SER a 95 " (cutoff:3.500A) Processing helix chain 'a' and resid 115 through 130 Processing helix chain 'a' and resid 145 through 156 removed outlier: 3.549A pdb=" N ASP a 149 " --> pdb=" O ASN a 145 " (cutoff:3.500A) Processing helix chain 'a' and resid 163 through 173 Processing helix chain 'a' and resid 188 through 193 Processing helix chain 'a' and resid 197 through 207 removed outlier: 4.168A pdb=" N TYR a 207 " --> pdb=" O ASP a 203 " (cutoff:3.500A) Processing helix chain 'a' and resid 222 through 229 removed outlier: 3.623A pdb=" N MET a 228 " --> pdb=" O GLU a 224 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 232 No H-bonds generated for 'chain 'a' and resid 230 through 232' Processing helix chain 'a' and resid 242 through 246 removed outlier: 3.619A pdb=" N LEU a 246 " --> pdb=" O ARG a 243 " (cutoff:3.500A) Processing helix chain 'a' and resid 260 through 262 No H-bonds generated for 'chain 'a' and resid 260 through 262' Processing helix chain 'a' and resid 263 through 271 removed outlier: 3.555A pdb=" N ASP a 270 " --> pdb=" O ASP a 266 " (cutoff:3.500A) Processing helix chain 'a' and resid 271 through 276 Processing helix chain 'a' and resid 286 through 300 Processing helix chain 'a' and resid 312 through 325 Processing helix chain 'a' and resid 335 through 338 Processing helix chain 'a' and resid 357 through 366 removed outlier: 3.693A pdb=" N TYR a 361 " --> pdb=" O ASN a 357 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE a 362 " --> pdb=" O ARG a 358 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS a 363 " --> pdb=" O GLU a 359 " (cutoff:3.500A) Processing helix chain 'a' and resid 385 through 397 Processing helix chain 'b' and resid 53 through 68 Processing helix chain 'b' and resid 69 through 72 Processing helix chain 'b' and resid 106 through 112 removed outlier: 3.677A pdb=" N VAL b 110 " --> pdb=" O SER b 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 115 through 142 removed outlier: 3.524A pdb=" N GLN b 127 " --> pdb=" O TYR b 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 85 through 94 Processing helix chain 'c' and resid 123 through 135 Processing helix chain 'd' and resid 118 through 127 Processing helix chain 'd' and resid 155 through 167 removed outlier: 3.708A pdb=" N ALA d 159 " --> pdb=" O ARG d 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 43 removed outlier: 3.823A pdb=" N THR F 42 " --> pdb=" O THR F 39 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET F 43 " --> pdb=" O PHE F 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 39 through 43' Processing helix chain 'F' and resid 46 through 57 Processing helix chain 'F' and resid 64 through 74 removed outlier: 3.965A pdb=" N ILE F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LYS F 70 " --> pdb=" O GLN F 66 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 99 removed outlier: 3.598A pdb=" N PHE F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 130 Processing helix chain 'F' and resid 145 through 156 removed outlier: 3.866A pdb=" N ASP F 149 " --> pdb=" O ASN F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 173 Processing helix chain 'F' and resid 188 through 193 Processing helix chain 'F' and resid 197 through 207 removed outlier: 4.170A pdb=" N TYR F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 229 removed outlier: 3.589A pdb=" N MET F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR F 229 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 242 through 246 removed outlier: 3.620A pdb=" N LEU F 246 " --> pdb=" O ARG F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 262 No H-bonds generated for 'chain 'F' and resid 260 through 262' Processing helix chain 'F' and resid 263 through 271 Processing helix chain 'F' and resid 271 through 276 Processing helix chain 'F' and resid 286 through 300 removed outlier: 3.525A pdb=" N ARG F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 325 Processing helix chain 'F' and resid 335 through 338 Processing helix chain 'F' and resid 357 through 366 removed outlier: 3.618A pdb=" N TYR F 361 " --> pdb=" O ASN F 357 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 362 " --> pdb=" O ARG F 358 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS F 363 " --> pdb=" O GLU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 397 Processing helix chain 'G' and resid 53 through 68 Processing helix chain 'G' and resid 69 through 72 Processing helix chain 'G' and resid 106 through 112 removed outlier: 3.759A pdb=" N VAL G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 142 removed outlier: 3.503A pdb=" N VAL G 121 " --> pdb=" O GLU G 117 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN G 127 " --> pdb=" O TYR G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 Processing helix chain 'H' and resid 123 through 135 Processing helix chain 'I' and resid 118 through 127 Processing helix chain 'I' and resid 155 through 167 removed outlier: 3.711A pdb=" N ALA I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 39 through 43 removed outlier: 3.554A pdb=" N THR f 42 " --> pdb=" O THR f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 46 through 57 Processing helix chain 'f' and resid 64 through 74 removed outlier: 3.968A pdb=" N ILE f 69 " --> pdb=" O GLN f 65 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS f 70 " --> pdb=" O GLN f 66 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLN f 71 " --> pdb=" O ARG f 67 " (cutoff:3.500A) Processing helix chain 'f' and resid 87 through 99 removed outlier: 3.640A pdb=" N PHE f 92 " --> pdb=" O LYS f 88 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS f 99 " --> pdb=" O SER f 95 " (cutoff:3.500A) Processing helix chain 'f' and resid 115 through 130 Processing helix chain 'f' and resid 145 through 156 removed outlier: 3.562A pdb=" N ASP f 149 " --> pdb=" O ASN f 145 " (cutoff:3.500A) Processing helix chain 'f' and resid 163 through 173 Processing helix chain 'f' and resid 188 through 193 Processing helix chain 'f' and resid 197 through 207 removed outlier: 4.242A pdb=" N TYR f 207 " --> pdb=" O ASP f 203 " (cutoff:3.500A) Processing helix chain 'f' and resid 222 through 229 removed outlier: 3.514A pdb=" N MET f 228 " --> pdb=" O GLU f 224 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR f 229 " --> pdb=" O ILE f 225 " (cutoff:3.500A) Processing helix chain 'f' and resid 230 through 232 No H-bonds generated for 'chain 'f' and resid 230 through 232' Processing helix chain 'f' and resid 260 through 262 No H-bonds generated for 'chain 'f' and resid 260 through 262' Processing helix chain 'f' and resid 263 through 271 Processing helix chain 'f' and resid 271 through 277 removed outlier: 3.845A pdb=" N ILE f 277 " --> pdb=" O ASP f 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 286 through 300 Processing helix chain 'f' and resid 312 through 325 Processing helix chain 'f' and resid 335 through 338 Processing helix chain 'f' and resid 357 through 366 removed outlier: 3.706A pdb=" N TYR f 361 " --> pdb=" O ASN f 357 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE f 362 " --> pdb=" O ARG f 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS f 363 " --> pdb=" O GLU f 359 " (cutoff:3.500A) Processing helix chain 'f' and resid 385 through 397 Processing helix chain 'g' and resid 53 through 68 removed outlier: 3.570A pdb=" N MET g 57 " --> pdb=" O HIS g 53 " (cutoff:3.500A) Processing helix chain 'g' and resid 69 through 72 Processing helix chain 'g' and resid 106 through 112 removed outlier: 3.669A pdb=" N VAL g 110 " --> pdb=" O SER g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 142 removed outlier: 3.536A pdb=" N GLN g 127 " --> pdb=" O TYR g 123 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 94 Processing helix chain 'h' and resid 123 through 135 Processing helix chain 'i' and resid 118 through 127 Processing helix chain 'i' and resid 155 through 167 removed outlier: 3.640A pdb=" N ALA i 159 " --> pdb=" O ARG i 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 57 Processing helix chain 'K' and resid 64 through 74 removed outlier: 3.974A pdb=" N ILE K 69 " --> pdb=" O GLN K 65 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS K 70 " --> pdb=" O GLN K 66 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 99 removed outlier: 3.604A pdb=" N PHE K 92 " --> pdb=" O LYS K 88 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS K 99 " --> pdb=" O SER K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 130 Processing helix chain 'K' and resid 145 through 156 Processing helix chain 'K' and resid 163 through 173 Processing helix chain 'K' and resid 188 through 193 Processing helix chain 'K' and resid 197 through 207 removed outlier: 4.187A pdb=" N TYR K 207 " --> pdb=" O ASP K 203 " (cutoff:3.500A) Processing helix chain 'K' and resid 222 through 229 removed outlier: 3.720A pdb=" N MET K 228 " --> pdb=" O GLU K 224 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR K 229 " --> pdb=" O ILE K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 230 through 232 No H-bonds generated for 'chain 'K' and resid 230 through 232' Processing helix chain 'K' and resid 242 through 246 removed outlier: 3.644A pdb=" N LEU K 246 " --> pdb=" O ARG K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 262 No H-bonds generated for 'chain 'K' and resid 260 through 262' Processing helix chain 'K' and resid 263 through 271 Processing helix chain 'K' and resid 271 through 276 Processing helix chain 'K' and resid 286 through 300 Processing helix chain 'K' and resid 312 through 325 Processing helix chain 'K' and resid 335 through 338 Processing helix chain 'K' and resid 357 through 366 removed outlier: 3.607A pdb=" N TYR K 361 " --> pdb=" O ASN K 357 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE K 362 " --> pdb=" O ARG K 358 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS K 363 " --> pdb=" O GLU K 359 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 397 Processing helix chain 'L' and resid 53 through 68 Processing helix chain 'L' and resid 69 through 72 Processing helix chain 'L' and resid 106 through 112 removed outlier: 3.726A pdb=" N VAL L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 142 removed outlier: 3.527A pdb=" N GLN L 127 " --> pdb=" O TYR L 123 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 123 through 135 removed outlier: 3.510A pdb=" N ALA M 127 " --> pdb=" O THR M 123 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 127 Processing helix chain 'N' and resid 155 through 167 removed outlier: 3.691A pdb=" N ALA N 159 " --> pdb=" O ARG N 155 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 43 Processing helix chain 'k' and resid 46 through 57 Processing helix chain 'k' and resid 64 through 74 removed outlier: 3.983A pdb=" N ILE k 69 " --> pdb=" O GLN k 65 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS k 70 " --> pdb=" O GLN k 66 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN k 71 " --> pdb=" O ARG k 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 99 removed outlier: 3.609A pdb=" N PHE k 92 " --> pdb=" O LYS k 88 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS k 99 " --> pdb=" O SER k 95 " (cutoff:3.500A) Processing helix chain 'k' and resid 115 through 130 Processing helix chain 'k' and resid 145 through 156 removed outlier: 3.537A pdb=" N ASP k 149 " --> pdb=" O ASN k 145 " (cutoff:3.500A) Processing helix chain 'k' and resid 163 through 173 Processing helix chain 'k' and resid 188 through 193 Processing helix chain 'k' and resid 197 through 207 removed outlier: 4.081A pdb=" N TYR k 207 " --> pdb=" O ASP k 203 " (cutoff:3.500A) Processing helix chain 'k' and resid 222 through 229 removed outlier: 3.684A pdb=" N MET k 228 " --> pdb=" O GLU k 224 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR k 229 " --> pdb=" O ILE k 225 " (cutoff:3.500A) Processing helix chain 'k' and resid 230 through 232 No H-bonds generated for 'chain 'k' and resid 230 through 232' Processing helix chain 'k' and resid 260 through 262 No H-bonds generated for 'chain 'k' and resid 260 through 262' Processing helix chain 'k' and resid 263 through 271 removed outlier: 3.801A pdb=" N ASP k 270 " --> pdb=" O ASP k 266 " (cutoff:3.500A) Processing helix chain 'k' and resid 271 through 276 Processing helix chain 'k' and resid 286 through 300 Processing helix chain 'k' and resid 312 through 325 Processing helix chain 'k' and resid 357 through 366 removed outlier: 3.581A pdb=" N TYR k 361 " --> pdb=" O ASN k 357 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE k 362 " --> pdb=" O ARG k 358 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS k 363 " --> pdb=" O GLU k 359 " (cutoff:3.500A) Processing helix chain 'k' and resid 385 through 397 Processing helix chain 'l' and resid 53 through 68 Processing helix chain 'l' and resid 69 through 72 Processing helix chain 'l' and resid 106 through 112 removed outlier: 3.744A pdb=" N VAL l 110 " --> pdb=" O SER l 106 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN l 112 " --> pdb=" O ILE l 108 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 142 removed outlier: 3.558A pdb=" N GLN l 127 " --> pdb=" O TYR l 123 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 123 through 135 Processing helix chain 'n' and resid 118 through 127 Processing helix chain 'n' and resid 155 through 167 removed outlier: 3.742A pdb=" N ALA n 159 " --> pdb=" O ARG n 155 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 137 through 140 removed outlier: 6.067A pdb=" N HIS A 138 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA A 109 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N GLY A 162 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE A 111 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 78 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N SER A 218 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA A 80 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 306 through 307 removed outlier: 6.145A pdb=" N GLN A 279 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 348 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LYS A 252 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASN A 379 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE A 254 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL A 381 " --> pdb=" O PHE A 254 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL A 256 " --> pdb=" O VAL A 381 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N ASP A 401 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN A 253 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.619A pdb=" N GLY B 18 " --> pdb=" O GLY B 15 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 95 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 99 through 103 removed outlier: 4.217A pdb=" N ASN C 101 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 138 through 139 removed outlier: 3.552A pdb=" N GLN C 142 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 132 through 139 removed outlier: 5.050A pdb=" N THR D 148 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY D 106 " --> pdb=" O PHE D 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 170 through 171 Processing sheet with id=AA8, first strand: chain 'a' and resid 137 through 140 removed outlier: 6.019A pdb=" N HIS a 138 " --> pdb=" O ALA a 161 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA a 109 " --> pdb=" O VAL a 160 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY a 162 " --> pdb=" O ALA a 109 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE a 111 " --> pdb=" O GLY a 162 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL a 78 " --> pdb=" O LEU a 216 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER a 218 " --> pdb=" O VAL a 78 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA a 80 " --> pdb=" O SER a 218 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'a' and resid 305 through 307 removed outlier: 6.145A pdb=" N SER a 305 " --> pdb=" O ILE a 332 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLN a 279 " --> pdb=" O SER a 347 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE a 349 " --> pdb=" O GLN a 279 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL a 281 " --> pdb=" O ILE a 349 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ASN a 351 " --> pdb=" O VAL a 281 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N PHE a 283 " --> pdb=" O ASN a 351 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LYS a 252 " --> pdb=" O ALA a 377 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASN a 379 " --> pdb=" O LYS a 252 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N PHE a 254 " --> pdb=" O ASN a 379 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL a 381 " --> pdb=" O PHE a 254 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL a 256 " --> pdb=" O VAL a 381 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N ASP a 401 " --> pdb=" O ILE a 251 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLN a 253 " --> pdb=" O ASP a 401 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 46 through 51 removed outlier: 3.506A pdb=" N GLY b 18 " --> pdb=" O GLY b 15 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU b 95 " --> pdb=" O ILE b 92 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 99 through 103 removed outlier: 4.093A pdb=" N ASN c 101 " --> pdb=" O GLU c 120 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 138 through 139 Processing sheet with id=AB4, first strand: chain 'd' and resid 132 through 139 removed outlier: 6.585A pdb=" N HIS d 152 " --> pdb=" O LYS d 133 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA d 135 " --> pdb=" O ASP d 150 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP d 150 " --> pdb=" O ALA d 135 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N VAL d 137 " --> pdb=" O THR d 148 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N THR d 148 " --> pdb=" O VAL d 137 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TYR d 139 " --> pdb=" O LEU d 146 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LEU d 146 " --> pdb=" O TYR d 139 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY d 106 " --> pdb=" O PHE d 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'd' and resid 170 through 171 Processing sheet with id=AB6, first strand: chain 'F' and resid 137 through 140 removed outlier: 6.010A pdb=" N HIS F 138 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA F 109 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N GLY F 162 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE F 111 " --> pdb=" O GLY F 162 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU F 110 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASP F 187 " --> pdb=" O LEU F 110 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU F 112 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL F 78 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N SER F 218 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA F 80 " --> pdb=" O SER F 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 305 through 307 removed outlier: 6.133A pdb=" N SER F 305 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN F 279 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER F 347 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE F 378 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE F 349 " --> pdb=" O ILE F 378 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N PHE F 380 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASN F 351 " --> pdb=" O PHE F 380 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LYS F 252 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASN F 379 " --> pdb=" O LYS F 252 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE F 254 " --> pdb=" O ASN F 379 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL F 381 " --> pdb=" O PHE F 254 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL F 256 " --> pdb=" O VAL F 381 " (cutoff:3.500A) removed outlier: 9.110A pdb=" N ASP F 401 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLN F 253 " --> pdb=" O ASP F 401 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 46 through 51 removed outlier: 3.530A pdb=" N GLU G 95 " --> pdb=" O ILE G 92 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 99 through 103 removed outlier: 4.102A pdb=" N ASN H 101 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 138 through 139 Processing sheet with id=AC2, first strand: chain 'I' and resid 132 through 139 removed outlier: 3.504A pdb=" N LYS I 134 " --> pdb=" O HIS I 152 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THR I 148 " --> pdb=" O HIS I 138 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY I 106 " --> pdb=" O PHE I 153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 170 through 171 Processing sheet with id=AC4, first strand: chain 'f' and resid 137 through 140 removed outlier: 6.079A pdb=" N HIS f 138 " --> pdb=" O ALA f 161 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA f 109 " --> pdb=" O VAL f 160 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N GLY f 162 " --> pdb=" O ALA f 109 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE f 111 " --> pdb=" O GLY f 162 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL f 78 " --> pdb=" O LEU f 216 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N SER f 218 " --> pdb=" O VAL f 78 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA f 80 " --> pdb=" O SER f 218 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'f' and resid 305 through 307 removed outlier: 6.227A pdb=" N SER f 305 " --> pdb=" O ILE f 332 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN f 279 " --> pdb=" O VAL f 346 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS f 252 " --> pdb=" O ALA f 377 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ASN f 379 " --> pdb=" O LYS f 252 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N PHE f 254 " --> pdb=" O ASN f 379 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N VAL f 381 " --> pdb=" O PHE f 254 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL f 256 " --> pdb=" O VAL f 381 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N ASP f 401 " --> pdb=" O ILE f 251 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLN f 253 " --> pdb=" O ASP f 401 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 46 through 51 removed outlier: 3.612A pdb=" N GLY g 18 " --> pdb=" O GLY g 15 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU g 95 " --> pdb=" O ILE g 92 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'h' and resid 99 through 103 removed outlier: 4.216A pdb=" N ASN h 101 " --> pdb=" O GLU h 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 138 through 139 Processing sheet with id=AC9, first strand: chain 'i' and resid 132 through 139 removed outlier: 3.591A pdb=" N LYS i 134 " --> pdb=" O HIS i 152 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N THR i 148 " --> pdb=" O HIS i 138 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY i 106 " --> pdb=" O PHE i 153 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'i' and resid 170 through 171 Processing sheet with id=AD2, first strand: chain 'K' and resid 137 through 140 removed outlier: 6.140A pdb=" N HIS K 138 " --> pdb=" O ALA K 161 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA K 109 " --> pdb=" O VAL K 160 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLY K 162 " --> pdb=" O ALA K 109 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE K 111 " --> pdb=" O GLY K 162 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU K 110 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N ASP K 187 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU K 112 " --> pdb=" O ASP K 187 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL K 78 " --> pdb=" O LEU K 216 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER K 218 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA K 80 " --> pdb=" O SER K 218 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 305 through 307 removed outlier: 6.220A pdb=" N SER K 305 " --> pdb=" O ILE K 332 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLN K 279 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYS K 252 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASN K 379 " --> pdb=" O LYS K 252 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE K 254 " --> pdb=" O ASN K 379 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL K 381 " --> pdb=" O PHE K 254 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL K 256 " --> pdb=" O VAL K 381 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N ASP K 401 " --> pdb=" O ILE K 251 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN K 253 " --> pdb=" O ASP K 401 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 46 through 51 removed outlier: 3.522A pdb=" N GLY L 18 " --> pdb=" O GLY L 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 95 " --> pdb=" O ILE L 92 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 99 through 103 removed outlier: 4.100A pdb=" N ASN M 101 " --> pdb=" O GLU M 120 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 138 through 139 Processing sheet with id=AD7, first strand: chain 'N' and resid 132 through 139 removed outlier: 3.559A pdb=" N LYS N 134 " --> pdb=" O HIS N 152 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR N 148 " --> pdb=" O HIS N 138 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY N 106 " --> pdb=" O PHE N 153 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 170 through 171 Processing sheet with id=AD9, first strand: chain 'k' and resid 137 through 140 removed outlier: 6.013A pdb=" N HIS k 138 " --> pdb=" O ALA k 161 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA k 109 " --> pdb=" O VAL k 160 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY k 162 " --> pdb=" O ALA k 109 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE k 111 " --> pdb=" O GLY k 162 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU k 110 " --> pdb=" O VAL k 185 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ASP k 187 " --> pdb=" O LEU k 110 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU k 112 " --> pdb=" O ASP k 187 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL k 78 " --> pdb=" O LEU k 216 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N SER k 218 " --> pdb=" O VAL k 78 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA k 80 " --> pdb=" O SER k 218 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'k' and resid 305 through 307 removed outlier: 6.030A pdb=" N SER k 305 " --> pdb=" O ILE k 332 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN k 279 " --> pdb=" O VAL k 346 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS k 252 " --> pdb=" O ALA k 377 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASN k 379 " --> pdb=" O LYS k 252 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N PHE k 254 " --> pdb=" O ASN k 379 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL k 381 " --> pdb=" O PHE k 254 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL k 256 " --> pdb=" O VAL k 381 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N ASP k 401 " --> pdb=" O ILE k 251 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN k 253 " --> pdb=" O ASP k 401 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'l' and resid 46 through 51 removed outlier: 3.522A pdb=" N GLY l 18 " --> pdb=" O GLY l 15 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'm' and resid 99 through 103 removed outlier: 4.141A pdb=" N ASN m 101 " --> pdb=" O GLU m 120 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'm' and resid 138 through 139 Processing sheet with id=AE5, first strand: chain 'n' and resid 132 through 139 removed outlier: 5.104A pdb=" N THR n 148 " --> pdb=" O HIS n 138 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY n 106 " --> pdb=" O PHE n 153 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'n' and resid 170 through 171 1485 hydrogen bonds defined for protein. 4272 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: 6.65 Time building geometry restraints manager: 3.60 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: 11485 1.34 - 1.46: 8175 1.46 - 1.59: 15811 1.59 - 1.71: 73 1.71 - 1.83: 270 Bond restraints: 35814 Sorted by residual: bond pdb=" O3A ANP a 502 " pdb=" PB ANP a 502 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" O3A ANP F 502 " pdb=" PB ANP F 502 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.33e+01 bond pdb=" O3A ANP K 502 " pdb=" PB ANP K 502 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" O3A ANP f 502 " pdb=" PB ANP f 502 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" O3A ANP k 502 " pdb=" PB ANP k 502 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 ... (remaining 35809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 48267 4.18 - 8.36: 207 8.36 - 12.54: 36 12.54 - 16.72: 9 16.72 - 20.90: 3 Bond angle restraints: 48522 Sorted by residual: angle pdb=" CB LYS D 161 " pdb=" CG LYS D 161 " pdb=" CD LYS D 161 " ideal model delta sigma weight residual 111.30 125.70 -14.40 2.30e+00 1.89e-01 3.92e+01 angle pdb=" C PHE f 58 " pdb=" N GLU f 59 " pdb=" CA GLU f 59 " ideal model delta sigma weight residual 121.54 133.05 -11.51 1.91e+00 2.74e-01 3.63e+01 angle pdb=" CA LEU D 91 " pdb=" CB LEU D 91 " pdb=" CG LEU D 91 " ideal model delta sigma weight residual 116.30 137.20 -20.90 3.50e+00 8.16e-02 3.56e+01 angle pdb=" C PHE A 58 " pdb=" N GLU A 59 " pdb=" CA GLU A 59 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C PHE F 58 " pdb=" N GLU F 59 " pdb=" CA GLU F 59 " ideal model delta sigma weight residual 121.54 132.69 -11.15 1.91e+00 2.74e-01 3.41e+01 ... (remaining 48517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 18941 17.70 - 35.39: 1912 35.39 - 53.09: 635 53.09 - 70.78: 220 70.78 - 88.48: 96 Dihedral angle restraints: 21804 sinusoidal: 9540 harmonic: 12264 Sorted by residual: dihedral pdb=" CA TRP i 87 " pdb=" C TRP i 87 " pdb=" N GLN i 88 " pdb=" CA GLN i 88 " ideal model delta harmonic sigma weight residual -180.00 -154.93 -25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA TRP n 87 " pdb=" C TRP n 87 " pdb=" N GLN n 88 " pdb=" CA GLN n 88 " ideal model delta harmonic sigma weight residual -180.00 -156.03 -23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA TRP N 87 " pdb=" C TRP N 87 " pdb=" N GLN N 88 " pdb=" CA GLN N 88 " ideal model delta harmonic sigma weight residual 180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 21801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4153 0.051 - 0.102: 935 0.102 - 0.152: 268 0.152 - 0.203: 8 0.203 - 0.254: 6 Chirality restraints: 5370 Sorted by residual: chirality pdb=" C3' ANP F 502 " pdb=" C2' ANP F 502 " pdb=" C4' ANP F 502 " pdb=" O3' ANP F 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" C3' ANP a 502 " pdb=" C2' ANP a 502 " pdb=" C4' ANP a 502 " pdb=" O3' ANP a 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C3' ANP A 502 " pdb=" C2' ANP A 502 " pdb=" C4' ANP A 502 " pdb=" O3' ANP A 502 " both_signs ideal model delta sigma weight residual False -2.36 -2.60 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 5367 not shown) Planarity restraints: 6150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE k 265 " 0.027 2.00e-02 2.50e+03 3.50e-02 2.14e+01 pdb=" CG PHE k 265 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE k 265 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE k 265 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE k 265 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE k 265 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE k 265 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU I 91 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C LEU I 91 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU I 91 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE I 92 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 58 " -0.012 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C PHE A 58 " 0.042 2.00e-02 2.50e+03 pdb=" O PHE A 58 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 59 " -0.014 2.00e-02 2.50e+03 ... (remaining 6147 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 376 2.65 - 3.22: 28787 3.22 - 3.78: 53569 3.78 - 4.34: 80616 4.34 - 4.90: 126082 Nonbonded interactions: 289430 Sorted by model distance: nonbonded pdb="MG MG A 501 " pdb=" O3G ANP A 502 " model vdw 2.092 2.170 nonbonded pdb="MG MG f 501 " pdb=" O3G ANP f 502 " model vdw 2.098 2.170 nonbonded pdb="MG MG k 501 " pdb=" O3G ANP k 502 " model vdw 2.108 2.170 nonbonded pdb="MG MG K 501 " pdb=" O2B ANP K 502 " model vdw 2.133 2.170 nonbonded pdb="MG MG a 501 " pdb=" O2B ANP a 502 " model vdw 2.139 2.170 ... (remaining 289425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' selection = chain 'a' selection = chain 'f' selection = chain 'k' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' selection = chain 'b' selection = chain 'g' selection = chain 'l' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' selection = chain 'c' selection = chain 'h' selection = chain 'm' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' selection = chain 'd' selection = chain 'i' selection = chain 'n' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' selection = chain 'e' selection = chain 'j' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.060 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: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 30.230 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 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 : 0.004 0.146 35814 Z= 0.218 Angle : 0.824 20.896 48522 Z= 0.432 Chirality : 0.047 0.254 5370 Planarity : 0.005 0.084 6150 Dihedral : 17.775 88.479 13920 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.83 % Allowed : 17.42 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.12), residues: 4182 helix: -3.13 (0.07), residues: 1536 sheet: 1.28 (0.16), residues: 912 loop : 0.16 (0.15), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG a 329 TYR 0.034 0.002 TYR a 155 PHE 0.080 0.002 PHE k 265 TRP 0.038 0.002 TRP k 337 HIS 0.009 0.001 HIS i 89 Details of bonding type rmsd covalent geometry : bond 0.00439 (35814) covalent geometry : angle 0.82418 (48522) hydrogen bonds : bond 0.26919 ( 1485) hydrogen bonds : angle 8.01503 ( 4272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 625 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7149 (pt0) cc_final: 0.6532 (mt-10) REVERT: A 288 ARG cc_start: 0.6777 (ttp80) cc_final: 0.6372 (tmt170) REVERT: A 297 MET cc_start: 0.6880 (mmm) cc_final: 0.6622 (mtp) REVERT: C 120 GLU cc_start: 0.8688 (tt0) cc_final: 0.8409 (tt0) REVERT: a 202 TYR cc_start: 0.6046 (t80) cc_final: 0.5498 (t80) REVERT: a 329 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7262 (mmm160) REVERT: F 329 ARG cc_start: 0.7312 (mtp85) cc_final: 0.7097 (mmm160) REVERT: H 140 MET cc_start: 0.7449 (mpt) cc_final: 0.6908 (mpt) REVERT: f 224 GLU cc_start: 0.7071 (pt0) cc_final: 0.6624 (mt-10) REVERT: g 127 GLN cc_start: 0.8404 (mt0) cc_final: 0.8168 (mt0) REVERT: h 120 GLU cc_start: 0.8588 (tt0) cc_final: 0.8347 (tt0) REVERT: K 117 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6993 (mt-10) REVERT: K 320 MET cc_start: 0.7070 (tpt) cc_final: 0.6851 (mmm) REVERT: K 354 LEU cc_start: 0.7133 (mp) cc_final: 0.6868 (tt) REVERT: M 120 GLU cc_start: 0.8624 (tt0) cc_final: 0.8406 (tt0) REVERT: k 288 ARG cc_start: 0.6563 (ttp80) cc_final: 0.6281 (tmt170) REVERT: l 57 MET cc_start: 0.8395 (mmm) cc_final: 0.8145 (mmt) REVERT: l 107 LEU cc_start: 0.8550 (tp) cc_final: 0.8330 (mt) REVERT: m 140 MET cc_start: 0.7332 (mpt) cc_final: 0.7039 (mpp) outliers start: 31 outliers final: 7 residues processed: 641 average time/residue: 0.8837 time to fit residues: 656.4206 Evaluate side-chains 545 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 538 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain a residue 50 LEU Chi-restraints excluded: chain a residue 247 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain n residue 158 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 4.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS B 42 ASN C 128 GLN D 123 GLN ** a 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 351 ASN b 140 HIS c 101 ASN c 128 GLN d 179 GLN G 96 HIS G 140 HIS H 101 ASN H 128 GLN I 179 GLN g 42 ASN g 112 GLN h 128 GLN i 152 HIS i 179 GLN L 42 ASN ** L 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN L 112 GLN L 140 HIS M 128 GLN N 177 ASN N 179 GLN k 213 GLN k 308 HIS k 351 ASN l 42 ASN l 96 HIS l 140 HIS n 179 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.200938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.166816 restraints weight = 29294.958| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.16 r_work: 0.3557 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35814 Z= 0.175 Angle : 0.670 15.083 48522 Z= 0.354 Chirality : 0.048 0.159 5370 Planarity : 0.005 0.051 6150 Dihedral : 11.178 65.367 5423 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.63 % Allowed : 14.27 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.12), residues: 4182 helix: -0.54 (0.11), residues: 1572 sheet: 1.71 (0.16), residues: 912 loop : 0.06 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 329 TYR 0.017 0.002 TYR l 9 PHE 0.029 0.002 PHE f 92 TRP 0.019 0.002 TRP k 292 HIS 0.012 0.001 HIS i 152 Details of bonding type rmsd covalent geometry : bond 0.00393 (35814) covalent geometry : angle 0.67040 (48522) hydrogen bonds : bond 0.05700 ( 1485) hydrogen bonds : angle 4.98277 ( 4272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 557 time to evaluate : 1.265 Fit side-chains REVERT: A 224 GLU cc_start: 0.7220 (pt0) cc_final: 0.6362 (mt-10) REVERT: A 233 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6897 (mtt) REVERT: A 288 ARG cc_start: 0.6924 (ttp80) cc_final: 0.6308 (tmt170) REVERT: A 289 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7327 (tmtm) REVERT: a 148 GLU cc_start: 0.6688 (tp30) cc_final: 0.6322 (mp0) REVERT: a 288 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.5917 (ttt180) REVERT: a 383 ASN cc_start: 0.6359 (m-40) cc_final: 0.6024 (m110) REVERT: c 103 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6801 (m90) REVERT: c 128 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8013 (tm130) REVERT: d 161 LYS cc_start: 0.7646 (mttt) cc_final: 0.7380 (mmpt) REVERT: F 23 MET cc_start: 0.5956 (ptt) cc_final: 0.5115 (ptp) REVERT: F 288 ARG cc_start: 0.7183 (ttp-110) cc_final: 0.6976 (tmt170) REVERT: F 298 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6303 (mtt90) REVERT: H 103 HIS cc_start: 0.6887 (OUTLIER) cc_final: 0.6630 (m90) REVERT: H 128 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8048 (tm130) REVERT: I 161 LYS cc_start: 0.7711 (mttt) cc_final: 0.7411 (mmpt) REVERT: f 23 MET cc_start: 0.5682 (ptt) cc_final: 0.4974 (ptp) REVERT: f 43 MET cc_start: 0.8683 (mtt) cc_final: 0.8131 (mtt) REVERT: f 224 GLU cc_start: 0.7149 (pt0) cc_final: 0.6493 (mt-10) REVERT: f 288 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6179 (ttt180) REVERT: f 289 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7458 (tmtm) REVERT: g 111 ASN cc_start: 0.8218 (m-40) cc_final: 0.7960 (m110) REVERT: h 140 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6894 (mpt) REVERT: i 111 SER cc_start: 0.8608 (m) cc_final: 0.8398 (p) REVERT: K 74 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.7188 (mttp) REVERT: K 105 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6966 (ttt180) REVERT: K 148 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6579 (mp0) REVERT: K 170 MET cc_start: 0.7440 (mmt) cc_final: 0.6821 (mmt) REVERT: K 191 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: K 288 ARG cc_start: 0.7064 (ttp-110) cc_final: 0.6752 (tmt170) REVERT: K 329 ARG cc_start: 0.7805 (mtp85) cc_final: 0.7407 (mmm160) REVERT: K 354 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7097 (tt) REVERT: N 161 LYS cc_start: 0.7627 (mmpt) cc_final: 0.7253 (mmtp) REVERT: k 148 GLU cc_start: 0.6700 (tp30) cc_final: 0.6370 (mp0) REVERT: k 191 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7283 (tp30) REVERT: k 279 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: k 287 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7897 (ttmt) REVERT: k 315 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7147 (tp30) REVERT: k 329 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7486 (mmm160) REVERT: k 337 TRP cc_start: 0.7699 (OUTLIER) cc_final: 0.6554 (m100) REVERT: k 364 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7975 (mtp180) REVERT: l 57 MET cc_start: 0.8652 (mmm) cc_final: 0.8311 (mmt) REVERT: l 107 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8036 (mt) REVERT: m 98 GLU cc_start: 0.6591 (tt0) cc_final: 0.6192 (pm20) REVERT: m 140 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.7041 (mpt) REVERT: m 152 ARG cc_start: 0.7279 (mmm-85) cc_final: 0.7018 (tpt-90) REVERT: n 161 LYS cc_start: 0.7672 (mttt) cc_final: 0.7371 (mmpt) outliers start: 135 outliers final: 54 residues processed: 624 average time/residue: 0.8431 time to fit residues: 612.7676 Evaluate side-chains 590 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 512 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 288 ARG Chi-restraints excluded: chain a residue 307 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 228 MET Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 289 LYS Chi-restraints excluded: chain f residue 319 ILE Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain f residue 360 LEU Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 140 MET Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain i residue 180 LEU Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 279 GLN Chi-restraints excluded: chain k residue 287 LYS Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 220 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 187 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 413 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 96 HIS B 140 HIS C 128 GLN D 179 GLN a 213 GLN b 42 ASN b 111 ASN c 101 ASN d 179 GLN G 42 ASN G 111 ASN H 101 ASN I 179 GLN g 42 ASN g 140 HIS h 101 ASN h 128 GLN ** i 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 177 ASN L 111 ASN L 112 GLN l 111 ASN m 103 HIS n 179 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.196246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.162063 restraints weight = 29066.265| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 1.28 r_work: 0.3473 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35814 Z= 0.168 Angle : 0.644 14.979 48522 Z= 0.341 Chirality : 0.047 0.155 5370 Planarity : 0.005 0.044 6150 Dihedral : 11.052 64.532 5412 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.98 % Allowed : 13.22 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.12), residues: 4182 helix: 0.35 (0.12), residues: 1554 sheet: 1.40 (0.16), residues: 966 loop : 0.17 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 105 TYR 0.024 0.002 TYR K 155 PHE 0.026 0.002 PHE k 92 TRP 0.015 0.001 TRP k 292 HIS 0.006 0.001 HIS i 89 Details of bonding type rmsd covalent geometry : bond 0.00383 (35814) covalent geometry : angle 0.64421 (48522) hydrogen bonds : bond 0.05283 ( 1485) hydrogen bonds : angle 4.80537 ( 4272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 550 time to evaluate : 1.438 Fit side-chains REVERT: A 148 GLU cc_start: 0.6639 (tp30) cc_final: 0.6188 (mp0) REVERT: A 288 ARG cc_start: 0.6818 (OUTLIER) cc_final: 0.6308 (tmt170) REVERT: A 289 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7339 (tmtm) REVERT: B 111 ASN cc_start: 0.8110 (m-40) cc_final: 0.7850 (m110) REVERT: C 128 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8232 (tm130) REVERT: D 111 SER cc_start: 0.8556 (m) cc_final: 0.8348 (p) REVERT: a 23 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.5331 (ptp) REVERT: a 148 GLU cc_start: 0.6731 (tp30) cc_final: 0.6301 (mp0) REVERT: a 191 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7250 (tp30) REVERT: a 195 LYS cc_start: 0.7177 (mmtt) cc_final: 0.6525 (mmpt) REVERT: a 224 GLU cc_start: 0.7253 (pt0) cc_final: 0.6455 (mt-10) REVERT: a 288 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.5899 (ttt180) REVERT: c 71 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7261 (mt-10) REVERT: c 92 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7457 (tptp) REVERT: d 161 LYS cc_start: 0.7591 (mttt) cc_final: 0.7306 (mmpt) REVERT: F 23 MET cc_start: 0.5744 (ptt) cc_final: 0.4924 (ptp) REVERT: F 74 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6850 (mttp) REVERT: F 148 GLU cc_start: 0.6971 (mp0) cc_final: 0.6647 (mp0) REVERT: F 191 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7283 (tp30) REVERT: F 288 ARG cc_start: 0.7181 (ttp-110) cc_final: 0.6820 (tmt170) REVERT: F 298 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6351 (mtt90) REVERT: F 315 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7227 (tp30) REVERT: H 98 GLU cc_start: 0.6809 (tt0) cc_final: 0.6501 (tm-30) REVERT: H 140 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6844 (mpt) REVERT: I 161 LYS cc_start: 0.7627 (mttt) cc_final: 0.7296 (mmpt) REVERT: f 43 MET cc_start: 0.8639 (mtt) cc_final: 0.8072 (mtt) REVERT: f 74 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7335 (mttp) REVERT: f 224 GLU cc_start: 0.7230 (pt0) cc_final: 0.6503 (mt-10) REVERT: f 288 ARG cc_start: 0.6971 (OUTLIER) cc_final: 0.6205 (ttt180) REVERT: f 289 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7342 (tmtm) REVERT: f 317 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6867 (mt-10) REVERT: g 54 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.8072 (mttt) REVERT: g 111 ASN cc_start: 0.8183 (m-40) cc_final: 0.7909 (m110) REVERT: i 111 SER cc_start: 0.8611 (m) cc_final: 0.8361 (p) REVERT: K 74 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7191 (mttp) REVERT: K 148 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: K 191 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7369 (tp30) REVERT: K 288 ARG cc_start: 0.7054 (ttp-110) cc_final: 0.6740 (tmt170) REVERT: K 329 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7438 (mmm160) REVERT: K 354 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7209 (tt) REVERT: M 103 HIS cc_start: 0.7035 (OUTLIER) cc_final: 0.6668 (m-70) REVERT: M 140 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7165 (mpt) REVERT: N 181 VAL cc_start: 0.4272 (OUTLIER) cc_final: 0.3979 (p) REVERT: k 148 GLU cc_start: 0.6892 (tp30) cc_final: 0.6415 (mp0) REVERT: k 191 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7310 (tp30) REVERT: k 306 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8247 (t) REVERT: k 307 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7477 (ttp) REVERT: k 315 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7174 (tp30) REVERT: k 317 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6951 (mt-10) REVERT: k 335 ASP cc_start: 0.7961 (m-30) cc_final: 0.7632 (m-30) REVERT: k 337 TRP cc_start: 0.7878 (OUTLIER) cc_final: 0.6661 (m100) REVERT: l 57 MET cc_start: 0.8689 (mmm) cc_final: 0.8390 (mmt) REVERT: l 107 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7905 (mt) REVERT: m 92 LYS cc_start: 0.7963 (ttmm) cc_final: 0.7745 (tptt) REVERT: m 152 ARG cc_start: 0.7474 (mmm-85) cc_final: 0.7216 (tpt-90) REVERT: n 161 LYS cc_start: 0.7759 (mttt) cc_final: 0.7385 (mmpt) outliers start: 148 outliers final: 65 residues processed: 616 average time/residue: 0.8526 time to fit residues: 609.3961 Evaluate side-chains 623 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 529 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 73 ILE Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 191 GLU Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 288 ARG Chi-restraints excluded: chain a residue 307 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 92 LYS Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 73 ILE Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 228 MET Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 289 LYS Chi-restraints excluded: chain f residue 319 ILE Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain f residue 360 LEU Chi-restraints excluded: chain g residue 54 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 78 THR Chi-restraints excluded: chain h residue 101 ASN Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 354 LEU Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 103 HIS Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 306 SER Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 98 GLU Chi-restraints excluded: chain m residue 103 HIS Chi-restraints excluded: chain m residue 128 GLN Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 110 optimal weight: 3.9990 chunk 409 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 284 optimal weight: 0.0050 chunk 288 optimal weight: 0.0050 chunk 105 optimal weight: 0.7980 chunk 300 optimal weight: 0.9980 chunk 264 optimal weight: 8.9990 chunk 417 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.5610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN D 177 ASN D 179 GLN b 42 ASN b 111 ASN c 101 ASN d 179 GLN G 42 ASN I 179 GLN g 42 ASN h 103 HIS h 128 GLN ** i 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 177 ASN i 179 GLN L 112 GLN l 86 GLN n 179 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.199638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.166014 restraints weight = 29211.083| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.17 r_work: 0.3549 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 35814 Z= 0.094 Angle : 0.515 13.433 48522 Z= 0.272 Chirality : 0.043 0.146 5370 Planarity : 0.003 0.035 6150 Dihedral : 9.490 68.167 5412 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.15 % Allowed : 14.00 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.13), residues: 4182 helix: 1.02 (0.13), residues: 1554 sheet: 1.39 (0.16), residues: 996 loop : 0.43 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 329 TYR 0.018 0.001 TYR K 155 PHE 0.022 0.001 PHE k 92 TRP 0.015 0.001 TRP k 337 HIS 0.015 0.001 HIS m 103 Details of bonding type rmsd covalent geometry : bond 0.00193 (35814) covalent geometry : angle 0.51476 (48522) hydrogen bonds : bond 0.03742 ( 1485) hydrogen bonds : angle 4.49530 ( 4272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 573 time to evaluate : 1.311 Fit side-chains REVERT: A 148 GLU cc_start: 0.6720 (tp30) cc_final: 0.6125 (mp0) REVERT: A 224 GLU cc_start: 0.7311 (pt0) cc_final: 0.6492 (mt-10) REVERT: A 288 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6368 (tmt170) REVERT: A 289 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7318 (tmtm) REVERT: A 329 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7421 (mmm160) REVERT: B 111 ASN cc_start: 0.8026 (m-40) cc_final: 0.7715 (m110) REVERT: a 148 GLU cc_start: 0.6778 (tp30) cc_final: 0.6216 (mp0) REVERT: a 195 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6398 (mmpt) REVERT: a 224 GLU cc_start: 0.7211 (pt0) cc_final: 0.6395 (mt-10) REVERT: a 337 TRP cc_start: 0.7976 (OUTLIER) cc_final: 0.7414 (m100) REVERT: c 92 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7354 (tptp) REVERT: c 98 GLU cc_start: 0.6782 (tm-30) cc_final: 0.6312 (tm-30) REVERT: c 120 GLU cc_start: 0.8718 (tt0) cc_final: 0.8422 (tt0) REVERT: c 131 MET cc_start: 0.8600 (ttt) cc_final: 0.8290 (ttp) REVERT: d 161 LYS cc_start: 0.7461 (mttt) cc_final: 0.7206 (mmpt) REVERT: F 23 MET cc_start: 0.5671 (ptt) cc_final: 0.4844 (ptp) REVERT: F 148 GLU cc_start: 0.7050 (mp0) cc_final: 0.6746 (mp0) REVERT: F 315 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7349 (tp30) REVERT: F 335 ASP cc_start: 0.7688 (m-30) cc_final: 0.7408 (m-30) REVERT: F 337 TRP cc_start: 0.7978 (OUTLIER) cc_final: 0.7506 (m100) REVERT: G 117 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7184 (mm-30) REVERT: H 98 GLU cc_start: 0.6947 (tt0) cc_final: 0.6489 (tm-30) REVERT: H 140 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.6774 (mpt) REVERT: I 161 LYS cc_start: 0.7534 (mttt) cc_final: 0.7258 (mmpt) REVERT: f 43 MET cc_start: 0.8686 (mtt) cc_final: 0.8080 (mtt) REVERT: f 74 LYS cc_start: 0.7597 (mmtm) cc_final: 0.7257 (mttp) REVERT: f 148 GLU cc_start: 0.6940 (mp0) cc_final: 0.6734 (mp0) REVERT: f 224 GLU cc_start: 0.7251 (pt0) cc_final: 0.6475 (mt-10) REVERT: f 297 MET cc_start: 0.6558 (mmm) cc_final: 0.6211 (mmm) REVERT: g 49 GLU cc_start: 0.8471 (pt0) cc_final: 0.7965 (mp0) REVERT: g 111 ASN cc_start: 0.8123 (m-40) cc_final: 0.7816 (m110) REVERT: i 161 LYS cc_start: 0.7582 (mmpt) cc_final: 0.7208 (mptt) REVERT: K 74 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7182 (mttm) REVERT: K 148 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: K 170 MET cc_start: 0.7527 (OUTLIER) cc_final: 0.6859 (mmt) REVERT: K 173 ARG cc_start: 0.6597 (OUTLIER) cc_final: 0.6040 (mtt-85) REVERT: K 288 ARG cc_start: 0.7043 (ttp-110) cc_final: 0.6770 (tmt170) REVERT: K 329 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7441 (mmm160) REVERT: K 337 TRP cc_start: 0.7920 (OUTLIER) cc_final: 0.7370 (m100) REVERT: K 353 ASP cc_start: 0.7982 (m-30) cc_final: 0.7748 (m-30) REVERT: M 103 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6717 (m-70) REVERT: k 74 LYS cc_start: 0.7485 (mptt) cc_final: 0.7055 (mttp) REVERT: k 148 GLU cc_start: 0.6905 (tp30) cc_final: 0.6329 (mp0) REVERT: k 315 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7127 (tp30) REVERT: k 337 TRP cc_start: 0.7897 (OUTLIER) cc_final: 0.6592 (m100) REVERT: k 353 ASP cc_start: 0.8089 (m-30) cc_final: 0.7815 (m-30) REVERT: k 364 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8113 (mtp180) REVERT: l 57 MET cc_start: 0.8631 (mmm) cc_final: 0.8416 (mmt) REVERT: l 107 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7781 (mt) REVERT: m 152 ARG cc_start: 0.7522 (mmm-85) cc_final: 0.7280 (tpt-90) REVERT: n 161 LYS cc_start: 0.7769 (mttt) cc_final: 0.7289 (mmpt) outliers start: 117 outliers final: 43 residues processed: 617 average time/residue: 0.8218 time to fit residues: 589.5098 Evaluate side-chains 599 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 538 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain a residue 297 MET Chi-restraints excluded: chain a residue 307 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain c residue 92 LYS Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain h residue 103 HIS Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 148 GLU Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 170 MET Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 401 ASP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain M residue 103 HIS Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 140 ASP Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 288 ARG Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 401 ASP Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 103 HIS Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 122 optimal weight: 0.4980 chunk 192 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 311 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 chunk 406 optimal weight: 5.9990 chunk 359 optimal weight: 9.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN C 128 GLN D 179 GLN b 42 ASN b 96 HIS d 179 GLN G 42 ASN H 101 ASN H 128 GLN I 179 GLN g 42 ASN h 101 ASN h 128 GLN ** i 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 177 ASN i 179 GLN L 112 GLN k 213 GLN l 86 GLN l 111 ASN m 103 HIS n 179 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.193502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.159815 restraints weight = 28983.198| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.25 r_work: 0.3440 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 35814 Z= 0.243 Angle : 0.733 16.583 48522 Z= 0.388 Chirality : 0.052 0.180 5370 Planarity : 0.006 0.071 6150 Dihedral : 11.934 72.826 5412 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.09 % Allowed : 13.79 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.13), residues: 4182 helix: 0.72 (0.13), residues: 1548 sheet: 1.44 (0.16), residues: 906 loop : -0.00 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 243 TYR 0.021 0.003 TYR K 371 PHE 0.025 0.003 PHE k 92 TRP 0.017 0.002 TRP k 292 HIS 0.010 0.002 HIS h 103 Details of bonding type rmsd covalent geometry : bond 0.00563 (35814) covalent geometry : angle 0.73337 (48522) hydrogen bonds : bond 0.05889 ( 1485) hydrogen bonds : angle 4.88734 ( 4272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 548 time to evaluate : 1.425 Fit side-chains REVERT: A 148 GLU cc_start: 0.6715 (tp30) cc_final: 0.6132 (mp0) REVERT: A 288 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6534 (tmt170) REVERT: A 329 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7383 (mmm160) REVERT: B 45 MET cc_start: 0.8957 (tpp) cc_final: 0.8723 (tpp) REVERT: B 111 ASN cc_start: 0.8264 (m-40) cc_final: 0.8020 (m110) REVERT: a 23 MET cc_start: 0.5898 (OUTLIER) cc_final: 0.5191 (ptp) REVERT: a 33 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: a 148 GLU cc_start: 0.6760 (tp30) cc_final: 0.6333 (mp0) REVERT: a 191 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7285 (tp30) REVERT: a 195 LYS cc_start: 0.7145 (mmtt) cc_final: 0.6508 (mmpt) REVERT: a 224 GLU cc_start: 0.7190 (pt0) cc_final: 0.6457 (mt-10) REVERT: a 249 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: c 92 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7724 (tptp) REVERT: c 120 GLU cc_start: 0.8564 (tt0) cc_final: 0.8102 (tt0) REVERT: c 122 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: d 161 LYS cc_start: 0.7645 (mttt) cc_final: 0.7367 (mmpt) REVERT: F 74 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6909 (mttp) REVERT: F 148 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: F 191 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7317 (tp30) REVERT: F 249 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: F 315 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7332 (tp30) REVERT: H 98 GLU cc_start: 0.6850 (tt0) cc_final: 0.6551 (tm-30) REVERT: H 100 LYS cc_start: 0.7082 (tttt) cc_final: 0.6857 (mmpt) REVERT: H 120 GLU cc_start: 0.8539 (tt0) cc_final: 0.8082 (tt0) REVERT: H 140 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.6827 (mpt) REVERT: I 161 LYS cc_start: 0.7695 (mttt) cc_final: 0.7393 (mmpt) REVERT: f 43 MET cc_start: 0.8652 (mtt) cc_final: 0.8156 (mtt) REVERT: f 74 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7350 (mttp) REVERT: f 224 GLU cc_start: 0.7256 (pt0) cc_final: 0.6535 (mt-10) REVERT: f 288 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.6193 (ttt180) REVERT: f 296 LYS cc_start: 0.6619 (OUTLIER) cc_final: 0.5671 (mmpt) REVERT: h 92 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7797 (tptp) REVERT: h 103 HIS cc_start: 0.7010 (OUTLIER) cc_final: 0.6742 (t-90) REVERT: i 180 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7001 (tp) REVERT: K 74 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7216 (mttp) REVERT: K 173 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6308 (mtt-85) REVERT: K 191 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: K 288 ARG cc_start: 0.7030 (ttp-110) cc_final: 0.6730 (tmt170) REVERT: K 315 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7183 (tt0) REVERT: M 95 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7340 (tm-30) REVERT: N 161 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7544 (mmpt) REVERT: N 181 VAL cc_start: 0.4835 (OUTLIER) cc_final: 0.4411 (p) REVERT: k 148 GLU cc_start: 0.6966 (tp30) cc_final: 0.6474 (mp0) REVERT: k 191 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: k 288 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6015 (ttt180) REVERT: k 306 SER cc_start: 0.8588 (OUTLIER) cc_final: 0.8367 (t) REVERT: k 307 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7594 (ttp) REVERT: k 315 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: k 337 TRP cc_start: 0.7914 (OUTLIER) cc_final: 0.7054 (t60) REVERT: k 364 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8084 (mtp180) REVERT: l 61 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7689 (mttt) REVERT: l 107 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7989 (mt) REVERT: l 112 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6916 (pt0) REVERT: m 95 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7247 (tm-30) REVERT: m 140 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7327 (mpp) REVERT: n 161 LYS cc_start: 0.7824 (mttt) cc_final: 0.7415 (mmpt) outliers start: 152 outliers final: 65 residues processed: 618 average time/residue: 0.8765 time to fit residues: 626.7420 Evaluate side-chains 633 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 535 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 33 GLU Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 191 GLU Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 249 GLU Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 92 LYS Chi-restraints excluded: chain c residue 98 GLU Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 122 GLU Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 296 LYS Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 228 MET Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 296 LYS Chi-restraints excluded: chain f residue 319 ILE Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain f residue 386 ILE Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 103 HIS Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain i residue 180 LEU Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 315 GLU Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 161 LYS Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 288 ARG Chi-restraints excluded: chain k residue 306 SER Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 85 optimal weight: 1.9990 chunk 392 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 308 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 337 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 340 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 112 GLN C 128 GLN a 213 GLN d 177 ASN d 179 GLN G 42 ASN G 111 ASN H 101 ASN I 179 GLN g 42 ASN g 111 ASN h 103 HIS ** i 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 177 ASN i 179 GLN L 111 ASN L 112 GLN k 279 GLN l 111 ASN m 103 HIS n 179 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.195482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161362 restraints weight = 29091.374| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.22 r_work: 0.3475 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35814 Z= 0.141 Angle : 0.593 15.770 48522 Z= 0.314 Chirality : 0.046 0.151 5370 Planarity : 0.004 0.041 6150 Dihedral : 10.782 65.036 5412 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.45 % Allowed : 14.92 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.13), residues: 4182 helix: 1.02 (0.13), residues: 1548 sheet: 1.33 (0.16), residues: 966 loop : 0.20 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG k 329 TYR 0.019 0.002 TYR K 155 PHE 0.022 0.002 PHE K 92 TRP 0.018 0.001 TRP k 292 HIS 0.006 0.001 HIS K 308 Details of bonding type rmsd covalent geometry : bond 0.00317 (35814) covalent geometry : angle 0.59346 (48522) hydrogen bonds : bond 0.04583 ( 1485) hydrogen bonds : angle 4.66450 ( 4272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 541 time to evaluate : 1.399 Fit side-chains REVERT: A 148 GLU cc_start: 0.6773 (tp30) cc_final: 0.6219 (mp0) REVERT: A 224 GLU cc_start: 0.7221 (pt0) cc_final: 0.6498 (mt-10) REVERT: A 288 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6430 (tmt170) REVERT: A 289 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7398 (tmtm) REVERT: A 329 ARG cc_start: 0.7828 (mtp85) cc_final: 0.7426 (mmm160) REVERT: B 111 ASN cc_start: 0.8286 (m-40) cc_final: 0.8014 (m110) REVERT: a 23 MET cc_start: 0.5878 (OUTLIER) cc_final: 0.5159 (ptp) REVERT: a 148 GLU cc_start: 0.6798 (tp30) cc_final: 0.6410 (mp0) REVERT: a 195 LYS cc_start: 0.7070 (mmtt) cc_final: 0.6491 (mmpt) REVERT: a 224 GLU cc_start: 0.7230 (pt0) cc_final: 0.6482 (mt-10) REVERT: a 289 LYS cc_start: 0.7296 (tppt) cc_final: 0.7062 (tppt) REVERT: a 303 THR cc_start: 0.7313 (p) cc_final: 0.6793 (t) REVERT: a 337 TRP cc_start: 0.7913 (OUTLIER) cc_final: 0.7371 (m100) REVERT: a 360 LEU cc_start: 0.8642 (tp) cc_final: 0.8317 (mt) REVERT: c 128 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: d 176 MET cc_start: 0.8106 (ptp) cc_final: 0.7866 (ptp) REVERT: F 74 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6823 (mttm) REVERT: F 148 GLU cc_start: 0.6964 (mp0) cc_final: 0.6643 (mp0) REVERT: F 315 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7302 (tp30) REVERT: F 329 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7421 (mmm160) REVERT: F 337 TRP cc_start: 0.7898 (OUTLIER) cc_final: 0.7398 (m100) REVERT: F 360 LEU cc_start: 0.8621 (tp) cc_final: 0.8297 (mt) REVERT: H 120 GLU cc_start: 0.8543 (tt0) cc_final: 0.8248 (tt0) REVERT: H 128 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7986 (tm-30) REVERT: H 131 MET cc_start: 0.8448 (ttp) cc_final: 0.8187 (ttp) REVERT: H 140 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.6855 (mpt) REVERT: f 43 MET cc_start: 0.8641 (mtt) cc_final: 0.8144 (mtt) REVERT: f 74 LYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7281 (mttt) REVERT: f 224 GLU cc_start: 0.7205 (pt0) cc_final: 0.6464 (mt-10) REVERT: f 288 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6188 (ttt180) REVERT: f 296 LYS cc_start: 0.6650 (OUTLIER) cc_final: 0.5694 (mmpt) REVERT: g 111 ASN cc_start: 0.8153 (m-40) cc_final: 0.7944 (m110) REVERT: h 92 LYS cc_start: 0.7970 (ttmm) cc_final: 0.7750 (tptp) REVERT: h 122 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: i 180 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6968 (tp) REVERT: K 74 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7162 (mttp) REVERT: K 170 MET cc_start: 0.7616 (mmp) cc_final: 0.7256 (mmt) REVERT: K 173 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.6095 (mtt-85) REVERT: K 288 ARG cc_start: 0.6996 (ttp-110) cc_final: 0.6709 (tmt170) REVERT: K 329 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7372 (mmm160) REVERT: N 161 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7440 (mmpt) REVERT: k 148 GLU cc_start: 0.6981 (tp30) cc_final: 0.6524 (mp0) REVERT: k 191 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7172 (tp30) REVERT: k 307 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7372 (ttp) REVERT: k 315 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7071 (tp30) REVERT: k 335 ASP cc_start: 0.7762 (m-30) cc_final: 0.7546 (m-30) REVERT: k 337 TRP cc_start: 0.7918 (OUTLIER) cc_final: 0.6459 (m100) REVERT: k 364 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8176 (mtp180) REVERT: l 57 MET cc_start: 0.8556 (mmm) cc_final: 0.8325 (mmt) REVERT: l 107 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7965 (mt) REVERT: l 112 GLN cc_start: 0.7229 (mm-40) cc_final: 0.7002 (pt0) REVERT: n 161 LYS cc_start: 0.7771 (mttt) cc_final: 0.7412 (mmpt) outliers start: 128 outliers final: 65 residues processed: 598 average time/residue: 0.8730 time to fit residues: 605.5863 Evaluate side-chains 612 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 524 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 288 ARG Chi-restraints excluded: chain a residue 297 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 92 LYS Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 289 LYS Chi-restraints excluded: chain f residue 296 LYS Chi-restraints excluded: chain f residue 319 ILE Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain f residue 386 ILE Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 103 HIS Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain i residue 180 LEU Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 288 ARG Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 128 GLN Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 309 optimal weight: 4.9990 chunk 412 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 398 optimal weight: 3.9990 chunk 409 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 375 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 112 GLN D 179 GLN b 42 ASN d 179 GLN F 213 GLN G 42 ASN G 111 ASN H 101 ASN I 179 GLN g 42 ASN h 103 HIS i 177 ASN i 179 GLN L 112 GLN l 111 ASN m 103 HIS n 179 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.192979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.159307 restraints weight = 29005.383| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.24 r_work: 0.3439 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35814 Z= 0.226 Angle : 0.712 17.170 48522 Z= 0.376 Chirality : 0.051 0.190 5370 Planarity : 0.006 0.061 6150 Dihedral : 11.661 69.814 5412 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.63 % Allowed : 14.75 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.13), residues: 4182 helix: 0.81 (0.13), residues: 1548 sheet: 1.39 (0.17), residues: 906 loop : -0.04 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 329 TYR 0.020 0.003 TYR K 371 PHE 0.023 0.003 PHE f 92 TRP 0.021 0.002 TRP k 292 HIS 0.013 0.002 HIS h 103 Details of bonding type rmsd covalent geometry : bond 0.00523 (35814) covalent geometry : angle 0.71190 (48522) hydrogen bonds : bond 0.05644 ( 1485) hydrogen bonds : angle 4.85766 ( 4272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 529 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6810 (tp30) cc_final: 0.6265 (mp0) REVERT: A 288 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6402 (tmt170) REVERT: A 329 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7359 (mmm160) REVERT: B 57 MET cc_start: 0.8564 (mmm) cc_final: 0.8337 (mmm) REVERT: C 100 LYS cc_start: 0.7595 (mmpt) cc_final: 0.7087 (mtpt) REVERT: C 128 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: a 23 MET cc_start: 0.5579 (OUTLIER) cc_final: 0.4848 (ptp) REVERT: a 148 GLU cc_start: 0.6819 (tp30) cc_final: 0.6427 (mp0) REVERT: a 224 GLU cc_start: 0.7168 (pt0) cc_final: 0.6512 (mt-10) REVERT: a 249 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: a 303 THR cc_start: 0.7323 (p) cc_final: 0.6801 (t) REVERT: a 307 MET cc_start: 0.8095 (mtp) cc_final: 0.7887 (ttt) REVERT: c 67 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: c 98 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6458 (tm-30) REVERT: c 120 GLU cc_start: 0.8518 (tt0) cc_final: 0.8075 (tt0) REVERT: c 128 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: c 140 MET cc_start: 0.7738 (OUTLIER) cc_final: 0.6912 (mpt) REVERT: F 74 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6897 (mttp) REVERT: F 249 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7812 (mm-30) REVERT: F 315 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7314 (tp30) REVERT: F 329 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7454 (mmm160) REVERT: H 67 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: H 98 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6652 (tm-30) REVERT: H 101 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7288 (t0) REVERT: H 120 GLU cc_start: 0.8519 (tt0) cc_final: 0.8210 (tt0) REVERT: H 128 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7987 (tm-30) REVERT: H 140 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6896 (mpt) REVERT: f 43 MET cc_start: 0.8665 (mtt) cc_final: 0.8164 (mtt) REVERT: f 74 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7363 (mttp) REVERT: f 224 GLU cc_start: 0.7226 (pt0) cc_final: 0.6462 (mt-10) REVERT: f 288 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6099 (ttt180) REVERT: f 296 LYS cc_start: 0.6654 (OUTLIER) cc_final: 0.5682 (mmpt) REVERT: h 122 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7515 (tm-30) REVERT: K 74 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7222 (mttp) REVERT: K 170 MET cc_start: 0.7559 (mmp) cc_final: 0.7224 (mmt) REVERT: K 173 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6250 (mtt-85) REVERT: K 288 ARG cc_start: 0.7043 (ttp-110) cc_final: 0.6748 (tmt170) REVERT: K 315 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7167 (tt0) REVERT: K 329 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7478 (mmm160) REVERT: M 100 LYS cc_start: 0.7406 (mmpt) cc_final: 0.6853 (mtpt) REVERT: N 161 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7536 (mmpt) REVERT: k 148 GLU cc_start: 0.6993 (tp30) cc_final: 0.6539 (mp0) REVERT: k 170 MET cc_start: 0.7538 (mmp) cc_final: 0.7184 (mmt) REVERT: k 191 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7315 (tp30) REVERT: k 288 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.5841 (ttt180) REVERT: k 307 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7617 (ttp) REVERT: k 315 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: k 337 TRP cc_start: 0.7916 (OUTLIER) cc_final: 0.7021 (t60) REVERT: k 364 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8181 (mtp180) REVERT: l 57 MET cc_start: 0.8631 (mmm) cc_final: 0.8405 (mmt) REVERT: l 107 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8003 (mt) REVERT: m 100 LYS cc_start: 0.7487 (mmpt) cc_final: 0.6951 (mtpt) REVERT: n 161 LYS cc_start: 0.7793 (mttt) cc_final: 0.7446 (mmpt) outliers start: 135 outliers final: 73 residues processed: 590 average time/residue: 0.8843 time to fit residues: 603.2638 Evaluate side-chains 625 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 522 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 249 GLU Chi-restraints excluded: chain a residue 288 ARG Chi-restraints excluded: chain a residue 296 LYS Chi-restraints excluded: chain a residue 297 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 67 GLN Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 GLU Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 140 MET Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 296 LYS Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 59 GLU Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 228 MET Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 289 LYS Chi-restraints excluded: chain f residue 296 LYS Chi-restraints excluded: chain f residue 319 ILE Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 315 GLU Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 128 GLN Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 288 ARG Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 101 ASN Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Chi-restraints excluded: chain m residue 152 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 50 optimal weight: 2.9990 chunk 210 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 383 optimal weight: 0.7980 chunk 326 optimal weight: 5.9990 chunk 364 optimal weight: 20.0000 chunk 228 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 111 ASN B 112 GLN D 179 GLN b 42 ASN d 179 GLN G 42 ASN I 179 GLN g 42 ASN g 111 ASN g 112 GLN ** i 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 177 ASN i 179 GLN L 111 ASN L 112 GLN l 111 ASN l 112 GLN m 103 HIS n 179 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.192977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.158816 restraints weight = 29068.540| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.23 r_work: 0.3441 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 35814 Z= 0.214 Angle : 0.698 17.371 48522 Z= 0.369 Chirality : 0.050 0.189 5370 Planarity : 0.006 0.056 6150 Dihedral : 11.591 84.060 5412 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.45 % Allowed : 15.27 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.13), residues: 4182 helix: 0.80 (0.13), residues: 1548 sheet: 1.36 (0.17), residues: 906 loop : -0.10 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 329 TYR 0.021 0.003 TYR K 155 PHE 0.022 0.003 PHE f 92 TRP 0.024 0.002 TRP k 292 HIS 0.007 0.002 HIS K 308 Details of bonding type rmsd covalent geometry : bond 0.00495 (35814) covalent geometry : angle 0.69831 (48522) hydrogen bonds : bond 0.05479 ( 1485) hydrogen bonds : angle 4.85248 ( 4272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 538 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6820 (tp30) cc_final: 0.6270 (mp0) REVERT: A 288 ARG cc_start: 0.6972 (OUTLIER) cc_final: 0.6511 (tmt170) REVERT: A 329 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7373 (mmm160) REVERT: C 128 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: a 23 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.4883 (ptp) REVERT: a 148 GLU cc_start: 0.6865 (tp30) cc_final: 0.6486 (mp0) REVERT: a 191 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: a 224 GLU cc_start: 0.7126 (pt0) cc_final: 0.6516 (mt-10) REVERT: a 249 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: a 303 THR cc_start: 0.7347 (p) cc_final: 0.6839 (t) REVERT: c 67 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: c 98 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.6614 (tm-30) REVERT: c 100 LYS cc_start: 0.7711 (mmpt) cc_final: 0.7156 (mtpt) REVERT: c 128 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: F 74 LYS cc_start: 0.7084 (OUTLIER) cc_final: 0.6877 (mttp) REVERT: F 191 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7295 (tp30) REVERT: F 249 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7827 (mm-30) REVERT: F 315 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7328 (tp30) REVERT: F 329 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7453 (mmm160) REVERT: H 67 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: H 120 GLU cc_start: 0.8527 (tt0) cc_final: 0.8229 (tt0) REVERT: H 128 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7990 (tm-30) REVERT: H 140 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.6963 (mpt) REVERT: f 43 MET cc_start: 0.8661 (mtt) cc_final: 0.8150 (mtt) REVERT: f 74 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7302 (mttt) REVERT: f 224 GLU cc_start: 0.7251 (pt0) cc_final: 0.6520 (mt-10) REVERT: f 288 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6178 (ttt180) REVERT: f 296 LYS cc_start: 0.6694 (OUTLIER) cc_final: 0.5724 (mmpt) REVERT: g 57 MET cc_start: 0.8601 (mmm) cc_final: 0.8381 (mmm) REVERT: h 128 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8280 (tm-30) REVERT: K 74 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7213 (mttp) REVERT: K 173 ARG cc_start: 0.6761 (OUTLIER) cc_final: 0.6260 (mtt-85) REVERT: K 191 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7277 (tp30) REVERT: K 288 ARG cc_start: 0.7075 (ttp-110) cc_final: 0.6782 (tmt170) REVERT: K 329 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7494 (mmm160) REVERT: L 54 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8113 (mttt) REVERT: M 100 LYS cc_start: 0.7394 (mmpt) cc_final: 0.6885 (mtpt) REVERT: N 161 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7551 (mmpt) REVERT: k 148 GLU cc_start: 0.6986 (tp30) cc_final: 0.6567 (mp0) REVERT: k 191 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7252 (tp30) REVERT: k 288 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.5936 (ttt180) REVERT: k 307 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7656 (ttp) REVERT: k 315 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: k 337 TRP cc_start: 0.7928 (OUTLIER) cc_final: 0.6976 (t60) REVERT: k 364 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8157 (mtp180) REVERT: l 54 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8151 (mttt) REVERT: l 107 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7968 (mt) REVERT: m 100 LYS cc_start: 0.7479 (mmpt) cc_final: 0.6963 (mtpt) REVERT: n 161 LYS cc_start: 0.7813 (mttt) cc_final: 0.7463 (mmpt) outliers start: 128 outliers final: 75 residues processed: 595 average time/residue: 0.8832 time to fit residues: 607.5856 Evaluate side-chains 638 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 531 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 288 ARG Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 191 GLU Chi-restraints excluded: chain a residue 228 MET Chi-restraints excluded: chain a residue 249 GLU Chi-restraints excluded: chain a residue 288 ARG Chi-restraints excluded: chain a residue 297 MET Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 67 GLN Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 98 GLU Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 74 LYS Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 191 GLU Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 296 LYS Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 98 SER Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 59 GLU Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 228 MET Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 296 LYS Chi-restraints excluded: chain f residue 319 ILE Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain f residue 386 ILE Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 128 GLN Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain h residue 152 ARG Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain L residue 54 LYS Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 101 ASN Chi-restraints excluded: chain M residue 128 GLN Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 161 LYS Chi-restraints excluded: chain k residue 33 GLU Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 191 GLU Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 288 ARG Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 98 GLU Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Chi-restraints excluded: chain m residue 152 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 74 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 0.0570 chunk 256 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 chunk 399 optimal weight: 10.0000 chunk 369 optimal weight: 6.9990 chunk 325 optimal weight: 0.9990 chunk 386 optimal weight: 0.8980 chunk 251 optimal weight: 1.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 111 ASN B 112 GLN D 177 ASN D 179 GLN b 42 ASN d 179 GLN G 42 ASN H 101 ASN I 179 GLN g 42 ASN g 111 ASN g 112 GLN h 103 HIS ** i 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 177 ASN i 179 GLN L 111 ASN L 112 GLN l 111 ASN m 103 HIS n 179 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.197220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.161205 restraints weight = 29232.474| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.15 r_work: 0.3532 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 35814 Z= 0.101 Angle : 0.531 15.931 48522 Z= 0.280 Chirality : 0.044 0.145 5370 Planarity : 0.004 0.037 6150 Dihedral : 9.556 76.395 5412 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.67 % Allowed : 16.10 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.13), residues: 4182 helix: 1.25 (0.13), residues: 1548 sheet: 1.33 (0.16), residues: 966 loop : 0.30 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG k 329 TYR 0.017 0.002 TYR F 155 PHE 0.020 0.002 PHE f 92 TRP 0.028 0.001 TRP k 292 HIS 0.005 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00214 (35814) covalent geometry : angle 0.53146 (48522) hydrogen bonds : bond 0.03687 ( 1485) hydrogen bonds : angle 4.50859 ( 4272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 564 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6941 (tp30) cc_final: 0.6217 (mp0) REVERT: A 202 TYR cc_start: 0.6074 (t80) cc_final: 0.5206 (t80) REVERT: A 224 GLU cc_start: 0.7300 (pt0) cc_final: 0.6512 (mt-10) REVERT: A 288 ARG cc_start: 0.7022 (ttp80) cc_final: 0.6426 (tmt170) REVERT: A 289 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7453 (tmtm) REVERT: A 329 ARG cc_start: 0.7810 (mtp85) cc_final: 0.7380 (mmm160) REVERT: B 111 ASN cc_start: 0.8098 (m-40) cc_final: 0.7848 (m110) REVERT: C 98 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6927 (tt0) REVERT: C 100 LYS cc_start: 0.7526 (mmpt) cc_final: 0.6961 (mtpt) REVERT: C 122 GLU cc_start: 0.7988 (pm20) cc_final: 0.7701 (tp30) REVERT: a 23 MET cc_start: 0.5431 (OUTLIER) cc_final: 0.4693 (ptp) REVERT: a 148 GLU cc_start: 0.6978 (tp30) cc_final: 0.6348 (mp0) REVERT: a 224 GLU cc_start: 0.7229 (pt0) cc_final: 0.6598 (mt-10) REVERT: a 337 TRP cc_start: 0.8000 (OUTLIER) cc_final: 0.7465 (m100) REVERT: a 360 LEU cc_start: 0.8660 (tp) cc_final: 0.8361 (mt) REVERT: c 100 LYS cc_start: 0.7667 (mmpt) cc_final: 0.7080 (mtpt) REVERT: c 120 GLU cc_start: 0.8705 (tt0) cc_final: 0.8406 (tt0) REVERT: c 122 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: c 128 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: c 131 MET cc_start: 0.8526 (ttt) cc_final: 0.8307 (ttp) REVERT: F 315 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7426 (tp30) REVERT: F 337 TRP cc_start: 0.7998 (OUTLIER) cc_final: 0.7490 (m100) REVERT: F 360 LEU cc_start: 0.8636 (tp) cc_final: 0.8315 (mt) REVERT: G 117 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7222 (mm-30) REVERT: H 67 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: H 101 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7307 (t0) REVERT: H 120 GLU cc_start: 0.8711 (tt0) cc_final: 0.8461 (tt0) REVERT: H 140 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.6866 (mpt) REVERT: f 43 MET cc_start: 0.8698 (mtt) cc_final: 0.8114 (mtt) REVERT: f 74 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7182 (mttt) REVERT: f 224 GLU cc_start: 0.7422 (pt0) cc_final: 0.6463 (mt-10) REVERT: f 288 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6184 (ttt180) REVERT: g 49 GLU cc_start: 0.8343 (pt0) cc_final: 0.7883 (mp0) REVERT: g 111 ASN cc_start: 0.8018 (m-40) cc_final: 0.7802 (m110) REVERT: g 113 SER cc_start: 0.6875 (t) cc_final: 0.6607 (p) REVERT: h 98 GLU cc_start: 0.7130 (tt0) cc_final: 0.6878 (tm-30) REVERT: h 122 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7655 (tm-30) REVERT: i 161 LYS cc_start: 0.7784 (mmpt) cc_final: 0.7350 (mptt) REVERT: K 74 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7169 (mttp) REVERT: K 288 ARG cc_start: 0.6967 (ttp-110) cc_final: 0.6706 (tmt170) REVERT: K 329 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7436 (mmm160) REVERT: K 337 TRP cc_start: 0.7889 (OUTLIER) cc_final: 0.7330 (m100) REVERT: K 353 ASP cc_start: 0.8212 (m-30) cc_final: 0.7977 (m-30) REVERT: L 54 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8057 (mttt) REVERT: M 98 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: M 100 LYS cc_start: 0.7381 (mmpt) cc_final: 0.6879 (mtpt) REVERT: N 125 LEU cc_start: 0.8213 (tt) cc_final: 0.7917 (tm) REVERT: N 161 LYS cc_start: 0.7747 (mmtt) cc_final: 0.7440 (mmpt) REVERT: k 148 GLU cc_start: 0.7049 (tp30) cc_final: 0.6471 (mp0) REVERT: k 307 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7318 (ttp) REVERT: k 315 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: k 335 ASP cc_start: 0.7602 (m-30) cc_final: 0.7382 (m-30) REVERT: k 337 TRP cc_start: 0.7962 (OUTLIER) cc_final: 0.6288 (m100) REVERT: k 364 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8114 (mtp180) REVERT: l 49 GLU cc_start: 0.8134 (pt0) cc_final: 0.7524 (mp0) REVERT: l 54 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8042 (mttt) REVERT: l 107 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7841 (mt) REVERT: m 100 LYS cc_start: 0.7330 (mmpt) cc_final: 0.6841 (mtpt) REVERT: n 111 SER cc_start: 0.8718 (m) cc_final: 0.8497 (p) REVERT: n 125 LEU cc_start: 0.8143 (tt) cc_final: 0.7928 (tm) REVERT: n 161 LYS cc_start: 0.7774 (mttt) cc_final: 0.7383 (mmpt) outliers start: 99 outliers final: 50 residues processed: 606 average time/residue: 0.8798 time to fit residues: 618.5314 Evaluate side-chains 619 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 544 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 122 GLU Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain d residue 140 ASP Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain I residue 140 ASP Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 289 LYS Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain h residue 103 HIS Chi-restraints excluded: chain h residue 122 GLU Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain h residue 152 ARG Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain L residue 54 LYS Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 288 ARG Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 315 GLU Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Chi-restraints excluded: chain m residue 152 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 241 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 330 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 112 GLN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN d 179 GLN G 42 ASN G 111 ASN G 112 GLN ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 42 ASN g 112 GLN h 103 HIS ** i 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 179 GLN L 112 GLN l 111 ASN m 103 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.195119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.161221 restraints weight = 29100.224| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.21 r_work: 0.3470 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35814 Z= 0.142 Angle : 0.605 15.987 48522 Z= 0.318 Chirality : 0.046 0.153 5370 Planarity : 0.004 0.036 6150 Dihedral : 9.924 71.291 5412 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.40 % Allowed : 16.77 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 4182 helix: 1.21 (0.13), residues: 1548 sheet: 1.46 (0.16), residues: 936 loop : 0.24 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 329 TYR 0.018 0.002 TYR A 155 PHE 0.020 0.002 PHE f 92 TRP 0.033 0.001 TRP k 292 HIS 0.014 0.001 HIS h 103 Details of bonding type rmsd covalent geometry : bond 0.00319 (35814) covalent geometry : angle 0.60524 (48522) hydrogen bonds : bond 0.04487 ( 1485) hydrogen bonds : angle 4.61476 ( 4272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8364 Ramachandran restraints generated. 4182 Oldfield, 0 Emsley, 4182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 539 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6783 (tp30) cc_final: 0.6266 (mp0) REVERT: A 224 GLU cc_start: 0.7232 (pt0) cc_final: 0.6476 (mt-10) REVERT: A 288 ARG cc_start: 0.6932 (ttp80) cc_final: 0.6365 (tmt170) REVERT: A 289 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7447 (tmtm) REVERT: A 329 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7385 (mmm160) REVERT: B 111 ASN cc_start: 0.8201 (m-40) cc_final: 0.7945 (m110) REVERT: C 98 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7262 (tm-30) REVERT: a 23 MET cc_start: 0.5603 (OUTLIER) cc_final: 0.4868 (ptp) REVERT: a 148 GLU cc_start: 0.6910 (tp30) cc_final: 0.6458 (mp0) REVERT: a 224 GLU cc_start: 0.7146 (pt0) cc_final: 0.6584 (mt-10) REVERT: a 289 LYS cc_start: 0.7282 (tppt) cc_final: 0.7045 (tppt) REVERT: a 337 TRP cc_start: 0.7916 (OUTLIER) cc_final: 0.7404 (m100) REVERT: a 360 LEU cc_start: 0.8661 (tp) cc_final: 0.8387 (mt) REVERT: c 120 GLU cc_start: 0.8489 (tt0) cc_final: 0.8054 (tt0) REVERT: c 128 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7967 (tm-30) REVERT: F 183 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6472 (ptp) REVERT: F 315 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7332 (tp30) REVERT: F 337 TRP cc_start: 0.7939 (OUTLIER) cc_final: 0.7438 (m100) REVERT: F 360 LEU cc_start: 0.8610 (tp) cc_final: 0.8318 (mt) REVERT: G 117 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.7212 (mm-30) REVERT: H 67 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: H 140 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.6839 (mpt) REVERT: f 43 MET cc_start: 0.8650 (mtt) cc_final: 0.8060 (mtt) REVERT: f 74 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7255 (mttt) REVERT: f 224 GLU cc_start: 0.7221 (pt0) cc_final: 0.6471 (mt-10) REVERT: f 288 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6031 (ttt180) REVERT: g 111 ASN cc_start: 0.8142 (m-40) cc_final: 0.7927 (m110) REVERT: g 113 SER cc_start: 0.7073 (t) cc_final: 0.6744 (p) REVERT: i 161 LYS cc_start: 0.7825 (mmpt) cc_final: 0.7367 (mptt) REVERT: K 74 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7193 (mttp) REVERT: K 288 ARG cc_start: 0.7056 (ttp-110) cc_final: 0.6785 (tmt170) REVERT: K 329 ARG cc_start: 0.7823 (mtp85) cc_final: 0.7485 (mmm160) REVERT: L 54 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8010 (mttt) REVERT: M 98 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: M 100 LYS cc_start: 0.7392 (mmpt) cc_final: 0.6884 (mtpt) REVERT: N 161 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7527 (mmpt) REVERT: k 148 GLU cc_start: 0.7019 (tp30) cc_final: 0.6590 (mp0) REVERT: k 307 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7307 (ttp) REVERT: k 337 TRP cc_start: 0.7907 (OUTLIER) cc_final: 0.6475 (m100) REVERT: k 364 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8132 (mtp180) REVERT: l 49 GLU cc_start: 0.8000 (pt0) cc_final: 0.7455 (mp0) REVERT: l 54 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8060 (mttt) REVERT: l 107 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7973 (mt) REVERT: m 100 LYS cc_start: 0.7306 (mmpt) cc_final: 0.6868 (mtpt) REVERT: n 161 LYS cc_start: 0.7662 (mttt) cc_final: 0.7441 (mmpt) outliers start: 89 outliers final: 53 residues processed: 576 average time/residue: 0.8500 time to fit residues: 567.2156 Evaluate side-chains 598 residues out of total 3720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 524 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 289 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 337 TRP Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 103 HIS Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 163 THR Chi-restraints excluded: chain a residue 325 SER Chi-restraints excluded: chain a residue 337 TRP Chi-restraints excluded: chain a residue 402 GLU Chi-restraints excluded: chain b residue 54 LYS Chi-restraints excluded: chain c residue 70 VAL Chi-restraints excluded: chain c residue 103 HIS Chi-restraints excluded: chain c residue 128 GLN Chi-restraints excluded: chain c residue 145 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 228 MET Chi-restraints excluded: chain F residue 315 GLU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 337 TRP Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain F residue 402 GLU Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 103 HIS Chi-restraints excluded: chain H residue 140 MET Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 74 LYS Chi-restraints excluded: chain f residue 163 THR Chi-restraints excluded: chain f residue 288 ARG Chi-restraints excluded: chain f residue 289 LYS Chi-restraints excluded: chain f residue 319 ILE Chi-restraints excluded: chain f residue 325 SER Chi-restraints excluded: chain f residue 337 TRP Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 145 SER Chi-restraints excluded: chain h residue 152 ARG Chi-restraints excluded: chain i residue 140 ASP Chi-restraints excluded: chain K residue 23 MET Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 325 SER Chi-restraints excluded: chain K residue 337 TRP Chi-restraints excluded: chain K residue 402 GLU Chi-restraints excluded: chain L residue 54 LYS Chi-restraints excluded: chain M residue 67 GLN Chi-restraints excluded: chain M residue 70 VAL Chi-restraints excluded: chain M residue 98 GLU Chi-restraints excluded: chain M residue 140 MET Chi-restraints excluded: chain M residue 145 SER Chi-restraints excluded: chain k residue 163 THR Chi-restraints excluded: chain k residue 228 MET Chi-restraints excluded: chain k residue 288 ARG Chi-restraints excluded: chain k residue 307 MET Chi-restraints excluded: chain k residue 325 SER Chi-restraints excluded: chain k residue 337 TRP Chi-restraints excluded: chain k residue 364 ARG Chi-restraints excluded: chain k residue 402 GLU Chi-restraints excluded: chain l residue 54 LYS Chi-restraints excluded: chain l residue 107 LEU Chi-restraints excluded: chain m residue 67 GLN Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 98 GLU Chi-restraints excluded: chain m residue 140 MET Chi-restraints excluded: chain m residue 145 SER Chi-restraints excluded: chain m residue 152 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 178 optimal weight: 0.6980 chunk 401 optimal weight: 0.9980 chunk 399 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 76 optimal weight: 1.9990 chunk 358 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 351 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN ** D 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 ASN d 179 GLN G 42 ASN G 111 ASN G 112 GLN H 101 ASN ** I 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 179 GLN g 42 ASN g 112 GLN h 103 HIS ** i 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 179 GLN L 112 GLN N 177 ASN l 111 ASN m 103 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.195067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.160762 restraints weight = 29121.373| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.20 r_work: 0.3471 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35814 Z= 0.142 Angle : 0.599 15.867 48522 Z= 0.316 Chirality : 0.046 0.152 5370 Planarity : 0.004 0.036 6150 Dihedral : 10.106 64.792 5412 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.40 % Allowed : 16.91 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.13), residues: 4182 helix: 1.16 (0.13), residues: 1548 sheet: 1.44 (0.16), residues: 936 loop : 0.24 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 329 TYR 0.022 0.002 TYR a 205 PHE 0.021 0.002 PHE k 92 TRP 0.035 0.001 TRP k 292 HIS 0.006 0.001 HIS K 308 Details of bonding type rmsd covalent geometry : bond 0.00317 (35814) covalent geometry : angle 0.59927 (48522) hydrogen bonds : bond 0.04488 ( 1485) hydrogen bonds : angle 4.62896 ( 4272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14559.38 seconds wall clock time: 247 minutes 57.14 seconds (14877.14 seconds total)