Starting phenix.real_space_refine on Mon Jul 6 20:47:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k22_36825/07_2026/8k22_36825.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k22_36825/07_2026/8k22_36825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k22_36825/07_2026/8k22_36825.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k22_36825/07_2026/8k22_36825.map" model { file = "/net/cci-nas-00/data/ceres_data/8k22_36825/07_2026/8k22_36825.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k22_36825/07_2026/8k22_36825.cif" } resolution = 2.92 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= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 468 atoms to isotropic. 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 Mn 2 7.51 5 P 175 5.49 5 S 161 5.16 5 C 24316 2.51 5 N 6699 2.21 5 O 7932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 87 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 39285 Number of models: 1 Model: "" Number of chains: 21 Chain: "B" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1415 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1903 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2323 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2313 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 295, 2313 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 2349 Chain: "E" Number of atoms: 2329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2329 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2314 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1290 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "I" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2298 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "J" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2318 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2318 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2307 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2314 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1260 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 18, 'rna3p_pur': 15, 'rna3p_pyr': 17} Link IDs: {'rna2p': 27, 'rna3p': 32} Chain: "Q" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 898 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain: "R" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 620 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "a" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 579 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "d" Number of atoms: 2337 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 295, 2327 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 Conformer: "B" Number of residues, atoms: 295, 2327 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 19 bond proxies already assigned to first conformer: 2363 Chain: "e" Number of atoms: 2324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2324 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 289} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 7278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7278 Classifications: {'peptide': 929} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 22, 'TRANS': 906} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'PHE:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 52 Chain: "U" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 439 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "V" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 419 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Time building chain proxies: 9.40, per 1000 atoms: 0.24 Number of scatterers: 39285 At special positions: 0 Unit cell: (154, 217.8, 178.2, 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) Mn 2 24.99 S 161 16.00 P 175 15.00 O 7932 8.00 N 6699 7.00 C 24316 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: 2.72 Conformation dependent library (CDL) restraints added in 1.9 seconds 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8462 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 42 sheets defined 38.8% alpha, 9.9% beta 33 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 5.55 Creating SS restraints... Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.648A pdb=" N LYS B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.715A pdb=" N VAL B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 81 through 92 Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.788A pdb=" N ASN B 151 " --> pdb=" O ASN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 159 Processing helix chain 'C' and resid 28 through 43 removed outlier: 3.601A pdb=" N PHE C 32 " --> pdb=" O PRO C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 122 removed outlier: 3.506A pdb=" N LEU C 113 " --> pdb=" O CYS C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 154 Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.965A pdb=" N ASP C 173 " --> pdb=" O ASN C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 225 through 229 Processing helix chain 'D' and resid 6 through 10 removed outlier: 3.655A pdb=" N LYS D 10 " --> pdb=" O THR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 98 through 110 removed outlier: 3.595A pdb=" N ASP D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 132 removed outlier: 3.713A pdb=" N ARG D 125 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 158 removed outlier: 3.792A pdb=" N GLN D 158 " --> pdb=" O LYS D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 184 Processing helix chain 'D' and resid 196 through 221 removed outlier: 4.016A pdb=" N LEU D 202 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU D 220 " --> pdb=" O SER D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 244 removed outlier: 3.581A pdb=" N ASP D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 264 through 279 removed outlier: 3.567A pdb=" N ASN D 279 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'E' and resid 58 through 67 Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 110 through 132 Processing helix chain 'E' and resid 142 through 159 Processing helix chain 'E' and resid 161 through 184 Processing helix chain 'E' and resid 196 through 220 removed outlier: 3.753A pdb=" N LEU E 220 " --> pdb=" O SER E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 248 removed outlier: 3.616A pdb=" N PHE E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE E 245 " --> pdb=" O ASP E 241 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE E 246 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR E 248 " --> pdb=" O ASP E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 262 Processing helix chain 'E' and resid 264 through 280 Processing helix chain 'E' and resid 280 through 295 Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.921A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 179 removed outlier: 3.932A pdb=" N MET G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY G 179 " --> pdb=" O GLY G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 234 Processing helix chain 'G' and resid 269 through 278 Processing helix chain 'G' and resid 284 through 298 Processing helix chain 'H' and resid 15 through 30 removed outlier: 3.641A pdb=" N VAL H 19 " --> pdb=" O GLY H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 removed outlier: 3.963A pdb=" N LEU H 65 " --> pdb=" O ASP H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 98 through 108 Processing helix chain 'H' and resid 112 through 121 removed outlier: 3.590A pdb=" N TYR H 120 " --> pdb=" O ALA H 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 58 removed outlier: 4.381A pdb=" N ASP I 58 " --> pdb=" O ASN I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 107 Processing helix chain 'I' and resid 111 through 125 removed outlier: 3.674A pdb=" N LEU I 115 " --> pdb=" O ASP I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 178 removed outlier: 3.574A pdb=" N ALA I 167 " --> pdb=" O ASP I 163 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET I 172 " --> pdb=" O GLU I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 234 Processing helix chain 'I' and resid 269 through 280 Processing helix chain 'I' and resid 284 through 298 Processing helix chain 'J' and resid 53 through 58 removed outlier: 4.364A pdb=" N ASP J 58 " --> pdb=" O ASN J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 98 through 106 Processing helix chain 'J' and resid 111 through 125 removed outlier: 3.506A pdb=" N LEU J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 179 removed outlier: 3.895A pdb=" N ALA J 167 " --> pdb=" O ASP J 163 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N MET J 172 " --> pdb=" O GLU J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 225 through 234 Processing helix chain 'J' and resid 269 through 279 Processing helix chain 'J' and resid 284 through 298 Processing helix chain 'K' and resid 98 through 106 Processing helix chain 'K' and resid 111 through 125 removed outlier: 3.945A pdb=" N LEU K 115 " --> pdb=" O ASP K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 179 removed outlier: 3.925A pdb=" N MET K 172 " --> pdb=" O GLU K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 225 through 234 Processing helix chain 'K' and resid 269 through 279 Processing helix chain 'K' and resid 284 through 298 Processing helix chain 'L' and resid 53 through 57 removed outlier: 3.610A pdb=" N ASP L 56 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA L 57 " --> pdb=" O PRO L 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 53 through 57' Processing helix chain 'L' and resid 99 through 105 Processing helix chain 'L' and resid 111 through 125 removed outlier: 3.717A pdb=" N LEU L 115 " --> pdb=" O ASP L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 179 removed outlier: 3.975A pdb=" N MET L 172 " --> pdb=" O GLU L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 234 Processing helix chain 'L' and resid 269 through 279 Processing helix chain 'L' and resid 284 through 298 Processing helix chain 'M' and resid 98 through 107 Processing helix chain 'M' and resid 111 through 125 removed outlier: 3.597A pdb=" N LEU M 115 " --> pdb=" O ASP M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 179 removed outlier: 3.930A pdb=" N MET M 172 " --> pdb=" O GLU M 168 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY M 179 " --> pdb=" O GLY M 175 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 234 removed outlier: 3.502A pdb=" N ARG M 234 " --> pdb=" O GLY M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 280 removed outlier: 3.670A pdb=" N LEU M 273 " --> pdb=" O ASP M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 298 Processing helix chain 'a' and resid 12 through 22 Processing helix chain 'a' and resid 38 through 51 Processing helix chain 'd' and resid 6 through 10 Processing helix chain 'd' and resid 58 through 68 removed outlier: 3.551A pdb=" N ASN d 67 " --> pdb=" O MET d 63 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 110 removed outlier: 3.987A pdb=" N ASP d 110 " --> pdb=" O ARG d 106 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 132 removed outlier: 3.752A pdb=" N ARG d 125 " --> pdb=" O ILE d 121 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL d 126 " --> pdb=" O LEU d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 142 through 158 Processing helix chain 'd' and resid 161 through 184 Processing helix chain 'd' and resid 196 through 220 removed outlier: 3.538A pdb=" N LEU d 202 " --> pdb=" O TYR d 198 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU d 220 " --> pdb=" O SER d 216 " (cutoff:3.500A) Processing helix chain 'd' and resid 238 through 243 Processing helix chain 'd' and resid 250 through 262 Processing helix chain 'd' and resid 264 through 279 removed outlier: 4.124A pdb=" N PHE d 268 " --> pdb=" O SER d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 280 through 294 Processing helix chain 'e' and resid 58 through 66 Processing helix chain 'e' and resid 98 through 110 Processing helix chain 'e' and resid 110 through 132 Processing helix chain 'e' and resid 142 through 158 Processing helix chain 'e' and resid 161 through 184 Processing helix chain 'e' and resid 196 through 219 Processing helix chain 'e' and resid 236 through 248 removed outlier: 3.558A pdb=" N PHE e 240 " --> pdb=" O GLY e 236 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE e 245 " --> pdb=" O ASP e 241 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE e 246 " --> pdb=" O VAL e 242 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR e 248 " --> pdb=" O ASP e 244 " (cutoff:3.500A) Processing helix chain 'e' and resid 250 through 262 Processing helix chain 'e' and resid 265 through 280 removed outlier: 3.620A pdb=" N ASN e 279 " --> pdb=" O TYR e 275 " (cutoff:3.500A) Processing helix chain 'e' and resid 280 through 294 Processing helix chain 'A' and resid 10 through 14 removed outlier: 3.683A pdb=" N ALA A 14 " --> pdb=" O GLN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 25 removed outlier: 3.598A pdb=" N TYR A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 51 Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.707A pdb=" N LYS A 115 " --> pdb=" O ASP A 112 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 116 " --> pdb=" O LEU A 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 112 through 116' Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 173 through 185 Processing helix chain 'A' and resid 194 through 201 Processing helix chain 'A' and resid 203 through 209 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 236 through 254 removed outlier: 3.744A pdb=" N VAL A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 286 removed outlier: 3.663A pdb=" N ASP A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 329 Processing helix chain 'A' and resid 346 through 358 removed outlier: 4.802A pdb=" N TRP A 351 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 353 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 355 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 388 removed outlier: 3.937A pdb=" N PHE A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 414 removed outlier: 3.636A pdb=" N THR A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.577A pdb=" N SER A 455 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A 456 " --> pdb=" O SER A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.552A pdb=" N LYS A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 488 removed outlier: 4.194A pdb=" N VAL A 484 " --> pdb=" O ASP A 481 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LYS A 485 " --> pdb=" O HIS A 482 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER A 487 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 505 removed outlier: 3.849A pdb=" N HIS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 515 Processing helix chain 'A' and resid 516 through 532 Processing helix chain 'A' and resid 545 through 567 Processing helix chain 'A' and resid 592 through 610 removed outlier: 4.192A pdb=" N LEU A 596 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 640 Processing helix chain 'A' and resid 654 through 667 Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 704 through 709 removed outlier: 3.598A pdb=" N LYS A 707 " --> pdb=" O ASP A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 Processing helix chain 'A' and resid 773 through 777 Processing helix chain 'A' and resid 800 through 805 Processing helix chain 'A' and resid 813 through 819 removed outlier: 4.190A pdb=" N GLY A 819 " --> pdb=" O ASN A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 840 Processing helix chain 'A' and resid 858 through 863 Processing helix chain 'A' and resid 910 through 915 removed outlier: 3.673A pdb=" N ASP A 915 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 15 through 17 removed outlier: 3.525A pdb=" N LEU B 15 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'B' and resid 104 through 107 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 112 through 117 current: chain 'C' and resid 93 through 104 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 93 through 104 current: chain 'C' and resid 129 through 133 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 129 through 133 current: chain 'C' and resid 205 through 219 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 205 through 219 current: chain 'C' and resid 238 through 241 Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 142 Processing sheet with id=AA5, first strand: chain 'D' and resid 12 through 16 removed outlier: 8.111A pdb=" N ASN D 12 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE D 48 " --> pdb=" O ASN D 12 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR D 14 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU D 50 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU D 16 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 70 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE D 87 " --> pdb=" O TRP D 73 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N MET E 81 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS E 75 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL E 46 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE E 72 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE E 48 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR E 74 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU E 50 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ASN E 12 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLY E 49 " --> pdb=" O ASN E 12 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TYR E 14 " --> pdb=" O GLY E 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 37 through 39 removed outlier: 7.354A pdb=" N VAL D 23 " --> pdb=" O THR D 57 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL E 23 " --> pdb=" O THR E 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AA8, first strand: chain 'G' and resid 21 through 26 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 35 through 36 current: chain 'G' and resid 149 through 152 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 149 through 152 current: chain 'G' and resid 221 through 224 Processing sheet with id=AA9, first strand: chain 'G' and resid 40 through 46 removed outlier: 7.383A pdb=" N SER G 212 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N THR G 64 " --> pdb=" O SER G 212 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN G 214 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASN G 66 " --> pdb=" O GLN G 214 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN G 214 " --> pdb=" O GLU G 204 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 254 through 255 removed outlier: 3.666A pdb=" N VAL G 260 " --> pdb=" O VAL G 255 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 2 through 8 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 2 through 8 current: chain 'H' and resid 51 through 54 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'H' and resid 90 through 93 removed outlier: 3.652A pdb=" N PHE H 147 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AB5, first strand: chain 'I' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 16 through 18 current: chain 'I' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 35 through 36 current: chain 'I' and resid 149 through 152 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 149 through 152 current: chain 'I' and resid 221 through 224 No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'I' and resid 40 through 45 removed outlier: 4.647A pdb=" N ALA I 68 " --> pdb=" O VAL I 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 11 through 12 Processing sheet with id=AB8, first strand: chain 'J' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 16 through 18 current: chain 'J' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 35 through 36 current: chain 'J' and resid 149 through 152 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 149 through 152 current: chain 'J' and resid 221 through 224 No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 39 through 47 Processing sheet with id=AC1, first strand: chain 'J' and resid 254 through 255 removed outlier: 3.713A pdb=" N VAL J 255 " --> pdb=" O VAL J 260 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL J 260 " --> pdb=" O VAL J 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'K' and resid 9 through 12 removed outlier: 3.799A pdb=" N LEU K 10 " --> pdb=" O PHE K 301 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 16 through 18 current: chain 'K' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 35 through 36 current: chain 'K' and resid 148 through 152 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 148 through 152 current: chain 'K' and resid 221 through 224 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'K' and resid 40 through 47 Processing sheet with id=AC5, first strand: chain 'K' and resid 254 through 255 Processing sheet with id=AC6, first strand: chain 'L' and resid 11 through 12 Processing sheet with id=AC7, first strand: chain 'L' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 16 through 18 current: chain 'L' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 35 through 36 current: chain 'L' and resid 149 through 152 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 149 through 152 current: chain 'L' and resid 221 through 224 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'L' and resid 40 through 45 removed outlier: 3.576A pdb=" N GLN L 63 " --> pdb=" O VAL L 44 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 203 through 204 removed outlier: 4.509A pdb=" N GLN L 214 " --> pdb=" O GLU L 204 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 254 through 255 removed outlier: 3.910A pdb=" N VAL L 260 " --> pdb=" O VAL L 255 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 11 through 12 Processing sheet with id=AD3, first strand: chain 'M' and resid 16 through 18 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 16 through 18 current: chain 'M' and resid 35 through 36 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 35 through 36 current: chain 'M' and resid 149 through 152 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 149 through 152 current: chain 'M' and resid 221 through 224 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'M' and resid 40 through 44 Processing sheet with id=AD5, first strand: chain 'M' and resid 254 through 255 removed outlier: 3.790A pdb=" N VAL M 255 " --> pdb=" O VAL M 260 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL M 260 " --> pdb=" O VAL M 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'a' and resid 32 through 36 removed outlier: 3.639A pdb=" N VAL a 58 " --> pdb=" O ILE a 70 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 37 through 39 removed outlier: 7.727A pdb=" N VAL d 23 " --> pdb=" O THR d 57 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 47 through 48 removed outlier: 6.509A pdb=" N ILE d 48 " --> pdb=" O PHE d 72 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE d 87 " --> pdb=" O TRP d 73 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'e' and resid 2 through 5 removed outlier: 6.332A pdb=" N ILE e 48 " --> pdb=" O PHE e 72 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR e 74 " --> pdb=" O ILE e 48 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU e 50 " --> pdb=" O THR e 74 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'e' and resid 19 through 24 Processing sheet with id=AE2, first strand: chain 'A' and resid 32 through 36 removed outlier: 3.707A pdb=" N VAL A 58 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N TYR A 62 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL A 66 " --> pdb=" O TYR A 62 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 298 through 299 removed outlier: 3.832A pdb=" N ASN A 298 " --> pdb=" O LYS A 306 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A 306 " --> pdb=" O ASN A 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'A' and resid 420 through 423 removed outlier: 7.049A pdb=" N CYS A 393 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR A 478 " --> pdb=" O CYS A 393 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N PHE A 395 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N SER A 394 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASP A 510 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLY A 396 " --> pdb=" O ASP A 510 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU A 507 " --> pdb=" O ILE A 538 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N SER A 540 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU A 509 " --> pdb=" O SER A 540 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 366 " --> pdb=" O VAL A 577 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TRP A 579 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE A 368 " --> pdb=" O TRP A 579 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 583 " --> pdb=" O ASP A 580 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 674 through 679 removed outlier: 5.833A pdb=" N LYS A 675 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL A 721 " --> pdb=" O LYS A 675 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU A 677 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER A 646 " --> pdb=" O TYR A 718 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 720 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLY A 648 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ALA A 722 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE A 650 " --> pdb=" O ALA A 722 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE A 647 " --> pdb=" O TRP A 736 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ILE A 738 " --> pdb=" O PHE A 647 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU A 649 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 737 " --> pdb=" O HIS A 768 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 881 through 882 1358 hydrogen bonds defined for protein. 3890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 9.14 Time building geometry restraints manager: 3.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6294 1.31 - 1.44: 11685 1.44 - 1.57: 21788 1.57 - 1.69: 368 1.69 - 1.82: 267 Bond restraints: 40402 Sorted by residual: bond pdb=" N3 DT V 2 " pdb=" C4 DT V 2 " ideal model delta sigma weight residual 1.382 1.322 0.060 8.00e-03 1.56e+04 5.61e+01 bond pdb=" N3 DT V 4 " pdb=" C4 DT V 4 " ideal model delta sigma weight residual 1.382 1.323 0.059 8.00e-03 1.56e+04 5.44e+01 bond pdb=" N1 DT V 2 " pdb=" C6 DT V 2 " ideal model delta sigma weight residual 1.378 1.327 0.051 7.00e-03 2.04e+04 5.40e+01 bond pdb=" CA LEU e 31 " pdb=" C LEU e 31 " ideal model delta sigma weight residual 1.528 1.436 0.092 1.32e-02 5.74e+03 4.85e+01 bond pdb=" N1 DT V 4 " pdb=" C6 DT V 4 " ideal model delta sigma weight residual 1.378 1.331 0.047 7.00e-03 2.04e+04 4.58e+01 ... (remaining 40397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 53686 2.75 - 5.50: 1440 5.50 - 8.25: 302 8.25 - 11.00: 74 11.00 - 13.74: 11 Bond angle restraints: 55513 Sorted by residual: angle pdb=" N1 DT V 4 " pdb=" C2 DT V 4 " pdb=" N3 DT V 4 " ideal model delta sigma weight residual 114.60 122.28 -7.68 6.00e-01 2.78e+00 1.64e+02 angle pdb=" C2 DT V 4 " pdb=" N3 DT V 4 " pdb=" C4 DT V 4 " ideal model delta sigma weight residual 127.20 120.32 6.88 6.00e-01 2.78e+00 1.31e+02 angle pdb=" N1 DT V 2 " pdb=" C2 DT V 2 " pdb=" N3 DT V 2 " ideal model delta sigma weight residual 114.60 121.23 -6.63 6.00e-01 2.78e+00 1.22e+02 angle pdb=" C2 DT V 2 " pdb=" N3 DT V 2 " pdb=" C4 DT V 2 " ideal model delta sigma weight residual 127.20 120.71 6.49 6.00e-01 2.78e+00 1.17e+02 angle pdb=" N GLU L 98 " pdb=" CA GLU L 98 " pdb=" C GLU L 98 " ideal model delta sigma weight residual 113.97 100.69 13.28 1.28e+00 6.10e-01 1.08e+02 ... (remaining 55508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 22151 35.59 - 71.18: 1478 71.18 - 106.77: 74 106.77 - 142.36: 5 142.36 - 177.95: 11 Dihedral angle restraints: 23719 sinusoidal: 10496 harmonic: 13223 Sorted by residual: dihedral pdb=" C5' C P 22 " pdb=" C4' C P 22 " pdb=" C3' C P 22 " pdb=" O3' C P 22 " ideal model delta sinusoidal sigma weight residual 147.00 73.44 73.56 1 8.00e+00 1.56e-02 1.08e+02 dihedral pdb=" C4' C P 22 " pdb=" C3' C P 22 " pdb=" C2' C P 22 " pdb=" C1' C P 22 " ideal model delta sinusoidal sigma weight residual -35.00 34.41 -69.41 1 8.00e+00 1.56e-02 9.73e+01 dihedral pdb=" O4' C P 22 " pdb=" C4' C P 22 " pdb=" C3' C P 22 " pdb=" C2' C P 22 " ideal model delta sinusoidal sigma weight residual 24.00 -39.03 63.03 1 8.00e+00 1.56e-02 8.20e+01 ... (remaining 23716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 6143 0.155 - 0.310: 175 0.310 - 0.466: 13 0.466 - 0.621: 1 0.621 - 0.776: 3 Chirality restraints: 6335 Sorted by residual: chirality pdb=" CB ILE a 13 " pdb=" CA ILE a 13 " pdb=" CG1 ILE a 13 " pdb=" CG2 ILE a 13 " both_signs ideal model delta sigma weight residual False 2.64 1.87 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" C3' C P 41 " pdb=" C4' C P 41 " pdb=" O3' C P 41 " pdb=" C2' C P 41 " both_signs ideal model delta sigma weight residual False -2.74 -2.08 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" C3' DA Q 52 " pdb=" C4' DA Q 52 " pdb=" O3' DA Q 52 " pdb=" C2' DA Q 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.08 -0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 6332 not shown) Planarity restraints: 6513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN I 53 " 0.094 5.00e-02 4.00e+02 1.44e-01 3.34e+01 pdb=" N PRO I 54 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO I 54 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO I 54 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN I 53 " 0.022 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C ASN I 53 " -0.076 2.00e-02 2.50e+03 pdb=" O ASN I 53 " 0.029 2.00e-02 2.50e+03 pdb=" N PRO I 54 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU e 169 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" CD GLU e 169 " -0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU e 169 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU e 169 " 0.023 2.00e-02 2.50e+03 ... (remaining 6510 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2723 2.72 - 3.27: 38085 3.27 - 3.81: 75576 3.81 - 4.36: 90724 4.36 - 4.90: 145649 Nonbonded interactions: 352757 Sorted by model distance: nonbonded pdb=" OD2 ASP A 112 " pdb="MN MN A1001 " model vdw 2.177 3.060 nonbonded pdb=" OD1 ASP A 280 " pdb="MN MN A1001 " model vdw 2.183 3.060 nonbonded pdb=" OD2 ASP H 10 " pdb=" ND2 ASN L 158 " model vdw 2.232 3.120 nonbonded pdb=" OG SER H 137 " pdb=" O GLN H 142 " model vdw 2.254 3.040 nonbonded pdb=" O2' C P 22 " pdb=" O4' C P 23 " model vdw 2.264 3.040 ... (remaining 352752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 8 or (resid 9 through 11 and (name N or name CA or name C o \ r name O or name CB )) or resid 12 through 31 or (resid 32 through 34 and (name \ N or name CA or name C or name O or name CB )) or resid 35 through 74 or (resid \ 75 and (name N or name CA or name C or name O or name CB )) or (resid 76 through \ 85 and (name N or name CA or name C or name O or name CB )) or resid 86 through \ 87 or (resid 88 through 94 and (name N or name CA or name C or name O or name C \ B )) or resid 95 through 105 or (resid 106 and (name N or name CA or name C or n \ ame O or name CB )) or resid 107 through 149 or resid 151 through 286 or resid 2 \ 88 through 295)) selection = (chain 'E' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 8 or (resid 9 through 11 and (name N or name CA or name C o \ r name O or name CB )) or resid 12 through 31 or (resid 32 through 34 and (name \ N or name CA or name C or name O or name CB )) or resid 35 through 74 or (resid \ 75 and (name N or name CA or name C or name O or name CB )) or resid 76 through \ 78 or (resid 79 through 85 and (name N or name CA or name C or name O or name CB \ )) or resid 86 through 111 or (resid 112 and (name N or name CA or name C or na \ me O or name CB )) or resid 113 through 149 or resid 151 through 192 or (resid 1 \ 93 and (name N or name CA or name C or name O or name CB )) or resid 194 through \ 269 or (resid 270 and (name N or name CA or name C or name O or name CB )) or r \ esid 271 through 286 or resid 288 through 293 or (resid 294 through 295 and (nam \ e N or name CA or name C or name O or name CB )))) selection = (chain 'd' and ((resid 1 and (name N or name CA or name C or name O or name CB ) \ ) or resid 2 through 8 or (resid 9 through 11 and (name N or name CA or name C o \ r name O or name CB )) or resid 12 through 31 or (resid 32 through 34 and (name \ N or name CA or name C or name O or name CB )) or resid 35 through 87 or (resid \ 88 through 94 and (name N or name CA or name C or name O or name CB )) or resid \ 95 through 105 or (resid 106 and (name N or name CA or name C or name O or name \ CB )) or resid 107 through 111 or (resid 112 and (name N or name CA or name C or \ name O or name CB )) or resid 113 through 149 or resid 151 through 192 or (resi \ d 193 and (name N or name CA or name C or name O or name CB )) or resid 194 thro \ ugh 269 or (resid 270 and (name N or name CA or name C or name O or name CB )) o \ r resid 271 through 286 or resid 288 through 293 or (resid 294 through 295 and ( \ name N or name CA or name C or name O or name CB )))) selection = (chain 'e' and (resid 1 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB )) or resid 76 through 78 or (resid 79 through 85 and (nam \ e N or name CA or name C or name O or name CB )) or resid 86 through 87 or (resi \ d 88 through 94 and (name N or name CA or name C or name O or name CB )) or resi \ d 95 through 105 or (resid 106 and (name N or name CA or name C or name O or nam \ e CB )) or resid 107 through 111 or (resid 112 and (name N or name CA or name C \ or name O or name CB )) or resid 113 through 149 or resid 151 through 192 or (re \ sid 193 and (name N or name CA or name C or name O or name CB )) or resid 194 th \ rough 269 or (resid 270 and (name N or name CA or name C or name O or name CB )) \ or resid 271 through 286 or resid 288 through 293 or (resid 294 through 295 and \ (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'G' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 or (resid 5 through 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 206 or (resid 207 through 211 and (name \ N or name CA or name C or name O or name CB )) or resid 212 through 266 or (res \ id 267 and (name N or name CA or name C or name O or name CB )) or resid 268 thr \ ough 303)) selection = (chain 'I' and (resid 2 through 58 or (resid 59 and (name N or name CA or name C \ or name O or name CB )) or resid 60 through 210 or (resid 211 and (name N or na \ me CA or name C or name O or name CB )) or resid 212 through 266 or (resid 267 a \ nd (name N or name CA or name C or name O or name CB )) or resid 268 through 303 \ )) selection = (chain 'J' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 or (resid 5 through 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 58 or (resid 59 and (name N or name CA \ or name C or name O or name CB )) or resid 60 through 206 or (resid 207 through \ 211 and (name N or name CA or name C or name O or name CB )) or resid 212 throug \ h 266 or (resid 267 and (name N or name CA or name C or name O or name CB )) or \ resid 268 through 303)) selection = (chain 'K' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 or (resid 5 through 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 58 or (resid 59 and (name N or name CA \ or name C or name O or name CB )) or resid 60 through 206 or (resid 207 through \ 211 and (name N or name CA or name C or name O or name CB )) or resid 212 throug \ h 266 or (resid 267 and (name N or name CA or name C or name O or name CB )) or \ resid 268 through 303)) selection = (chain 'L' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 or (resid 5 through 6 and (name N or name CA or name C or \ name O or name CB )) or resid 7 through 58 or (resid 59 and (name N or name CA \ or name C or name O or name CB )) or resid 60 through 206 or (resid 207 through \ 211 and (name N or name CA or name C or name O or name CB )) or resid 212 throug \ h 303)) selection = (chain 'M' and (resid 2 through 4 or (resid 5 through 6 and (name N or name CA o \ r name C or name O or name CB )) or resid 7 through 58 or (resid 59 and (name N \ or name CA or name C or name O or name CB )) or resid 60 through 206 or (resid 2 \ 07 through 211 and (name N or name CA or name C or name O or name CB )) or resid \ 212 through 266 or (resid 267 and (name N or name CA or name C or name O or nam \ e CB )) or resid 268 through 303)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.18 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: 2.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 40.900 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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:9.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 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 : 0.007 0.092 40402 Z= 0.435 Angle : 1.138 13.745 55513 Z= 0.712 Chirality : 0.067 0.776 6335 Planarity : 0.007 0.144 6513 Dihedral : 21.235 177.946 15257 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.36 % Favored : 94.27 % Rotamer: Outliers : 5.77 % Allowed : 26.38 % Favored : 67.84 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 1.92 % 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: -2.72 (0.10), residues: 4559 helix: -1.76 (0.10), residues: 1678 sheet: -0.82 (0.19), residues: 668 loop : -2.12 (0.11), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG G 257 TYR 0.056 0.003 TYR B 137 PHE 0.054 0.003 PHE G 205 TRP 0.030 0.003 TRP A 33 HIS 0.012 0.002 HIS H 28 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.44 (40402) covalent geometry : angle 1.13803 / 0.71 (55513) hydrogen bonds : bond 0.15249 / 10.35 ( 1438) hydrogen bonds : angle 6.79921 / 4.85 ( 4034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 221 poor density : 832 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8298 (tttt) REVERT: B 64 GLN cc_start: 0.9032 (mp10) cc_final: 0.8461 (mp10) REVERT: B 68 LYS cc_start: 0.8656 (pttp) cc_final: 0.8259 (pmtt) REVERT: B 126 SER cc_start: 0.8951 (t) cc_final: 0.8622 (m) REVERT: C 217 TYR cc_start: 0.8756 (m-80) cc_final: 0.8448 (m-80) REVERT: D 31 LEU cc_start: 0.8652 (tp) cc_final: 0.8371 (tp) REVERT: D 103 ASN cc_start: 0.8581 (m-40) cc_final: 0.8276 (m-40) REVERT: D 111 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7342 (mm-30) REVERT: D 119 LYS cc_start: 0.8826 (mttm) cc_final: 0.8280 (mttt) REVERT: D 127 ASP cc_start: 0.8128 (t70) cc_final: 0.7752 (OUTLIER) REVERT: D 169 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8789 (mm-30) REVERT: D 183 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8617 (tm-30) REVERT: D 185 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7966 (mm-30) REVERT: D 186 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8823 (pp) REVERT: D 191 ASP cc_start: 0.7927 (t0) cc_final: 0.7472 (t0) REVERT: D 194 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8453 (t) REVERT: D 224 ASN cc_start: 0.8599 (OUTLIER) cc_final: 0.8001 (t0) REVERT: D 225 SER cc_start: 0.8909 (OUTLIER) cc_final: 0.8699 (t) REVERT: D 257 HIS cc_start: 0.8481 (t70) cc_final: 0.7767 (t-170) REVERT: D 260 ASP cc_start: 0.8430 (t70) cc_final: 0.8195 (p0) REVERT: D 278 LYS cc_start: 0.8959 (ttpp) cc_final: 0.8601 (ttpp) REVERT: E 24 LYS cc_start: 0.8606 (ttmm) cc_final: 0.8402 (tppp) REVERT: E 59 GLU cc_start: 0.8264 (pm20) cc_final: 0.8010 (pm20) REVERT: E 120 GLU cc_start: 0.8503 (tp30) cc_final: 0.8193 (tp30) REVERT: E 124 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8059 (ptp) REVERT: E 127 ASP cc_start: 0.8313 (t70) cc_final: 0.7998 (t0) REVERT: E 154 LYS cc_start: 0.8842 (mttt) cc_final: 0.8343 (mmpt) REVERT: E 178 LYS cc_start: 0.9170 (tptp) cc_final: 0.8929 (tppp) REVERT: G 88 ASP cc_start: 0.7872 (t70) cc_final: 0.6136 (t0) REVERT: G 217 ASP cc_start: 0.7455 (p0) cc_final: 0.7231 (p0) REVERT: G 288 GLN cc_start: 0.8608 (mt0) cc_final: 0.8375 (mt0) REVERT: H 117 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8109 (mm-30) REVERT: I 84 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8675 (mttp) REVERT: I 283 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8134 (mt) REVERT: J 213 LYS cc_start: 0.8984 (ttpp) cc_final: 0.8616 (ttpp) REVERT: J 250 GLU cc_start: 0.7807 (mp0) cc_final: 0.7567 (mp0) REVERT: J 287 ASP cc_start: 0.7952 (t70) cc_final: 0.7720 (t0) REVERT: K 30 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7077 (p0) REVERT: K 33 ASN cc_start: 0.7906 (m-40) cc_final: 0.7634 (m-40) REVERT: K 53 ASN cc_start: 0.7251 (OUTLIER) cc_final: 0.6539 (t0) REVERT: K 58 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7558 (OUTLIER) REVERT: K 59 LYS cc_start: 0.9050 (ptpt) cc_final: 0.8831 (ptpp) REVERT: K 285 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6935 (tm-30) REVERT: K 289 MET cc_start: 0.8174 (mtp) cc_final: 0.7868 (mtp) REVERT: L 99 TYR cc_start: 0.8136 (t80) cc_final: 0.7711 (t80) REVERT: L 156 LEU cc_start: 0.8664 (mt) cc_final: 0.8298 (mm) REVERT: L 209 SER cc_start: 0.8022 (OUTLIER) cc_final: 0.7596 (p) REVERT: L 213 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8220 (ttmt) REVERT: L 266 ASN cc_start: 0.8317 (OUTLIER) cc_final: 0.7818 (p0) REVERT: a 47 THR cc_start: 0.8430 (m) cc_final: 0.8173 (t) REVERT: a 58 VAL cc_start: 0.8731 (t) cc_final: 0.8262 (t) REVERT: a 70 ILE cc_start: 0.9008 (mt) cc_final: 0.8699 (pp) REVERT: d 106 ARG cc_start: 0.8728 (mpp80) cc_final: 0.8469 (mpt-90) REVERT: d 119 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.7823 (mmtt) REVERT: d 123 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.7837 (mptt) REVERT: d 182 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8799 (pp) REVERT: d 183 GLU cc_start: 0.8509 (tp30) cc_final: 0.8256 (tm-30) REVERT: d 188 PHE cc_start: 0.8264 (t80) cc_final: 0.7918 (t80) REVERT: d 214 ARG cc_start: 0.9059 (mmm-85) cc_final: 0.8786 (mmm-85) REVERT: d 240 PHE cc_start: 0.6976 (m-10) cc_final: 0.6681 (m-10) REVERT: e 111 GLU cc_start: 0.8503 (tp30) cc_final: 0.8261 (tp30) REVERT: e 178 LYS cc_start: 0.8934 (ptmm) cc_final: 0.8585 (tmmm) REVERT: e 179 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8176 (pp20) REVERT: e 183 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7822 (pp20) REVERT: e 224 ASN cc_start: 0.8477 (p0) cc_final: 0.8175 (p0) REVERT: A 248 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8383 (mmtt) REVERT: A 510 ASP cc_start: 0.7442 (m-30) cc_final: 0.7177 (m-30) REVERT: A 520 MET cc_start: 0.8891 (ttm) cc_final: 0.8634 (mtm) REVERT: A 541 SER cc_start: 0.7302 (OUTLIER) cc_final: 0.6833 (p) REVERT: A 622 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7604 (mt0) REVERT: A 627 GLU cc_start: 0.7798 (pp20) cc_final: 0.7526 (pp20) REVERT: A 631 GLN cc_start: 0.8132 (tp40) cc_final: 0.7861 (tp40) REVERT: A 841 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8821 (p) REVERT: A 848 ASN cc_start: 0.6563 (OUTLIER) cc_final: 0.5265 (t0) REVERT: A 874 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8026 (t0) REVERT: A 885 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7264 (t0) REVERT: A 907 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7730 (tt) outliers start: 221 outliers final: 27 residues processed: 943 average time/residue: 0.7073 time to fit residues: 801.8693 Evaluate side-chains 772 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 722 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 189 LYS Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 225 SER Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain E residue 124 MET Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain I residue 84 LYS Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 283 LEU Chi-restraints excluded: chain I residue 284 THR Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 212 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 119 LYS Chi-restraints excluded: chain d residue 123 LYS Chi-restraints excluded: chain d residue 182 LEU Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 113 LYS Chi-restraints excluded: chain e residue 116 SER Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 ASN Chi-restraints excluded: chain A residue 874 ASP Chi-restraints excluded: chain A residue 885 ASN Chi-restraints excluded: chain A residue 907 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 HIS C 78 ASN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN E 44 ASN I 17 ASN I 63 GLN I 104 GLN I 203 GLN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 GLN K 53 ASN K 146 ASN L 109 ASN L 146 ASN L 288 GLN M 146 ASN d 9 GLN ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 261 GLN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN A 768 HIS A 833 HIS A 885 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.117502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105009 restraints weight = 154075.664| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 3.77 r_work: 0.3432 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 40402 Z= 0.174 Angle : 0.705 12.849 55513 Z= 0.387 Chirality : 0.045 0.344 6335 Planarity : 0.005 0.091 6513 Dihedral : 19.929 177.885 7228 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.50 % Favored : 95.28 % Rotamer: Outliers : 3.87 % Allowed : 27.90 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -1.79 (0.11), residues: 4559 helix: -0.54 (0.11), residues: 1705 sheet: -0.73 (0.20), residues: 669 loop : -1.84 (0.12), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 106 TYR 0.020 0.002 TYR H 132 PHE 0.015 0.001 PHE A 68 TRP 0.022 0.001 TRP A 897 HIS 0.008 0.001 HIS e 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (40402) covalent geometry : angle 0.70500 / 0.39 (55513) hydrogen bonds : bond 0.05233 / 3.55 ( 1438) hydrogen bonds : angle 5.04688 / 3.60 ( 4034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 762 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 GLN cc_start: 0.8894 (mp10) cc_final: 0.8612 (mp10) REVERT: B 83 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7371 (tm-30) REVERT: B 126 SER cc_start: 0.9093 (t) cc_final: 0.8696 (m) REVERT: C 1 MET cc_start: 0.7541 (tpp) cc_final: 0.7299 (tpp) REVERT: C 48 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8335 (pttm) REVERT: C 115 ASP cc_start: 0.8659 (t0) cc_final: 0.8337 (t0) REVERT: C 193 VAL cc_start: 0.8904 (m) cc_final: 0.8656 (p) REVERT: C 214 MET cc_start: 0.8171 (mmm) cc_final: 0.7799 (tpp) REVERT: D 4 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8370 (tm-30) REVERT: D 31 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8416 (tp) REVERT: D 34 ASP cc_start: 0.8483 (p0) cc_final: 0.8113 (p0) REVERT: D 113 LYS cc_start: 0.9318 (ttmm) cc_final: 0.8920 (ttpp) REVERT: D 120 GLU cc_start: 0.8856 (tt0) cc_final: 0.8524 (tm-30) REVERT: D 127 ASP cc_start: 0.8178 (t70) cc_final: 0.7698 (t0) REVERT: D 135 ASP cc_start: 0.8670 (p0) cc_final: 0.8380 (p0) REVERT: D 139 ASP cc_start: 0.8309 (p0) cc_final: 0.7834 (p0) REVERT: D 183 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8689 (tm-30) REVERT: D 186 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8794 (pp) REVERT: D 191 ASP cc_start: 0.7934 (t0) cc_final: 0.7204 (t0) REVERT: D 224 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.8150 (t0) REVERT: D 241 ASP cc_start: 0.9291 (t0) cc_final: 0.8994 (t0) REVERT: D 257 HIS cc_start: 0.8529 (t70) cc_final: 0.7877 (t-170) REVERT: D 260 ASP cc_start: 0.8503 (t70) cc_final: 0.8263 (p0) REVERT: D 278 LYS cc_start: 0.9177 (ttpp) cc_final: 0.8751 (ttpp) REVERT: D 280 ASP cc_start: 0.8820 (t0) cc_final: 0.8286 (t0) REVERT: E 6 LEU cc_start: 0.9026 (tp) cc_final: 0.8591 (tm) REVERT: E 59 GLU cc_start: 0.8695 (pm20) cc_final: 0.8358 (pm20) REVERT: E 102 GLN cc_start: 0.9147 (mt0) cc_final: 0.8514 (mp10) REVERT: E 120 GLU cc_start: 0.8684 (tp30) cc_final: 0.8207 (tp30) REVERT: E 124 MET cc_start: 0.8553 (ptp) cc_final: 0.8277 (ptp) REVERT: E 127 ASP cc_start: 0.8464 (t70) cc_final: 0.8144 (t0) REVERT: E 154 LYS cc_start: 0.9026 (mttt) cc_final: 0.8167 (mmmm) REVERT: E 178 LYS cc_start: 0.9335 (tptp) cc_final: 0.9044 (tppp) REVERT: E 183 GLU cc_start: 0.8648 (tp30) cc_final: 0.8358 (tp30) REVERT: E 261 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8233 (mm110) REVERT: E 294 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7663 (tmm) REVERT: G 111 ASP cc_start: 0.7997 (t70) cc_final: 0.7731 (p0) REVERT: G 217 ASP cc_start: 0.8252 (p0) cc_final: 0.7840 (p0) REVERT: H 117 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8480 (mm-30) REVERT: I 147 ASP cc_start: 0.8708 (t70) cc_final: 0.8489 (t70) REVERT: I 171 ASP cc_start: 0.8055 (m-30) cc_final: 0.7678 (m-30) REVERT: I 195 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7577 (tm-30) REVERT: I 217 ASP cc_start: 0.7627 (p0) cc_final: 0.7332 (p0) REVERT: I 241 GLU cc_start: 0.8135 (mp0) cc_final: 0.7861 (mp0) REVERT: I 250 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8198 (mm-30) REVERT: I 289 MET cc_start: 0.8576 (mtm) cc_final: 0.8375 (mtp) REVERT: J 88 ASP cc_start: 0.8309 (t0) cc_final: 0.8038 (t0) REVERT: J 91 LYS cc_start: 0.8968 (tttm) cc_final: 0.8766 (tttm) REVERT: J 137 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7201 (pp20) REVERT: J 165 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8494 (t0) REVERT: J 213 LYS cc_start: 0.9159 (ttpp) cc_final: 0.8654 (ttpp) REVERT: K 30 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7416 (p0) REVERT: K 33 ASN cc_start: 0.8426 (m-40) cc_final: 0.8200 (m-40) REVERT: K 56 ASP cc_start: 0.8624 (m-30) cc_final: 0.8398 (m-30) REVERT: K 58 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8044 (OUTLIER) REVERT: K 59 LYS cc_start: 0.8967 (ptpt) cc_final: 0.8563 (ptpp) REVERT: K 140 GLU cc_start: 0.8538 (tt0) cc_final: 0.8225 (tt0) REVERT: K 190 TYR cc_start: 0.8296 (m-80) cc_final: 0.7995 (m-10) REVERT: K 191 MET cc_start: 0.8646 (mtp) cc_final: 0.8389 (mtp) REVERT: K 285 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7687 (tm-30) REVERT: K 289 MET cc_start: 0.8663 (mtp) cc_final: 0.8313 (mtp) REVERT: L 12 TYR cc_start: 0.8765 (m-80) cc_final: 0.8553 (m-80) REVERT: L 30 ASP cc_start: 0.8267 (t70) cc_final: 0.8064 (t0) REVERT: L 156 LEU cc_start: 0.8856 (mt) cc_final: 0.8486 (mm) REVERT: L 188 GLU cc_start: 0.7995 (pm20) cc_final: 0.7636 (pm20) REVERT: L 213 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8412 (ttmt) REVERT: L 266 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8133 (p0) REVERT: M 88 ASP cc_start: 0.8480 (m-30) cc_final: 0.8216 (p0) REVERT: M 159 GLU cc_start: 0.8281 (pm20) cc_final: 0.8029 (pm20) REVERT: M 195 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7241 (tp30) REVERT: a 46 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.8107 (mm110) REVERT: a 47 THR cc_start: 0.8539 (m) cc_final: 0.8312 (t) REVERT: a 58 VAL cc_start: 0.9058 (t) cc_final: 0.8784 (m) REVERT: d 119 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7418 (mmtt) REVERT: d 123 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7808 (mptt) REVERT: d 151 LYS cc_start: 0.8488 (tmmm) cc_final: 0.8261 (pptt) REVERT: d 179 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8602 (tm-30) REVERT: d 183 GLU cc_start: 0.8754 (tp30) cc_final: 0.8436 (tm-30) REVERT: d 241 ASP cc_start: 0.8047 (t70) cc_final: 0.7839 (m-30) REVERT: e 24 LYS cc_start: 0.8896 (ttmm) cc_final: 0.8644 (mmmm) REVERT: e 59 GLU cc_start: 0.8199 (pp20) cc_final: 0.7922 (pp20) REVERT: e 98 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7763 (p) REVERT: e 99 LYS cc_start: 0.9130 (ptpp) cc_final: 0.8753 (ptmm) REVERT: e 111 GLU cc_start: 0.8668 (tp30) cc_final: 0.8304 (tp30) REVERT: e 127 ASP cc_start: 0.8382 (m-30) cc_final: 0.8077 (t0) REVERT: e 178 LYS cc_start: 0.9094 (ptmm) cc_final: 0.8539 (tptp) REVERT: e 179 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8541 (tm-30) REVERT: e 189 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8496 (tmmm) REVERT: e 261 GLN cc_start: 0.8810 (mp10) cc_final: 0.8538 (mp10) REVERT: e 278 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8647 (ptpp) REVERT: A 172 ASP cc_start: 0.7907 (p0) cc_final: 0.7658 (p0) REVERT: A 225 ASP cc_start: 0.8470 (m-30) cc_final: 0.8010 (p0) REVERT: A 248 LYS cc_start: 0.8910 (mppt) cc_final: 0.8463 (mmtm) REVERT: A 331 LYS cc_start: 0.8837 (mmpt) cc_final: 0.8622 (mmpt) REVERT: A 405 GLN cc_start: 0.8936 (tt0) cc_final: 0.8075 (tm-30) REVERT: A 422 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8800 (tpp) REVERT: A 511 GLU cc_start: 0.8401 (pm20) cc_final: 0.8152 (pm20) REVERT: A 520 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8957 (mtm) REVERT: A 541 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7464 (t) REVERT: A 621 ASP cc_start: 0.8870 (p0) cc_final: 0.8668 (p0) REVERT: A 622 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8070 (mp10) REVERT: A 631 GLN cc_start: 0.8906 (tp40) cc_final: 0.8480 (tp40) REVERT: A 700 ASN cc_start: 0.9029 (m-40) cc_final: 0.8681 (t160) REVERT: A 848 ASN cc_start: 0.6517 (OUTLIER) cc_final: 0.5067 (t0) REVERT: A 850 PHE cc_start: 0.7254 (m-10) cc_final: 0.6971 (m-10) outliers start: 148 outliers final: 50 residues processed: 859 average time/residue: 0.6684 time to fit residues: 694.6158 Evaluate side-chains 793 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 724 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 130 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 1 TYR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 284 THR Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 165 ASP Chi-restraints excluded: chain J residue 191 MET Chi-restraints excluded: chain J residue 227 GLN Chi-restraints excluded: chain J residue 267 LYS Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 146 ASN Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 171 ASP Chi-restraints excluded: chain L residue 197 SER Chi-restraints excluded: chain L residue 226 ASP Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 138 SER Chi-restraints excluded: chain M residue 146 ASN Chi-restraints excluded: chain M residue 197 SER Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain a residue 46 GLN Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 119 LYS Chi-restraints excluded: chain d residue 123 LYS Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 112 GLU Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 189 LYS Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 496 MET Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 848 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 135 optimal weight: 0.0070 chunk 184 optimal weight: 5.9990 chunk 380 optimal weight: 7.9990 chunk 257 optimal weight: 7.9990 chunk 297 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 271 optimal weight: 0.7980 chunk 461 optimal weight: 4.9990 chunk 351 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 12 ASN D 102 GLN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 17 ASN H 28 HIS I 63 GLN I 203 GLN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 ASN L 258 ASN L 288 GLN M 146 ASN ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 168 HIS e 150 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.111829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.098828 restraints weight = 160840.969| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 3.81 r_work: 0.3304 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 40402 Z= 0.290 Angle : 0.721 11.205 55513 Z= 0.396 Chirality : 0.048 0.362 6335 Planarity : 0.005 0.064 6513 Dihedral : 19.775 179.356 7173 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.57 % Favored : 95.28 % Rotamer: Outliers : 4.86 % Allowed : 26.36 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -1.41 (0.12), residues: 4559 helix: -0.00 (0.12), residues: 1709 sheet: -0.96 (0.19), residues: 699 loop : -1.67 (0.12), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 270 TYR 0.025 0.002 TYR J 99 PHE 0.029 0.002 PHE d 188 TRP 0.017 0.002 TRP d 218 HIS 0.008 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.29 (40402) covalent geometry : angle 0.72085 / 0.40 (55513) hydrogen bonds : bond 0.05290 / 3.47 ( 1438) hydrogen bonds : angle 4.81235 / 3.43 ( 4034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 762 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 LYS cc_start: 0.8884 (tttm) cc_final: 0.8665 (tppt) REVERT: B 35 LYS cc_start: 0.8753 (mppt) cc_final: 0.8540 (mppt) REVERT: B 58 GLU cc_start: 0.7080 (pm20) cc_final: 0.6869 (pm20) REVERT: B 70 ASN cc_start: 0.9108 (m-40) cc_final: 0.8781 (m110) REVERT: C 1 MET cc_start: 0.7678 (tpp) cc_final: 0.7186 (tpp) REVERT: C 37 GLU cc_start: 0.6458 (pp20) cc_final: 0.6202 (pp20) REVERT: C 48 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8571 (mtmt) REVERT: C 89 GLN cc_start: 0.9359 (mm-40) cc_final: 0.9146 (mm-40) REVERT: C 115 ASP cc_start: 0.8682 (t0) cc_final: 0.8411 (t0) REVERT: C 172 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7120 (mm-30) REVERT: C 173 ASP cc_start: 0.7526 (p0) cc_final: 0.7055 (p0) REVERT: C 180 GLN cc_start: 0.8254 (tt0) cc_final: 0.8018 (tt0) REVERT: C 214 MET cc_start: 0.8401 (mmm) cc_final: 0.7923 (tpp) REVERT: D 4 GLN cc_start: 0.9140 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 18 ARG cc_start: 0.9039 (ttm110) cc_final: 0.8757 (ttm-80) REVERT: D 34 ASP cc_start: 0.8715 (p0) cc_final: 0.8347 (p0) REVERT: D 110 ASP cc_start: 0.8389 (t0) cc_final: 0.8175 (OUTLIER) REVERT: D 113 LYS cc_start: 0.9270 (ttmm) cc_final: 0.9056 (ttmm) REVERT: D 120 GLU cc_start: 0.8857 (tt0) cc_final: 0.8469 (tm-30) REVERT: D 127 ASP cc_start: 0.8270 (t70) cc_final: 0.7951 (t0) REVERT: D 135 ASP cc_start: 0.8792 (p0) cc_final: 0.8540 (p0) REVERT: D 139 ASP cc_start: 0.8485 (p0) cc_final: 0.7939 (p0) REVERT: D 183 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8624 (tm-30) REVERT: D 186 ILE cc_start: 0.9162 (tp) cc_final: 0.8683 (pp) REVERT: D 189 LYS cc_start: 0.8926 (tppt) cc_final: 0.8698 (tppt) REVERT: D 191 ASP cc_start: 0.7834 (t0) cc_final: 0.7274 (t0) REVERT: D 224 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.7923 (t0) REVERT: D 225 SER cc_start: 0.9239 (m) cc_final: 0.8917 (t) REVERT: D 241 ASP cc_start: 0.9282 (t0) cc_final: 0.9014 (t0) REVERT: D 244 ASP cc_start: 0.8737 (m-30) cc_final: 0.8477 (m-30) REVERT: D 278 LYS cc_start: 0.9261 (ttpp) cc_final: 0.8888 (ttpp) REVERT: D 280 ASP cc_start: 0.8871 (t0) cc_final: 0.8328 (t0) REVERT: D 291 ARG cc_start: 0.8831 (mtm110) cc_final: 0.8508 (ttp80) REVERT: E 6 LEU cc_start: 0.9061 (tp) cc_final: 0.8602 (tm) REVERT: E 24 LYS cc_start: 0.8383 (mppt) cc_final: 0.8080 (mppt) REVERT: E 55 SER cc_start: 0.7371 (OUTLIER) cc_final: 0.5256 (p) REVERT: E 59 GLU cc_start: 0.8722 (pm20) cc_final: 0.8498 (pm20) REVERT: E 80 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8054 (t70) REVERT: E 120 GLU cc_start: 0.8734 (tp30) cc_final: 0.8282 (tp30) REVERT: E 124 MET cc_start: 0.8759 (ptp) cc_final: 0.8534 (ptp) REVERT: E 127 ASP cc_start: 0.8600 (t70) cc_final: 0.8281 (t0) REVERT: E 139 ASP cc_start: 0.8061 (t0) cc_final: 0.7696 (t0) REVERT: E 154 LYS cc_start: 0.9150 (mttt) cc_final: 0.8523 (mmpt) REVERT: E 178 LYS cc_start: 0.9345 (tptp) cc_final: 0.9119 (tppp) REVERT: E 183 GLU cc_start: 0.8661 (tp30) cc_final: 0.8350 (tp30) REVERT: E 189 LYS cc_start: 0.8911 (ptmm) cc_final: 0.8614 (ttpp) REVERT: E 261 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8515 (mp10) REVERT: E 263 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8132 (pmm) REVERT: E 278 LYS cc_start: 0.9126 (mtpp) cc_final: 0.8706 (mtmm) REVERT: E 294 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7489 (tmm) REVERT: G 111 ASP cc_start: 0.8203 (t70) cc_final: 0.7843 (p0) REVERT: G 137 GLU cc_start: 0.8211 (mp0) cc_final: 0.7797 (mp0) REVERT: G 159 GLU cc_start: 0.8461 (pm20) cc_final: 0.8062 (pm20) REVERT: G 205 PHE cc_start: 0.6890 (t80) cc_final: 0.6685 (t80) REVERT: G 217 ASP cc_start: 0.8450 (p0) cc_final: 0.8016 (p0) REVERT: H 83 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7815 (tm-30) REVERT: H 117 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8474 (mm-30) REVERT: I 156 LEU cc_start: 0.9043 (mm) cc_final: 0.8827 (mp) REVERT: I 171 ASP cc_start: 0.8202 (m-30) cc_final: 0.7860 (m-30) REVERT: I 217 ASP cc_start: 0.7815 (p0) cc_final: 0.7381 (p0) REVERT: I 241 GLU cc_start: 0.8170 (mp0) cc_final: 0.7785 (mp0) REVERT: I 250 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8147 (mm-30) REVERT: I 281 LYS cc_start: 0.8554 (tmmt) cc_final: 0.8184 (tmmt) REVERT: I 285 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7686 (tm-30) REVERT: J 30 ASP cc_start: 0.8574 (t0) cc_final: 0.7713 (t0) REVERT: J 61 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8672 (t0) REVERT: J 88 ASP cc_start: 0.8578 (t0) cc_final: 0.8250 (t0) REVERT: J 137 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7493 (tm-30) REVERT: J 165 ASP cc_start: 0.8768 (OUTLIER) cc_final: 0.8549 (t0) REVERT: J 284 THR cc_start: 0.8925 (p) cc_final: 0.8692 (p) REVERT: J 286 GLU cc_start: 0.8446 (pm20) cc_final: 0.8133 (pm20) REVERT: K 30 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7822 (p0) REVERT: K 33 ASN cc_start: 0.8693 (m-40) cc_final: 0.8452 (m-40) REVERT: K 58 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8452 (p0) REVERT: K 59 LYS cc_start: 0.9011 (ptpt) cc_final: 0.8690 (ptpp) REVERT: K 74 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8323 (mtpp) REVERT: K 108 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7924 (mm-30) REVERT: K 153 SER cc_start: 0.8876 (p) cc_final: 0.8437 (p) REVERT: K 186 LYS cc_start: 0.9199 (OUTLIER) cc_final: 0.8807 (mmmm) REVERT: K 250 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8238 (mp0) REVERT: K 285 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7618 (tm-30) REVERT: K 289 MET cc_start: 0.8653 (mtp) cc_final: 0.8366 (mtp) REVERT: L 12 TYR cc_start: 0.8814 (m-80) cc_final: 0.8581 (m-80) REVERT: L 30 ASP cc_start: 0.8501 (t70) cc_final: 0.8160 (t0) REVERT: L 156 LEU cc_start: 0.8831 (mt) cc_final: 0.8484 (mm) REVERT: L 188 GLU cc_start: 0.8117 (pm20) cc_final: 0.7719 (pm20) REVERT: L 192 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8152 (tm) REVERT: L 203 GLN cc_start: 0.8979 (mp10) cc_final: 0.8366 (mt0) REVERT: L 213 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8270 (ttmt) REVERT: L 241 GLU cc_start: 0.8523 (pm20) cc_final: 0.8113 (pm20) REVERT: L 242 ASP cc_start: 0.8441 (m-30) cc_final: 0.8232 (p0) REVERT: L 262 TYR cc_start: 0.9255 (m-80) cc_final: 0.8889 (m-80) REVERT: L 266 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8311 (p0) REVERT: M 63 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6069 (pm20) REVERT: M 88 ASP cc_start: 0.8703 (m-30) cc_final: 0.8435 (p0) REVERT: M 146 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8750 (p0) REVERT: M 195 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7487 (mm-30) REVERT: M 282 SER cc_start: 0.8871 (m) cc_final: 0.8664 (m) REVERT: a 47 THR cc_start: 0.8654 (m) cc_final: 0.8451 (t) REVERT: a 48 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8061 (ptpp) REVERT: a 57 LYS cc_start: 0.7881 (mmtt) cc_final: 0.7631 (mmmt) REVERT: d 102 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8208 (mp10) REVERT: d 123 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.7894 (mmmt) REVERT: d 151 LYS cc_start: 0.8591 (tmmm) cc_final: 0.8037 (tmmt) REVERT: d 178 LYS cc_start: 0.8843 (tmmm) cc_final: 0.8635 (tmmt) REVERT: d 179 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8385 (tm-30) REVERT: d 182 LEU cc_start: 0.9139 (tm) cc_final: 0.8869 (pp) REVERT: d 183 GLU cc_start: 0.8874 (tp30) cc_final: 0.8392 (tm-30) REVERT: d 188 PHE cc_start: 0.8041 (t80) cc_final: 0.7676 (t80) REVERT: d 240 PHE cc_start: 0.7207 (m-10) cc_final: 0.6823 (m-10) REVERT: e 8 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7857 (p) REVERT: e 13 MET cc_start: 0.8063 (ttt) cc_final: 0.7789 (ttt) REVERT: e 24 LYS cc_start: 0.8964 (ttmm) cc_final: 0.8648 (mmmm) REVERT: e 59 GLU cc_start: 0.8411 (pp20) cc_final: 0.8123 (pp20) REVERT: e 99 LYS cc_start: 0.9151 (ptpp) cc_final: 0.8737 (ptmm) REVERT: e 107 LEU cc_start: 0.8815 (tt) cc_final: 0.8605 (tm) REVERT: e 111 GLU cc_start: 0.8729 (tp30) cc_final: 0.8315 (tp30) REVERT: e 114 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8076 (mtpp) REVERT: e 127 ASP cc_start: 0.8408 (m-30) cc_final: 0.8103 (t0) REVERT: e 178 LYS cc_start: 0.9189 (ptmm) cc_final: 0.8706 (tptp) REVERT: e 189 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8496 (ptmm) REVERT: e 200 LYS cc_start: 0.9170 (pptt) cc_final: 0.8812 (pptt) REVERT: e 261 GLN cc_start: 0.8815 (mp10) cc_final: 0.8350 (mp10) REVERT: e 263 MET cc_start: 0.8262 (pmm) cc_final: 0.7939 (pmm) REVERT: e 278 LYS cc_start: 0.9035 (ttmt) cc_final: 0.8747 (mtpp) REVERT: A 172 ASP cc_start: 0.8180 (p0) cc_final: 0.7817 (p0) REVERT: A 225 ASP cc_start: 0.8549 (m-30) cc_final: 0.8106 (OUTLIER) REVERT: A 248 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8469 (mmpt) REVERT: A 287 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7045 (mm) REVERT: A 322 LYS cc_start: 0.9153 (mtmm) cc_final: 0.8855 (mtmm) REVERT: A 422 MET cc_start: 0.9146 (tmm) cc_final: 0.8653 (tpp) REVERT: A 541 SER cc_start: 0.8073 (OUTLIER) cc_final: 0.7613 (p) REVERT: A 622 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8088 (mt0) REVERT: A 631 GLN cc_start: 0.8914 (tp40) cc_final: 0.8526 (tp40) REVERT: A 675 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9086 (mmmm) REVERT: A 700 ASN cc_start: 0.9073 (m-40) cc_final: 0.8790 (t0) REVERT: A 807 LYS cc_start: 0.9177 (OUTLIER) cc_final: 0.8733 (tppp) REVERT: A 850 PHE cc_start: 0.7661 (m-10) cc_final: 0.7432 (m-10) REVERT: A 881 LYS cc_start: 0.5314 (mttt) cc_final: 0.5016 (tttt) outliers start: 186 outliers final: 62 residues processed: 883 average time/residue: 0.7087 time to fit residues: 752.1424 Evaluate side-chains 823 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 734 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 263 MET Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 1 TYR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 186 LYS Chi-restraints excluded: chain I residue 284 THR Chi-restraints excluded: chain J residue 61 ASN Chi-restraints excluded: chain J residue 148 GLN Chi-restraints excluded: chain J residue 165 ASP Chi-restraints excluded: chain J residue 191 MET Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain K residue 30 ASP Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 146 ASN Chi-restraints excluded: chain K residue 186 LYS Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 197 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 63 GLN Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 146 ASN Chi-restraints excluded: chain M residue 188 GLU Chi-restraints excluded: chain M residue 197 SER Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain a residue 48 LYS Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 102 GLN Chi-restraints excluded: chain d residue 122 LEU Chi-restraints excluded: chain d residue 123 LYS Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 189 LYS Chi-restraints excluded: chain e residue 294 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 675 LYS Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 807 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 51 optimal weight: 0.9980 chunk 180 optimal weight: 0.0770 chunk 224 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 389 optimal weight: 0.9990 chunk 306 optimal weight: 10.0000 chunk 430 optimal weight: 5.9990 chunk 374 optimal weight: 0.1980 chunk 386 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 222 ASN D 197 ASN ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN I 63 GLN I 294 ASN J 55 ASN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 ASN J 227 GLN K 27 ASN K 53 ASN K 148 GLN M 33 ASN M 146 ASN ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 92 GLN e 150 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 ASN ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.114583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.101873 restraints weight = 149304.831| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.70 r_work: 0.3366 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40402 Z= 0.150 Angle : 0.660 13.472 55513 Z= 0.359 Chirality : 0.045 0.353 6335 Planarity : 0.004 0.060 6513 Dihedral : 19.674 179.626 7160 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.48 % Favored : 95.35 % Rotamer: Outliers : 3.87 % Allowed : 27.51 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -1.23 (0.12), residues: 4559 helix: 0.26 (0.12), residues: 1718 sheet: -1.12 (0.19), residues: 706 loop : -1.59 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 133 TYR 0.028 0.001 TYR A 772 PHE 0.024 0.001 PHE d 188 TRP 0.021 0.001 TRP d 218 HIS 0.008 0.001 HIS e 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (40402) covalent geometry : angle 0.66027 / 0.36 (55513) hydrogen bonds : bond 0.04267 / 2.84 ( 1438) hydrogen bonds : angle 4.57198 / 3.26 ( 4034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 754 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LYS cc_start: 0.8721 (mppt) cc_final: 0.8446 (mppt) REVERT: B 64 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8642 (mp10) REVERT: B 130 TYR cc_start: 0.8032 (t80) cc_final: 0.7236 (t80) REVERT: C 1 MET cc_start: 0.7623 (tpp) cc_final: 0.7180 (tpp) REVERT: C 37 GLU cc_start: 0.6595 (pp20) cc_final: 0.6159 (pp20) REVERT: C 48 LYS cc_start: 0.8839 (mtmm) cc_final: 0.8511 (mtmm) REVERT: C 115 ASP cc_start: 0.8669 (t0) cc_final: 0.8407 (t0) REVERT: C 172 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7201 (mm-30) REVERT: C 180 GLN cc_start: 0.8320 (tt0) cc_final: 0.8022 (tt0) REVERT: D 4 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8192 (tm-30) REVERT: D 18 ARG cc_start: 0.9053 (ttm110) cc_final: 0.8817 (ttm-80) REVERT: D 88 CYS cc_start: 0.8862 (t) cc_final: 0.8617 (t) REVERT: D 109 LEU cc_start: 0.8671 (mm) cc_final: 0.8455 (mm) REVERT: D 110 ASP cc_start: 0.8307 (t0) cc_final: 0.8089 (t0) REVERT: D 113 LYS cc_start: 0.9268 (ttmm) cc_final: 0.8955 (ttmm) REVERT: D 120 GLU cc_start: 0.8787 (tt0) cc_final: 0.8493 (tm-30) REVERT: D 127 ASP cc_start: 0.8238 (t70) cc_final: 0.7927 (t0) REVERT: D 135 ASP cc_start: 0.8795 (p0) cc_final: 0.8549 (p0) REVERT: D 139 ASP cc_start: 0.8456 (p0) cc_final: 0.7919 (p0) REVERT: D 174 LYS cc_start: 0.9095 (ttmm) cc_final: 0.8757 (mmmm) REVERT: D 186 ILE cc_start: 0.9120 (tp) cc_final: 0.8617 (pp) REVERT: D 190 ARG cc_start: 0.7944 (tpt90) cc_final: 0.7649 (tpt90) REVERT: D 191 ASP cc_start: 0.7875 (t0) cc_final: 0.7296 (t0) REVERT: D 224 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8051 (t0) REVERT: D 225 SER cc_start: 0.9192 (m) cc_final: 0.8739 (p) REVERT: D 241 ASP cc_start: 0.9304 (t0) cc_final: 0.8800 (t0) REVERT: D 244 ASP cc_start: 0.8739 (m-30) cc_final: 0.8177 (p0) REVERT: D 260 ASP cc_start: 0.8505 (t70) cc_final: 0.8248 (p0) REVERT: D 278 LYS cc_start: 0.9213 (ttpp) cc_final: 0.8807 (ttpp) REVERT: D 280 ASP cc_start: 0.8838 (t0) cc_final: 0.8282 (t0) REVERT: E 59 GLU cc_start: 0.8651 (pm20) cc_final: 0.8406 (pm20) REVERT: E 120 GLU cc_start: 0.8685 (tp30) cc_final: 0.8197 (tp30) REVERT: E 124 MET cc_start: 0.8674 (ptp) cc_final: 0.8373 (ptp) REVERT: E 127 ASP cc_start: 0.8535 (t70) cc_final: 0.8229 (t0) REVERT: E 150 ASN cc_start: 0.8872 (m110) cc_final: 0.8217 (m-40) REVERT: E 154 LYS cc_start: 0.9098 (mttt) cc_final: 0.8486 (mmpt) REVERT: E 178 LYS cc_start: 0.9263 (tptp) cc_final: 0.9014 (tppp) REVERT: E 183 GLU cc_start: 0.8593 (tp30) cc_final: 0.8290 (tp30) REVERT: E 189 LYS cc_start: 0.8905 (ptmm) cc_final: 0.8571 (ttpp) REVERT: E 244 ASP cc_start: 0.8707 (m-30) cc_final: 0.8451 (m-30) REVERT: E 261 GLN cc_start: 0.8797 (mp10) cc_final: 0.8397 (mp10) REVERT: E 294 MET cc_start: 0.8042 (mmp) cc_final: 0.7490 (tmm) REVERT: G 47 THR cc_start: 0.8644 (p) cc_final: 0.7965 (p) REVERT: G 111 ASP cc_start: 0.8198 (t70) cc_final: 0.7804 (p0) REVERT: G 159 GLU cc_start: 0.8364 (pm20) cc_final: 0.8028 (pm20) REVERT: G 217 ASP cc_start: 0.8421 (p0) cc_final: 0.7968 (p0) REVERT: H 36 GLU cc_start: 0.8077 (pp20) cc_final: 0.7876 (pp20) REVERT: H 83 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7638 (tm-30) REVERT: H 117 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8403 (mm-30) REVERT: I 156 LEU cc_start: 0.8976 (mm) cc_final: 0.8761 (mp) REVERT: I 171 ASP cc_start: 0.8168 (m-30) cc_final: 0.7817 (m-30) REVERT: I 195 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7902 (mm-30) REVERT: I 217 ASP cc_start: 0.7732 (p0) cc_final: 0.7312 (p0) REVERT: I 250 GLU cc_start: 0.8520 (mm-30) cc_final: 0.7999 (mt-10) REVERT: I 281 LYS cc_start: 0.8560 (tmmt) cc_final: 0.8194 (tmmt) REVERT: J 30 ASP cc_start: 0.8590 (t0) cc_final: 0.7680 (t0) REVERT: J 80 LYS cc_start: 0.9234 (mtpm) cc_final: 0.8987 (mtmm) REVERT: J 88 ASP cc_start: 0.8520 (t0) cc_final: 0.8144 (t0) REVERT: J 165 ASP cc_start: 0.8760 (OUTLIER) cc_final: 0.8559 (t0) REVERT: J 186 LYS cc_start: 0.8964 (mmmm) cc_final: 0.8726 (mmmm) REVERT: J 286 GLU cc_start: 0.8410 (pm20) cc_final: 0.8184 (pp20) REVERT: K 30 ASP cc_start: 0.8269 (p0) cc_final: 0.7764 (p0) REVERT: K 58 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8417 (p0) REVERT: K 59 LYS cc_start: 0.8996 (ptpt) cc_final: 0.8694 (ptpp) REVERT: K 108 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7847 (mm-30) REVERT: K 153 SER cc_start: 0.8698 (p) cc_final: 0.8468 (p) REVERT: K 159 GLU cc_start: 0.7883 (pp20) cc_final: 0.7659 (pp20) REVERT: K 186 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8731 (mmmm) REVERT: K 207 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8381 (tm-30) REVERT: K 250 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8148 (mp0) REVERT: K 285 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7618 (tm-30) REVERT: K 289 MET cc_start: 0.8524 (mtp) cc_final: 0.8240 (mtp) REVERT: L 12 TYR cc_start: 0.8855 (m-80) cc_final: 0.8542 (m-80) REVERT: L 30 ASP cc_start: 0.8436 (t70) cc_final: 0.8030 (t0) REVERT: L 156 LEU cc_start: 0.8817 (mt) cc_final: 0.8544 (mm) REVERT: L 188 GLU cc_start: 0.8084 (pm20) cc_final: 0.7694 (pm20) REVERT: L 192 LEU cc_start: 0.9010 (tt) cc_final: 0.8315 (tp) REVERT: L 213 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8248 (ttmt) REVERT: L 262 TYR cc_start: 0.9237 (m-80) cc_final: 0.8927 (m-80) REVERT: L 266 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8319 (p0) REVERT: L 286 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8018 (mm-30) REVERT: M 81 TYR cc_start: 0.8669 (p90) cc_final: 0.8414 (p90) REVERT: M 88 ASP cc_start: 0.8573 (m-30) cc_final: 0.8326 (p0) REVERT: M 137 GLU cc_start: 0.8708 (tp30) cc_final: 0.8507 (mm-30) REVERT: M 159 GLU cc_start: 0.8319 (pm20) cc_final: 0.8036 (pm20) REVERT: M 195 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7351 (tp30) REVERT: a 28 THR cc_start: 0.5732 (OUTLIER) cc_final: 0.5383 (t) REVERT: a 48 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7876 (ptpp) REVERT: d 123 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7741 (mmmt) REVERT: d 151 LYS cc_start: 0.8380 (tmmm) cc_final: 0.8029 (tmmt) REVERT: d 154 LYS cc_start: 0.8470 (ptmm) cc_final: 0.7739 (ptpp) REVERT: d 178 LYS cc_start: 0.8883 (tmmm) cc_final: 0.8655 (tmmt) REVERT: d 179 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8322 (tm-30) REVERT: d 182 LEU cc_start: 0.9221 (tm) cc_final: 0.8885 (pp) REVERT: d 183 GLU cc_start: 0.8871 (tp30) cc_final: 0.8367 (tm-30) REVERT: d 187 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8169 (pp20) REVERT: d 188 PHE cc_start: 0.7895 (t80) cc_final: 0.7690 (t80) REVERT: d 240 PHE cc_start: 0.7092 (m-10) cc_final: 0.6755 (m-10) REVERT: e 13 MET cc_start: 0.7984 (ttt) cc_final: 0.7716 (ttt) REVERT: e 24 LYS cc_start: 0.8949 (ttmm) cc_final: 0.8640 (mmmm) REVERT: e 59 GLU cc_start: 0.8403 (pp20) cc_final: 0.8020 (pp20) REVERT: e 99 LYS cc_start: 0.9130 (ptpp) cc_final: 0.8713 (ptmm) REVERT: e 111 GLU cc_start: 0.8728 (tp30) cc_final: 0.8380 (tp30) REVERT: e 114 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7969 (mtpp) REVERT: e 127 ASP cc_start: 0.8429 (m-30) cc_final: 0.8117 (t0) REVERT: e 178 LYS cc_start: 0.9142 (ptmm) cc_final: 0.8639 (tptp) REVERT: e 189 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8507 (ptmm) REVERT: e 191 ASP cc_start: 0.8186 (t0) cc_final: 0.7897 (t0) REVERT: e 200 LYS cc_start: 0.9124 (pptt) cc_final: 0.8785 (pptt) REVERT: e 224 ASN cc_start: 0.8718 (p0) cc_final: 0.8190 (p0) REVERT: e 261 GLN cc_start: 0.8764 (mp10) cc_final: 0.8276 (mp10) REVERT: e 263 MET cc_start: 0.8199 (pmm) cc_final: 0.7870 (pmm) REVERT: e 278 LYS cc_start: 0.9005 (ttmt) cc_final: 0.8753 (mtpp) REVERT: A 172 ASP cc_start: 0.8179 (p0) cc_final: 0.7793 (p0) REVERT: A 225 ASP cc_start: 0.8504 (m-30) cc_final: 0.8070 (OUTLIER) REVERT: A 241 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8843 (mmmm) REVERT: A 248 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8678 (mmmt) REVERT: A 322 LYS cc_start: 0.9077 (mtmm) cc_final: 0.8845 (mtmm) REVERT: A 344 LYS cc_start: 0.8926 (mmmm) cc_final: 0.8683 (mmmt) REVERT: A 422 MET cc_start: 0.9097 (tmm) cc_final: 0.8604 (tpp) REVERT: A 541 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7670 (p) REVERT: A 622 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: A 631 GLN cc_start: 0.8912 (tp40) cc_final: 0.8576 (tp40) REVERT: A 675 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9070 (mmmm) REVERT: A 693 GLU cc_start: 0.8273 (pp20) cc_final: 0.8015 (pp20) REVERT: A 700 ASN cc_start: 0.9072 (m-40) cc_final: 0.8821 (t0) REVERT: A 807 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8858 (tppp) REVERT: A 848 ASN cc_start: 0.7348 (OUTLIER) cc_final: 0.4910 (t0) REVERT: A 913 LEU cc_start: 0.8833 (mt) cc_final: 0.8485 (tp) outliers start: 148 outliers final: 62 residues processed: 854 average time/residue: 0.7199 time to fit residues: 737.4745 Evaluate side-chains 807 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 729 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 64 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 1 TYR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 284 THR Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain J residue 148 GLN Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 165 ASP Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 197 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 188 GLU Chi-restraints excluded: chain M residue 197 SER Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain a residue 13 ILE Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 48 LYS Chi-restraints excluded: chain a residue 52 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 123 LYS Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 17 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 52 GLU Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 189 LYS Chi-restraints excluded: chain e residue 294 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 675 LYS Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 848 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 260 optimal weight: 4.9990 chunk 459 optimal weight: 0.6980 chunk 215 optimal weight: 0.6980 chunk 299 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 300 optimal weight: 10.0000 chunk 465 optimal weight: 8.9990 chunk 269 optimal weight: 0.8980 chunk 387 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN I 109 ASN I 294 ASN ** J 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN L 288 GLN M 33 ASN M 221 GLN ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 150 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 GLN A 460 ASN A 575 ASN ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.114159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.101578 restraints weight = 138555.801| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.54 r_work: 0.3365 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40402 Z= 0.162 Angle : 0.657 13.935 55513 Z= 0.355 Chirality : 0.044 0.355 6335 Planarity : 0.004 0.060 6513 Dihedral : 19.595 179.374 7155 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.43 % Favored : 95.37 % Rotamer: Outliers : 4.10 % Allowed : 27.93 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -1.08 (0.12), residues: 4559 helix: 0.43 (0.12), residues: 1716 sheet: -1.12 (0.20), residues: 685 loop : -1.50 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 599 TYR 0.024 0.001 TYR H 90 PHE 0.029 0.001 PHE A 776 TRP 0.024 0.001 TRP d 218 HIS 0.006 0.001 HIS e 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (40402) covalent geometry : angle 0.65732 / 0.35 (55513) hydrogen bonds : bond 0.04187 / 2.79 ( 1438) hydrogen bonds : angle 4.48473 / 3.19 ( 4034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 910 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 753 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LYS cc_start: 0.8725 (mppt) cc_final: 0.8467 (mppt) REVERT: B 83 GLU cc_start: 0.7942 (pp20) cc_final: 0.7713 (pp20) REVERT: C 1 MET cc_start: 0.7573 (tpp) cc_final: 0.7202 (tpp) REVERT: C 37 GLU cc_start: 0.6603 (pp20) cc_final: 0.6300 (pp20) REVERT: C 48 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8538 (mtmm) REVERT: C 75 ASP cc_start: 0.8705 (m-30) cc_final: 0.8307 (t0) REVERT: C 103 GLU cc_start: 0.8315 (tp30) cc_final: 0.8086 (tp30) REVERT: C 108 ASP cc_start: 0.8213 (m-30) cc_final: 0.7939 (m-30) REVERT: C 115 ASP cc_start: 0.8653 (t0) cc_final: 0.8361 (t0) REVERT: C 172 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7216 (mm-30) REVERT: C 180 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: D 4 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8183 (tm-30) REVERT: D 18 ARG cc_start: 0.9008 (ttm110) cc_final: 0.8790 (ttm-80) REVERT: D 120 GLU cc_start: 0.8786 (tt0) cc_final: 0.8475 (tm-30) REVERT: D 123 LYS cc_start: 0.8783 (mmmt) cc_final: 0.8380 (mmpt) REVERT: D 127 ASP cc_start: 0.8260 (t70) cc_final: 0.7935 (t0) REVERT: D 135 ASP cc_start: 0.8782 (p0) cc_final: 0.8578 (p0) REVERT: D 139 ASP cc_start: 0.8453 (p0) cc_final: 0.7919 (p0) REVERT: D 174 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8801 (mmmm) REVERT: D 186 ILE cc_start: 0.9087 (tp) cc_final: 0.8593 (pp) REVERT: D 191 ASP cc_start: 0.7907 (t0) cc_final: 0.7272 (t0) REVERT: D 224 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8033 (t0) REVERT: D 225 SER cc_start: 0.9179 (m) cc_final: 0.8742 (p) REVERT: D 241 ASP cc_start: 0.9272 (t0) cc_final: 0.8767 (t0) REVERT: D 244 ASP cc_start: 0.8734 (m-30) cc_final: 0.8210 (p0) REVERT: D 260 ASP cc_start: 0.8488 (t70) cc_final: 0.8244 (p0) REVERT: D 267 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7786 (mm-30) REVERT: D 278 LYS cc_start: 0.9241 (ttpp) cc_final: 0.8857 (ttpp) REVERT: D 280 ASP cc_start: 0.8846 (t0) cc_final: 0.8297 (t0) REVERT: E 120 GLU cc_start: 0.8706 (tp30) cc_final: 0.8225 (tp30) REVERT: E 124 MET cc_start: 0.8662 (ptp) cc_final: 0.8391 (ptp) REVERT: E 127 ASP cc_start: 0.8542 (t70) cc_final: 0.8244 (t0) REVERT: E 150 ASN cc_start: 0.8874 (m110) cc_final: 0.8263 (m-40) REVERT: E 154 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8562 (mttt) REVERT: E 178 LYS cc_start: 0.9258 (tptp) cc_final: 0.9049 (tppp) REVERT: E 183 GLU cc_start: 0.8525 (tp30) cc_final: 0.8192 (tp30) REVERT: E 189 LYS cc_start: 0.8876 (ptmm) cc_final: 0.8551 (ttpp) REVERT: E 261 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8470 (mp10) REVERT: E 278 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8666 (mtmm) REVERT: G 100 SER cc_start: 0.7971 (m) cc_final: 0.7433 (p) REVERT: G 111 ASP cc_start: 0.8185 (t70) cc_final: 0.7800 (p0) REVERT: G 140 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7702 (tp30) REVERT: G 217 ASP cc_start: 0.8400 (p0) cc_final: 0.7945 (p0) REVERT: H 83 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7643 (tm-30) REVERT: H 117 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8412 (mm-30) REVERT: I 108 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7479 (mm-30) REVERT: I 138 SER cc_start: 0.8722 (OUTLIER) cc_final: 0.8519 (p) REVERT: I 156 LEU cc_start: 0.8972 (mm) cc_final: 0.8748 (mp) REVERT: I 171 ASP cc_start: 0.8178 (m-30) cc_final: 0.7862 (m-30) REVERT: I 195 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7909 (mm-30) REVERT: I 217 ASP cc_start: 0.7695 (p0) cc_final: 0.7264 (p0) REVERT: I 250 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8034 (mm-30) REVERT: I 281 LYS cc_start: 0.8585 (tmmt) cc_final: 0.8236 (tmmt) REVERT: J 30 ASP cc_start: 0.8620 (t0) cc_final: 0.7684 (t0) REVERT: J 63 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7795 (mm-40) REVERT: J 80 LYS cc_start: 0.9215 (mtpm) cc_final: 0.8933 (mtmm) REVERT: J 88 ASP cc_start: 0.8508 (t0) cc_final: 0.8086 (t0) REVERT: J 147 ASP cc_start: 0.8675 (p0) cc_final: 0.8403 (p0) REVERT: J 165 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8555 (t0) REVERT: K 30 ASP cc_start: 0.8323 (p0) cc_final: 0.7853 (p0) REVERT: K 58 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8413 (p0) REVERT: K 59 LYS cc_start: 0.8991 (ptpt) cc_final: 0.8707 (ptpp) REVERT: K 91 LYS cc_start: 0.9224 (tppp) cc_final: 0.9020 (ttmm) REVERT: K 108 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7835 (mm-30) REVERT: K 153 SER cc_start: 0.8715 (p) cc_final: 0.8479 (p) REVERT: K 159 GLU cc_start: 0.7919 (pp20) cc_final: 0.7706 (pp20) REVERT: K 186 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8685 (mmmm) REVERT: K 250 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8142 (mm-30) REVERT: K 285 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7586 (tm-30) REVERT: K 289 MET cc_start: 0.8561 (mtp) cc_final: 0.8206 (mtp) REVERT: L 12 TYR cc_start: 0.8880 (m-80) cc_final: 0.8562 (m-80) REVERT: L 100 SER cc_start: 0.8807 (m) cc_final: 0.8515 (p) REVERT: L 156 LEU cc_start: 0.8831 (mt) cc_final: 0.8567 (mm) REVERT: L 171 ASP cc_start: 0.8139 (m-30) cc_final: 0.7716 (m-30) REVERT: L 188 GLU cc_start: 0.8065 (pm20) cc_final: 0.7696 (pm20) REVERT: L 192 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8679 (tp) REVERT: L 203 GLN cc_start: 0.8924 (mp10) cc_final: 0.8218 (mt0) REVERT: L 213 LYS cc_start: 0.8625 (ttmt) cc_final: 0.8235 (ttmt) REVERT: M 63 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.5848 (pm20) REVERT: M 81 TYR cc_start: 0.8653 (p90) cc_final: 0.8418 (p90) REVERT: M 88 ASP cc_start: 0.8587 (m-30) cc_final: 0.8345 (p0) REVERT: M 195 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7385 (tp30) REVERT: M 262 TYR cc_start: 0.9335 (m-80) cc_final: 0.9133 (m-10) REVERT: a 28 THR cc_start: 0.5724 (OUTLIER) cc_final: 0.5369 (t) REVERT: a 46 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7649 (tp40) REVERT: d 123 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7897 (mmpt) REVERT: d 154 LYS cc_start: 0.8475 (ptmm) cc_final: 0.8024 (ptpp) REVERT: d 177 TYR cc_start: 0.8491 (m-80) cc_final: 0.8282 (m-80) REVERT: d 178 LYS cc_start: 0.8885 (tmmm) cc_final: 0.8655 (tmmt) REVERT: d 179 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8296 (tm-30) REVERT: d 182 LEU cc_start: 0.9277 (tm) cc_final: 0.8897 (pp) REVERT: d 183 GLU cc_start: 0.8917 (tp30) cc_final: 0.8391 (tm-30) REVERT: d 187 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8159 (pp20) REVERT: d 188 PHE cc_start: 0.7837 (t80) cc_final: 0.7506 (t80) REVERT: d 189 LYS cc_start: 0.8391 (mppt) cc_final: 0.8123 (mppt) REVERT: d 234 ARG cc_start: 0.7057 (tpp80) cc_final: 0.6614 (tpp80) REVERT: d 240 PHE cc_start: 0.7156 (m-10) cc_final: 0.6495 (m-10) REVERT: d 241 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: e 8 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7792 (p) REVERT: e 13 MET cc_start: 0.8095 (ttt) cc_final: 0.7843 (ttt) REVERT: e 24 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8656 (mmmm) REVERT: e 59 GLU cc_start: 0.8403 (pp20) cc_final: 0.8014 (pp20) REVERT: e 61 MET cc_start: 0.8342 (tpt) cc_final: 0.7894 (tpt) REVERT: e 98 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7707 (p) REVERT: e 99 LYS cc_start: 0.9134 (ptpp) cc_final: 0.8745 (ptmm) REVERT: e 102 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8840 (mm-40) REVERT: e 111 GLU cc_start: 0.8737 (tp30) cc_final: 0.8352 (tp30) REVERT: e 114 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8015 (mtpp) REVERT: e 127 ASP cc_start: 0.8422 (m-30) cc_final: 0.8131 (t0) REVERT: e 178 LYS cc_start: 0.9151 (ptmm) cc_final: 0.8693 (tptp) REVERT: e 189 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8513 (ptmm) REVERT: e 191 ASP cc_start: 0.8180 (t0) cc_final: 0.7811 (t0) REVERT: e 193 LYS cc_start: 0.8792 (mmpt) cc_final: 0.8570 (mmpt) REVERT: e 200 LYS cc_start: 0.9117 (pptt) cc_final: 0.8776 (pptt) REVERT: e 261 GLN cc_start: 0.8758 (mp10) cc_final: 0.8215 (mp10) REVERT: e 278 LYS cc_start: 0.9016 (ttmt) cc_final: 0.8810 (mtpp) REVERT: A 172 ASP cc_start: 0.8141 (p0) cc_final: 0.7712 (p0) REVERT: A 225 ASP cc_start: 0.8516 (m-30) cc_final: 0.8077 (OUTLIER) REVERT: A 241 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8834 (mmmm) REVERT: A 248 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8669 (mmmt) REVERT: A 282 ASN cc_start: 0.8870 (t0) cc_final: 0.8587 (t0) REVERT: A 322 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8715 (mtmm) REVERT: A 422 MET cc_start: 0.9091 (tmm) cc_final: 0.8606 (tpp) REVERT: A 541 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.7712 (p) REVERT: A 622 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: A 627 GLU cc_start: 0.8537 (pp20) cc_final: 0.8040 (pp20) REVERT: A 631 GLN cc_start: 0.8919 (tp40) cc_final: 0.8573 (tp40) REVERT: A 675 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9073 (mmmm) REVERT: A 807 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8855 (tppp) REVERT: A 850 PHE cc_start: 0.7906 (m-10) cc_final: 0.7655 (m-10) REVERT: A 913 LEU cc_start: 0.8838 (mt) cc_final: 0.8516 (tt) outliers start: 157 outliers final: 67 residues processed: 855 average time/residue: 0.7103 time to fit residues: 729.6550 Evaluate side-chains 816 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 726 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 264 SER Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 270 ARG Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 1 TYR Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 44 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 84 LYS Chi-restraints excluded: chain I residue 104 GLN Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 165 ASP Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain K residue 44 VAL Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 284 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 197 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 63 GLN Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 188 GLU Chi-restraints excluded: chain M residue 197 SER Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 46 GLN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 122 LEU Chi-restraints excluded: chain d residue 123 LYS Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain d residue 241 ASP Chi-restraints excluded: chain e residue 8 SER Chi-restraints excluded: chain e residue 17 SER Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain e residue 52 GLU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 125 ARG Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 189 LYS Chi-restraints excluded: chain e residue 294 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 675 LYS Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 807 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 387 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 365 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 196 optimal weight: 0.8980 chunk 245 optimal weight: 0.2980 chunk 42 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 299 optimal weight: 10.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 228 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 294 ASN K 53 ASN K 148 GLN K 208 ASN L 288 GLN M 33 ASN ** M 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 150 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.113937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.101510 restraints weight = 134194.040| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.45 r_work: 0.3368 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 40402 Z= 0.170 Angle : 0.665 14.336 55513 Z= 0.358 Chirality : 0.044 0.358 6335 Planarity : 0.004 0.076 6513 Dihedral : 19.581 179.742 7153 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.72 % Favored : 95.08 % Rotamer: Outliers : 4.18 % Allowed : 28.71 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.97 (0.12), residues: 4559 helix: 0.54 (0.12), residues: 1718 sheet: -1.09 (0.20), residues: 680 loop : -1.45 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 133 TYR 0.024 0.001 TYR J 99 PHE 0.015 0.001 PHE d 188 TRP 0.026 0.001 TRP d 218 HIS 0.006 0.001 HIS e 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (40402) covalent geometry : angle 0.66495 / 0.36 (55513) hydrogen bonds : bond 0.04142 / 2.76 ( 1438) hydrogen bonds : angle 4.44338 / 3.16 ( 4034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 749 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 LYS cc_start: 0.8717 (mppt) cc_final: 0.8419 (mppt) REVERT: B 83 GLU cc_start: 0.7912 (pp20) cc_final: 0.7318 (tm-30) REVERT: B 126 SER cc_start: 0.8920 (t) cc_final: 0.8522 (m) REVERT: B 130 TYR cc_start: 0.8184 (t80) cc_final: 0.7498 (t80) REVERT: C 1 MET cc_start: 0.7586 (tpp) cc_final: 0.7168 (tpp) REVERT: C 37 GLU cc_start: 0.6601 (pp20) cc_final: 0.6284 (pp20) REVERT: C 48 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8516 (mtmm) REVERT: C 60 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8469 (mtp85) REVERT: C 108 ASP cc_start: 0.8257 (m-30) cc_final: 0.7980 (m-30) REVERT: C 115 ASP cc_start: 0.8623 (t0) cc_final: 0.8336 (t0) REVERT: C 172 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: C 173 ASP cc_start: 0.7622 (p0) cc_final: 0.6927 (p0) REVERT: C 177 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.8385 (ptm-80) REVERT: C 214 MET cc_start: 0.8576 (tpp) cc_final: 0.7907 (mpp) REVERT: D 4 GLN cc_start: 0.9133 (tm-30) cc_final: 0.8165 (tm-30) REVERT: D 113 LYS cc_start: 0.9224 (ttmm) cc_final: 0.8994 (ttmm) REVERT: D 120 GLU cc_start: 0.8760 (tt0) cc_final: 0.8476 (tm-30) REVERT: D 123 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8372 (mmpt) REVERT: D 139 ASP cc_start: 0.8475 (p0) cc_final: 0.7972 (p0) REVERT: D 174 LYS cc_start: 0.9111 (ttmm) cc_final: 0.8825 (mmmm) REVERT: D 186 ILE cc_start: 0.9091 (tp) cc_final: 0.8586 (pp) REVERT: D 191 ASP cc_start: 0.7894 (t0) cc_final: 0.7287 (t0) REVERT: D 224 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8117 (t0) REVERT: D 225 SER cc_start: 0.9218 (m) cc_final: 0.8762 (p) REVERT: D 241 ASP cc_start: 0.9278 (t0) cc_final: 0.9030 (t0) REVERT: D 260 ASP cc_start: 0.8511 (t70) cc_final: 0.8219 (p0) REVERT: D 278 LYS cc_start: 0.9232 (ttpp) cc_final: 0.8855 (ttpp) REVERT: D 280 ASP cc_start: 0.8867 (t0) cc_final: 0.8545 (t0) REVERT: E 111 GLU cc_start: 0.9122 (tp30) cc_final: 0.8921 (tp30) REVERT: E 120 GLU cc_start: 0.8695 (tp30) cc_final: 0.8175 (tp30) REVERT: E 124 MET cc_start: 0.8669 (ptp) cc_final: 0.8290 (ptp) REVERT: E 127 ASP cc_start: 0.8519 (t70) cc_final: 0.8225 (t0) REVERT: E 139 ASP cc_start: 0.8015 (t0) cc_final: 0.7631 (t0) REVERT: E 150 ASN cc_start: 0.8865 (m110) cc_final: 0.8258 (m-40) REVERT: E 154 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8589 (mttt) REVERT: E 178 LYS cc_start: 0.9254 (tptp) cc_final: 0.9013 (tppp) REVERT: E 183 GLU cc_start: 0.8496 (tp30) cc_final: 0.8176 (tp30) REVERT: E 189 LYS cc_start: 0.8851 (ptmm) cc_final: 0.8507 (ttpp) REVERT: E 261 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8398 (mp10) REVERT: E 278 LYS cc_start: 0.9094 (mtpp) cc_final: 0.8637 (mtmm) REVERT: G 9 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8559 (t) REVERT: G 100 SER cc_start: 0.7938 (m) cc_final: 0.7403 (p) REVERT: G 111 ASP cc_start: 0.8214 (t70) cc_final: 0.7814 (p0) REVERT: G 217 ASP cc_start: 0.8367 (p0) cc_final: 0.7930 (p0) REVERT: H 83 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7583 (tm-30) REVERT: H 90 TYR cc_start: 0.7845 (m-80) cc_final: 0.7636 (m-10) REVERT: H 117 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8404 (mm-30) REVERT: I 108 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7388 (mm-30) REVERT: I 138 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8522 (p) REVERT: I 156 LEU cc_start: 0.8981 (mm) cc_final: 0.8220 (mp) REVERT: I 159 GLU cc_start: 0.8005 (pm20) cc_final: 0.7554 (pm20) REVERT: I 171 ASP cc_start: 0.8155 (m-30) cc_final: 0.7860 (m-30) REVERT: I 193 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8842 (mm) REVERT: I 217 ASP cc_start: 0.7794 (p0) cc_final: 0.7383 (p0) REVERT: I 250 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8036 (mm-30) REVERT: I 281 LYS cc_start: 0.8589 (tmmt) cc_final: 0.8206 (tmmt) REVERT: J 30 ASP cc_start: 0.8624 (t0) cc_final: 0.7780 (t0) REVERT: J 80 LYS cc_start: 0.9186 (mtpm) cc_final: 0.8902 (mtmm) REVERT: J 84 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8654 (tppp) REVERT: J 88 ASP cc_start: 0.8472 (t0) cc_final: 0.8046 (t0) REVERT: J 165 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8547 (t0) REVERT: K 30 ASP cc_start: 0.8303 (p0) cc_final: 0.7857 (p0) REVERT: K 58 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8477 (p0) REVERT: K 59 LYS cc_start: 0.8980 (ptpt) cc_final: 0.8704 (ptpp) REVERT: K 74 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8285 (mtpp) REVERT: K 91 LYS cc_start: 0.9183 (tppp) cc_final: 0.8979 (ttmm) REVERT: K 108 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7900 (mm-30) REVERT: K 153 SER cc_start: 0.8695 (p) cc_final: 0.8447 (p) REVERT: K 159 GLU cc_start: 0.7934 (pp20) cc_final: 0.7671 (pp20) REVERT: K 186 LYS cc_start: 0.9098 (mmmm) cc_final: 0.8652 (mmmm) REVERT: K 250 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8086 (mp0) REVERT: K 285 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7568 (tm-30) REVERT: K 289 MET cc_start: 0.8547 (mtp) cc_final: 0.8240 (mtp) REVERT: L 12 TYR cc_start: 0.8904 (m-80) cc_final: 0.8569 (m-80) REVERT: L 13 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.9054 (p) REVERT: L 100 SER cc_start: 0.8790 (m) cc_final: 0.8554 (p) REVERT: L 156 LEU cc_start: 0.8836 (mt) cc_final: 0.8566 (mm) REVERT: L 171 ASP cc_start: 0.8179 (m-30) cc_final: 0.7751 (m-30) REVERT: L 188 GLU cc_start: 0.8020 (pm20) cc_final: 0.7704 (pm20) REVERT: L 203 GLN cc_start: 0.8931 (mp10) cc_final: 0.8668 (mt0) REVERT: L 213 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8165 (ttmt) REVERT: L 214 GLN cc_start: 0.8754 (mm110) cc_final: 0.8422 (mm-40) REVERT: L 241 GLU cc_start: 0.8365 (pm20) cc_final: 0.8047 (pm20) REVERT: L 245 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8877 (p) REVERT: L 262 TYR cc_start: 0.9196 (m-80) cc_final: 0.8798 (m-80) REVERT: L 266 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8207 (p0) REVERT: M 81 TYR cc_start: 0.8625 (p90) cc_final: 0.8408 (p90) REVERT: M 156 LEU cc_start: 0.8134 (mt) cc_final: 0.7658 (pp) REVERT: M 195 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7370 (tp30) REVERT: M 221 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: M 262 TYR cc_start: 0.9348 (m-80) cc_final: 0.9135 (m-10) REVERT: a 28 THR cc_start: 0.5701 (OUTLIER) cc_final: 0.5339 (t) REVERT: a 46 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7606 (tp40) REVERT: d 34 ASP cc_start: 0.8952 (p0) cc_final: 0.8658 (p0) REVERT: d 123 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.7826 (mmmt) REVERT: d 154 LYS cc_start: 0.8514 (ptmm) cc_final: 0.7992 (ptpp) REVERT: d 178 LYS cc_start: 0.8900 (tmmm) cc_final: 0.8661 (tmmt) REVERT: d 179 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8411 (tm-30) REVERT: d 182 LEU cc_start: 0.9295 (tm) cc_final: 0.8958 (pp) REVERT: d 183 GLU cc_start: 0.8913 (tp30) cc_final: 0.8399 (tm-30) REVERT: d 187 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8160 (pp20) REVERT: d 188 PHE cc_start: 0.7865 (t80) cc_final: 0.7503 (t80) REVERT: d 189 LYS cc_start: 0.8444 (mppt) cc_final: 0.8236 (mppt) REVERT: d 191 ASP cc_start: 0.8215 (t70) cc_final: 0.7999 (t0) REVERT: d 240 PHE cc_start: 0.7299 (m-10) cc_final: 0.6773 (m-10) REVERT: d 241 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8170 (m-30) REVERT: e 13 MET cc_start: 0.8194 (ttt) cc_final: 0.7277 (ttt) REVERT: e 24 LYS cc_start: 0.8955 (ttmm) cc_final: 0.8659 (mmmm) REVERT: e 59 GLU cc_start: 0.8417 (pp20) cc_final: 0.8083 (pp20) REVERT: e 61 MET cc_start: 0.8324 (tpt) cc_final: 0.7882 (tpt) REVERT: e 98 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7662 (p) REVERT: e 99 LYS cc_start: 0.9130 (ptpp) cc_final: 0.8786 (ptmm) REVERT: e 102 GLN cc_start: 0.9070 (mm-40) cc_final: 0.8808 (mm-40) REVERT: e 111 GLU cc_start: 0.8741 (tp30) cc_final: 0.8325 (tp30) REVERT: e 114 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8001 (mtpp) REVERT: e 127 ASP cc_start: 0.8444 (m-30) cc_final: 0.8173 (t0) REVERT: e 178 LYS cc_start: 0.9145 (ptmm) cc_final: 0.8679 (tptp) REVERT: e 189 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8511 (ptmm) REVERT: e 191 ASP cc_start: 0.8171 (t0) cc_final: 0.7830 (t0) REVERT: e 200 LYS cc_start: 0.9106 (pptt) cc_final: 0.8751 (pptt) REVERT: e 278 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8805 (mtpp) REVERT: A 172 ASP cc_start: 0.8193 (p0) cc_final: 0.7767 (p0) REVERT: A 225 ASP cc_start: 0.8499 (m-30) cc_final: 0.8059 (p0) REVERT: A 241 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8801 (mmmm) REVERT: A 248 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8682 (mmmt) REVERT: A 282 ASN cc_start: 0.8903 (t0) cc_final: 0.8575 (t0) REVERT: A 305 LEU cc_start: 0.8968 (tp) cc_final: 0.8659 (tp) REVERT: A 322 LYS cc_start: 0.9055 (mtmm) cc_final: 0.8840 (mtmm) REVERT: A 356 ASN cc_start: 0.8821 (m110) cc_final: 0.8478 (m-40) REVERT: A 422 MET cc_start: 0.9094 (tmm) cc_final: 0.8595 (tpp) REVERT: A 445 VAL cc_start: 0.8572 (t) cc_final: 0.8308 (p) REVERT: A 511 GLU cc_start: 0.8331 (pm20) cc_final: 0.8110 (pm20) REVERT: A 541 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.7714 (p) REVERT: A 591 ASP cc_start: 0.8323 (t0) cc_final: 0.7890 (t0) REVERT: A 622 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: A 631 GLN cc_start: 0.8884 (tp40) cc_final: 0.8541 (tp40) REVERT: A 675 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.9050 (mmmm) REVERT: A 693 GLU cc_start: 0.8315 (pp20) cc_final: 0.8026 (pp20) REVERT: A 807 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8674 (tppp) REVERT: A 850 PHE cc_start: 0.8046 (OUTLIER) cc_final: 0.7765 (m-10) REVERT: A 881 LYS cc_start: 0.5396 (mttt) cc_final: 0.5092 (tttt) REVERT: A 913 LEU cc_start: 0.8849 (mt) cc_final: 0.8572 (tt) REVERT: A 922 ASP cc_start: 0.7835 (t70) cc_final: 0.7258 (t0) outliers start: 160 outliers final: 65 residues processed: 847 average time/residue: 0.7168 time to fit residues: 728.2054 Evaluate side-chains 816 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 720 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 270 ARG Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 1 TYR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 84 LYS Chi-restraints excluded: chain I residue 104 GLN Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 165 ASP Chi-restraints excluded: chain J residue 191 MET Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 284 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 104 GLN Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 197 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 197 SER Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 221 GLN Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 46 GLN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 123 LYS Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain d residue 241 ASP Chi-restraints excluded: chain e residue 17 SER Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 52 GLU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 189 LYS Chi-restraints excluded: chain e residue 294 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 541 SER Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 675 LYS Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 850 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 154 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 225 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 chunk 256 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 306 optimal weight: 9.9990 chunk 252 optimal weight: 0.9990 chunk 139 optimal weight: 0.0470 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN I 294 ASN J 55 ASN ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 ASN K 148 GLN L 288 GLN ** M 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 221 GLN ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 ASN e 150 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.114574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.101599 restraints weight = 169136.218| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.84 r_work: 0.3353 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40402 Z= 0.152 Angle : 0.671 14.242 55513 Z= 0.359 Chirality : 0.044 0.357 6335 Planarity : 0.004 0.059 6513 Dihedral : 19.561 179.915 7153 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.63 % Favored : 95.17 % Rotamer: Outliers : 3.63 % Allowed : 29.70 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.93 (0.12), residues: 4559 helix: 0.60 (0.12), residues: 1724 sheet: -1.11 (0.20), residues: 692 loop : -1.43 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 18 TYR 0.024 0.001 TYR J 99 PHE 0.018 0.001 PHE C 4 TRP 0.031 0.001 TRP d 218 HIS 0.006 0.001 HIS e 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (40402) covalent geometry : angle 0.67116 / 0.36 (55513) hydrogen bonds : bond 0.04012 / 2.69 ( 1438) hydrogen bonds : angle 4.39517 / 3.12 ( 4034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 737 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8503 (mm-30) REVERT: B 35 LYS cc_start: 0.8761 (mppt) cc_final: 0.8412 (mppt) REVERT: B 46 MET cc_start: 0.8919 (mtm) cc_final: 0.8696 (mtm) REVERT: B 126 SER cc_start: 0.8952 (t) cc_final: 0.8570 (m) REVERT: C 1 MET cc_start: 0.7621 (tpp) cc_final: 0.7193 (tpp) REVERT: C 37 GLU cc_start: 0.6631 (pp20) cc_final: 0.6329 (pp20) REVERT: C 39 MET cc_start: 0.9027 (ttm) cc_final: 0.8743 (ttm) REVERT: C 48 LYS cc_start: 0.8889 (mtmm) cc_final: 0.8554 (mtmm) REVERT: C 60 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8488 (mtp85) REVERT: C 75 ASP cc_start: 0.8665 (m-30) cc_final: 0.8401 (t0) REVERT: C 103 GLU cc_start: 0.8147 (tp30) cc_final: 0.7860 (tp30) REVERT: C 115 ASP cc_start: 0.8663 (t0) cc_final: 0.8399 (t0) REVERT: C 172 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7344 (mm-30) REVERT: C 214 MET cc_start: 0.8650 (tpp) cc_final: 0.7993 (mpp) REVERT: D 4 GLN cc_start: 0.9148 (tm-30) cc_final: 0.8015 (tm-30) REVERT: D 18 ARG cc_start: 0.9014 (ttm110) cc_final: 0.8772 (ttm-80) REVERT: D 110 ASP cc_start: 0.8542 (t0) cc_final: 0.7984 (p0) REVERT: D 113 LYS cc_start: 0.9349 (ttmm) cc_final: 0.8775 (ttmm) REVERT: D 120 GLU cc_start: 0.8757 (tt0) cc_final: 0.8448 (tm-30) REVERT: D 139 ASP cc_start: 0.8471 (p0) cc_final: 0.7993 (p0) REVERT: D 174 LYS cc_start: 0.9116 (ttmm) cc_final: 0.8831 (mmmm) REVERT: D 186 ILE cc_start: 0.9098 (tp) cc_final: 0.8575 (pp) REVERT: D 191 ASP cc_start: 0.7927 (t0) cc_final: 0.7331 (t0) REVERT: D 224 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8049 (t0) REVERT: D 225 SER cc_start: 0.9195 (m) cc_final: 0.8929 (t) REVERT: D 241 ASP cc_start: 0.9345 (t0) cc_final: 0.9075 (t0) REVERT: D 257 HIS cc_start: 0.8608 (t70) cc_final: 0.7807 (t70) REVERT: D 260 ASP cc_start: 0.8535 (t70) cc_final: 0.8252 (p0) REVERT: D 278 LYS cc_start: 0.9250 (ttpp) cc_final: 0.8878 (ttpp) REVERT: D 280 ASP cc_start: 0.8876 (t0) cc_final: 0.8559 (t0) REVERT: E 59 GLU cc_start: 0.8305 (pm20) cc_final: 0.8087 (pm20) REVERT: E 75 LYS cc_start: 0.4315 (tptp) cc_final: 0.2171 (tptp) REVERT: E 120 GLU cc_start: 0.8705 (tp30) cc_final: 0.8246 (tp30) REVERT: E 124 MET cc_start: 0.8681 (ptp) cc_final: 0.8376 (ptp) REVERT: E 127 ASP cc_start: 0.8539 (t70) cc_final: 0.8246 (t0) REVERT: E 150 ASN cc_start: 0.8871 (m110) cc_final: 0.8416 (m-40) REVERT: E 154 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8617 (mttt) REVERT: E 178 LYS cc_start: 0.9261 (tptp) cc_final: 0.9043 (tmmt) REVERT: E 179 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8395 (mm-30) REVERT: E 183 GLU cc_start: 0.8518 (tp30) cc_final: 0.8205 (tp30) REVERT: E 189 LYS cc_start: 0.8877 (ptmm) cc_final: 0.8541 (ttpp) REVERT: E 261 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: E 278 LYS cc_start: 0.9078 (mtpp) cc_final: 0.8615 (mtmm) REVERT: G 9 VAL cc_start: 0.8877 (OUTLIER) cc_final: 0.8545 (t) REVERT: G 100 SER cc_start: 0.7856 (m) cc_final: 0.7319 (p) REVERT: G 111 ASP cc_start: 0.8235 (t70) cc_final: 0.7818 (p0) REVERT: G 140 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7674 (tp30) REVERT: G 159 GLU cc_start: 0.8399 (pm20) cc_final: 0.7995 (pm20) REVERT: G 217 ASP cc_start: 0.8410 (p0) cc_final: 0.7986 (p0) REVERT: H 83 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7640 (tm-30) REVERT: H 90 TYR cc_start: 0.7784 (m-80) cc_final: 0.7545 (m-10) REVERT: H 117 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8502 (mm-30) REVERT: I 138 SER cc_start: 0.8743 (OUTLIER) cc_final: 0.8531 (p) REVERT: I 156 LEU cc_start: 0.8944 (mm) cc_final: 0.8174 (mp) REVERT: I 159 GLU cc_start: 0.8022 (pm20) cc_final: 0.7547 (pm20) REVERT: I 171 ASP cc_start: 0.8217 (m-30) cc_final: 0.7925 (m-30) REVERT: I 193 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8794 (mm) REVERT: I 217 ASP cc_start: 0.7818 (p0) cc_final: 0.7411 (p0) REVERT: I 250 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8138 (mm-30) REVERT: I 281 LYS cc_start: 0.8596 (tmmt) cc_final: 0.8213 (tmmt) REVERT: J 30 ASP cc_start: 0.8696 (t0) cc_final: 0.7841 (t0) REVERT: J 80 LYS cc_start: 0.9187 (mtpm) cc_final: 0.8916 (mtmm) REVERT: J 84 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8648 (tppp) REVERT: J 88 ASP cc_start: 0.8525 (t0) cc_final: 0.8074 (t0) REVERT: K 30 ASP cc_start: 0.8317 (p0) cc_final: 0.7935 (p0) REVERT: K 58 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8534 (p0) REVERT: K 59 LYS cc_start: 0.8953 (ptpt) cc_final: 0.8688 (ptpp) REVERT: K 91 LYS cc_start: 0.9210 (tppp) cc_final: 0.8998 (ttmm) REVERT: K 108 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7897 (mm-30) REVERT: K 153 SER cc_start: 0.8685 (p) cc_final: 0.8442 (p) REVERT: K 159 GLU cc_start: 0.7935 (pp20) cc_final: 0.7642 (pp20) REVERT: K 186 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8686 (mmmm) REVERT: K 250 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8134 (mp0) REVERT: K 285 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7644 (tm-30) REVERT: K 289 MET cc_start: 0.8542 (mtp) cc_final: 0.8236 (mtp) REVERT: L 12 TYR cc_start: 0.8935 (m-80) cc_final: 0.8581 (m-80) REVERT: L 100 SER cc_start: 0.8812 (m) cc_final: 0.8562 (p) REVERT: L 156 LEU cc_start: 0.8815 (mt) cc_final: 0.8529 (mm) REVERT: L 171 ASP cc_start: 0.8241 (m-30) cc_final: 0.7734 (m-30) REVERT: L 203 GLN cc_start: 0.8941 (mp10) cc_final: 0.8690 (mt0) REVERT: L 213 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8136 (ttmt) REVERT: L 214 GLN cc_start: 0.8779 (mm110) cc_final: 0.8369 (mm-40) REVERT: L 241 GLU cc_start: 0.8514 (pm20) cc_final: 0.8214 (pm20) REVERT: L 262 TYR cc_start: 0.9239 (m-80) cc_final: 0.8837 (m-80) REVERT: L 274 MET cc_start: 0.8896 (mtm) cc_final: 0.8253 (ptp) REVERT: M 81 TYR cc_start: 0.8587 (p90) cc_final: 0.8342 (p90) REVERT: M 156 LEU cc_start: 0.8184 (mt) cc_final: 0.7689 (pp) REVERT: M 195 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7407 (tp30) REVERT: M 262 TYR cc_start: 0.9374 (m-80) cc_final: 0.9170 (m-10) REVERT: a 28 THR cc_start: 0.5725 (OUTLIER) cc_final: 0.5344 (t) REVERT: a 46 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7567 (tp40) REVERT: d 106 ARG cc_start: 0.8909 (tpp80) cc_final: 0.8691 (tpp80) REVERT: d 123 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.7939 (mmpt) REVERT: d 154 LYS cc_start: 0.8518 (ptmm) cc_final: 0.8030 (ptpp) REVERT: d 178 LYS cc_start: 0.8899 (tmmm) cc_final: 0.8636 (tmmt) REVERT: d 179 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8362 (tm-30) REVERT: d 182 LEU cc_start: 0.9331 (tm) cc_final: 0.8982 (pp) REVERT: d 183 GLU cc_start: 0.8948 (tp30) cc_final: 0.8455 (tm-30) REVERT: d 187 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8145 (pp20) REVERT: d 189 LYS cc_start: 0.8469 (mppt) cc_final: 0.8129 (mppt) REVERT: d 240 PHE cc_start: 0.7325 (m-10) cc_final: 0.6821 (m-10) REVERT: d 241 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8135 (m-30) REVERT: d 270 ARG cc_start: 0.8841 (ttm-80) cc_final: 0.8503 (ttm110) REVERT: e 24 LYS cc_start: 0.8971 (ttmm) cc_final: 0.8666 (mmmm) REVERT: e 59 GLU cc_start: 0.8493 (pp20) cc_final: 0.8066 (pp20) REVERT: e 98 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7616 (p) REVERT: e 99 LYS cc_start: 0.9136 (ptpp) cc_final: 0.8807 (ptmm) REVERT: e 102 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8808 (mm-40) REVERT: e 111 GLU cc_start: 0.8778 (tp30) cc_final: 0.8371 (tp30) REVERT: e 114 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8020 (mtpp) REVERT: e 125 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.7755 (ttp-170) REVERT: e 127 ASP cc_start: 0.8440 (m-30) cc_final: 0.8160 (t0) REVERT: e 169 GLU cc_start: 0.8056 (tp30) cc_final: 0.7647 (tp30) REVERT: e 174 LYS cc_start: 0.8592 (pttp) cc_final: 0.8311 (tppt) REVERT: e 178 LYS cc_start: 0.9170 (ptmm) cc_final: 0.8582 (tptp) REVERT: e 189 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8508 (ptmm) REVERT: e 191 ASP cc_start: 0.8202 (t0) cc_final: 0.7868 (t0) REVERT: e 200 LYS cc_start: 0.9112 (pptt) cc_final: 0.8771 (pptt) REVERT: e 261 GLN cc_start: 0.8716 (mp10) cc_final: 0.8126 (mp10) REVERT: e 278 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8818 (mtpp) REVERT: A 64 ASP cc_start: 0.8557 (p0) cc_final: 0.8140 (p0) REVERT: A 65 LYS cc_start: 0.8729 (pmmt) cc_final: 0.8429 (pmtt) REVERT: A 172 ASP cc_start: 0.8270 (p0) cc_final: 0.7852 (p0) REVERT: A 225 ASP cc_start: 0.8535 (m-30) cc_final: 0.8082 (p0) REVERT: A 241 LYS cc_start: 0.9071 (mmmm) cc_final: 0.8773 (mmmm) REVERT: A 248 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8744 (mmmt) REVERT: A 282 ASN cc_start: 0.8940 (t0) cc_final: 0.8620 (t0) REVERT: A 305 LEU cc_start: 0.8942 (tp) cc_final: 0.8636 (tp) REVERT: A 322 LYS cc_start: 0.9053 (mtmm) cc_final: 0.8652 (mtmm) REVERT: A 331 LYS cc_start: 0.9285 (tppp) cc_final: 0.9002 (mppt) REVERT: A 445 VAL cc_start: 0.8635 (t) cc_final: 0.8293 (p) REVERT: A 491 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7786 (mmmm) REVERT: A 591 ASP cc_start: 0.8404 (t0) cc_final: 0.7958 (t0) REVERT: A 622 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8203 (mt0) REVERT: A 627 GLU cc_start: 0.8659 (pp20) cc_final: 0.8216 (pp20) REVERT: A 631 GLN cc_start: 0.8924 (tp40) cc_final: 0.8576 (tp40) REVERT: A 675 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.9081 (mmmm) REVERT: A 807 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8682 (tppp) REVERT: A 850 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7804 (m-10) REVERT: A 881 LYS cc_start: 0.5816 (mttt) cc_final: 0.5535 (tttt) REVERT: A 913 LEU cc_start: 0.8842 (mt) cc_final: 0.8567 (tt) REVERT: A 922 ASP cc_start: 0.7886 (t70) cc_final: 0.7322 (t0) outliers start: 139 outliers final: 66 residues processed: 828 average time/residue: 0.7352 time to fit residues: 728.5803 Evaluate side-chains 822 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 733 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 110 ASP Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 270 ARG Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 1 TYR Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 84 LYS Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 294 ASN Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 191 MET Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 146 ASN Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 284 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 129 LEU Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 188 GLU Chi-restraints excluded: chain M residue 197 SER Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 46 GLN Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 123 LYS Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain d residue 241 ASP Chi-restraints excluded: chain e residue 17 SER Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 52 GLU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 189 LYS Chi-restraints excluded: chain e residue 294 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 675 LYS Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 850 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 362 optimal weight: 0.9980 chunk 281 optimal weight: 0.6980 chunk 215 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 399 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 366 optimal weight: 0.3980 chunk 84 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 452 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 228 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 HIS H 153 ASN I 55 ASN J 55 ASN ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN K 208 ASN ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 GLN M 33 ASN M 63 GLN d 25 ASN ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.114333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101387 restraints weight = 160867.499| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.83 r_work: 0.3352 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40402 Z= 0.164 Angle : 0.682 14.024 55513 Z= 0.364 Chirality : 0.044 0.359 6335 Planarity : 0.004 0.059 6513 Dihedral : 19.528 179.938 7149 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.65 % Favored : 95.15 % Rotamer: Outliers : 3.21 % Allowed : 30.36 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.90 (0.12), residues: 4559 helix: 0.64 (0.12), residues: 1724 sheet: -1.10 (0.20), residues: 691 loop : -1.43 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 133 TYR 0.023 0.001 TYR J 99 PHE 0.033 0.001 PHE L 205 TRP 0.037 0.001 TRP d 218 HIS 0.006 0.001 HIS e 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (40402) covalent geometry : angle 0.68199 / 0.36 (55513) hydrogen bonds : bond 0.04015 / 2.68 ( 1438) hydrogen bonds : angle 4.37493 / 3.11 ( 4034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 741 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8488 (mm-30) REVERT: B 35 LYS cc_start: 0.8758 (mppt) cc_final: 0.8401 (mppt) REVERT: B 46 MET cc_start: 0.8913 (mtm) cc_final: 0.8666 (mtm) REVERT: B 83 GLU cc_start: 0.8177 (pm20) cc_final: 0.7747 (pp20) REVERT: B 126 SER cc_start: 0.8936 (t) cc_final: 0.8564 (m) REVERT: C 1 MET cc_start: 0.7644 (tpp) cc_final: 0.7195 (tpp) REVERT: C 37 GLU cc_start: 0.6679 (pp20) cc_final: 0.6342 (pp20) REVERT: C 39 MET cc_start: 0.9046 (ttm) cc_final: 0.8772 (ttm) REVERT: C 48 LYS cc_start: 0.8885 (mtmm) cc_final: 0.8522 (mtmm) REVERT: C 60 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8499 (mtp85) REVERT: C 75 ASP cc_start: 0.8654 (m-30) cc_final: 0.8372 (t0) REVERT: C 108 ASP cc_start: 0.8283 (m-30) cc_final: 0.7990 (m-30) REVERT: C 115 ASP cc_start: 0.8651 (t0) cc_final: 0.8367 (t0) REVERT: C 163 ASP cc_start: 0.8727 (t0) cc_final: 0.8446 (t0) REVERT: C 172 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7341 (mm-30) REVERT: C 173 ASP cc_start: 0.7518 (p0) cc_final: 0.6963 (p0) REVERT: C 201 LYS cc_start: 0.9012 (ptpp) cc_final: 0.8673 (pptt) REVERT: C 214 MET cc_start: 0.8689 (tpp) cc_final: 0.8131 (mpp) REVERT: D 4 GLN cc_start: 0.9151 (tm-30) cc_final: 0.8035 (tm-30) REVERT: D 18 ARG cc_start: 0.9004 (ttm110) cc_final: 0.8726 (ttm-80) REVERT: D 113 LYS cc_start: 0.9313 (ttmm) cc_final: 0.9067 (ttmm) REVERT: D 120 GLU cc_start: 0.8775 (tt0) cc_final: 0.8472 (tm-30) REVERT: D 123 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8326 (mmpt) REVERT: D 139 ASP cc_start: 0.8499 (p0) cc_final: 0.8068 (p0) REVERT: D 174 LYS cc_start: 0.9119 (ttmm) cc_final: 0.8833 (mmmm) REVERT: D 186 ILE cc_start: 0.9108 (tp) cc_final: 0.8559 (pp) REVERT: D 191 ASP cc_start: 0.7949 (t0) cc_final: 0.7404 (t0) REVERT: D 224 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8073 (t0) REVERT: D 225 SER cc_start: 0.9211 (m) cc_final: 0.8782 (p) REVERT: D 241 ASP cc_start: 0.9322 (t0) cc_final: 0.9042 (t0) REVERT: D 257 HIS cc_start: 0.8618 (t70) cc_final: 0.7780 (t70) REVERT: D 260 ASP cc_start: 0.8532 (t70) cc_final: 0.8278 (p0) REVERT: D 278 LYS cc_start: 0.9251 (ttpp) cc_final: 0.8892 (ttpp) REVERT: D 280 ASP cc_start: 0.8883 (t0) cc_final: 0.8408 (t0) REVERT: E 59 GLU cc_start: 0.8344 (pm20) cc_final: 0.8108 (pm20) REVERT: E 75 LYS cc_start: 0.4385 (tptp) cc_final: 0.2591 (tptp) REVERT: E 120 GLU cc_start: 0.8708 (tp30) cc_final: 0.8312 (tp30) REVERT: E 124 MET cc_start: 0.8678 (ptp) cc_final: 0.8431 (ptm) REVERT: E 127 ASP cc_start: 0.8544 (t70) cc_final: 0.8253 (t0) REVERT: E 139 ASP cc_start: 0.8059 (t0) cc_final: 0.7663 (t0) REVERT: E 150 ASN cc_start: 0.8869 (m110) cc_final: 0.8422 (m-40) REVERT: E 154 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8629 (mttt) REVERT: E 179 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8483 (mm-30) REVERT: E 183 GLU cc_start: 0.8520 (tp30) cc_final: 0.8208 (tp30) REVERT: E 189 LYS cc_start: 0.8871 (ptmm) cc_final: 0.8459 (ttpp) REVERT: E 261 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8367 (mp10) REVERT: E 278 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8611 (mtmm) REVERT: G 9 VAL cc_start: 0.8885 (OUTLIER) cc_final: 0.8550 (t) REVERT: G 100 SER cc_start: 0.7869 (m) cc_final: 0.7340 (p) REVERT: G 111 ASP cc_start: 0.8244 (t70) cc_final: 0.7772 (p0) REVERT: G 159 GLU cc_start: 0.8407 (pm20) cc_final: 0.8050 (pm20) REVERT: G 217 ASP cc_start: 0.8422 (p0) cc_final: 0.8002 (p0) REVERT: G 289 MET cc_start: 0.8660 (mtm) cc_final: 0.8253 (mtp) REVERT: H 83 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7700 (tm-30) REVERT: H 90 TYR cc_start: 0.7793 (m-80) cc_final: 0.7580 (m-10) REVERT: H 117 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8546 (mm-30) REVERT: I 108 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7605 (mm-30) REVERT: I 138 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8552 (p) REVERT: I 156 LEU cc_start: 0.8969 (mm) cc_final: 0.8135 (mt) REVERT: I 159 GLU cc_start: 0.7986 (pm20) cc_final: 0.7483 (pm20) REVERT: I 171 ASP cc_start: 0.8261 (m-30) cc_final: 0.7959 (m-30) REVERT: I 193 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8789 (mm) REVERT: I 195 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7885 (mm-30) REVERT: I 217 ASP cc_start: 0.7845 (p0) cc_final: 0.7444 (p0) REVERT: I 241 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8215 (mp0) REVERT: I 250 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8124 (mm-30) REVERT: I 281 LYS cc_start: 0.8594 (tmmt) cc_final: 0.8244 (tmmt) REVERT: J 30 ASP cc_start: 0.8735 (t0) cc_final: 0.7863 (t0) REVERT: J 63 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7630 (mm110) REVERT: J 80 LYS cc_start: 0.9190 (mtpm) cc_final: 0.8928 (mtmm) REVERT: J 84 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8628 (tppp) REVERT: J 88 ASP cc_start: 0.8550 (t0) cc_final: 0.8091 (t0) REVERT: K 30 ASP cc_start: 0.8308 (p0) cc_final: 0.8038 (p0) REVERT: K 59 LYS cc_start: 0.8963 (ptpt) cc_final: 0.8709 (ptpp) REVERT: K 108 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7909 (mm-30) REVERT: K 153 SER cc_start: 0.8695 (p) cc_final: 0.8449 (p) REVERT: K 159 GLU cc_start: 0.7967 (pp20) cc_final: 0.7680 (pp20) REVERT: K 186 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8720 (mmmm) REVERT: K 250 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8141 (mp0) REVERT: K 285 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7635 (tm-30) REVERT: K 289 MET cc_start: 0.8548 (mtp) cc_final: 0.8215 (mtp) REVERT: L 12 TYR cc_start: 0.8934 (m-80) cc_final: 0.8570 (m-80) REVERT: L 100 SER cc_start: 0.8821 (m) cc_final: 0.8561 (p) REVERT: L 156 LEU cc_start: 0.8822 (mt) cc_final: 0.8573 (mm) REVERT: L 171 ASP cc_start: 0.8265 (m-30) cc_final: 0.7766 (m-30) REVERT: L 203 GLN cc_start: 0.8961 (mp10) cc_final: 0.8707 (mt0) REVERT: L 213 LYS cc_start: 0.8592 (ttmt) cc_final: 0.8150 (ttmt) REVERT: L 214 GLN cc_start: 0.8780 (mm110) cc_final: 0.8326 (mm-40) REVERT: L 245 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8868 (p) REVERT: L 274 MET cc_start: 0.8904 (mtm) cc_final: 0.8287 (ptp) REVERT: M 63 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6238 (pt0) REVERT: M 74 LYS cc_start: 0.8210 (mttp) cc_final: 0.7975 (mtpp) REVERT: M 81 TYR cc_start: 0.8574 (p90) cc_final: 0.8294 (p90) REVERT: M 156 LEU cc_start: 0.8208 (mt) cc_final: 0.7725 (pp) REVERT: M 195 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7459 (tp30) REVERT: M 262 TYR cc_start: 0.9370 (m-80) cc_final: 0.9165 (m-10) REVERT: a 28 THR cc_start: 0.5793 (OUTLIER) cc_final: 0.5403 (t) REVERT: d 14 TYR cc_start: 0.8071 (m-80) cc_final: 0.7833 (m-10) REVERT: d 25 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8517 (t0) REVERT: d 34 ASP cc_start: 0.8937 (p0) cc_final: 0.8683 (p0) REVERT: d 154 LYS cc_start: 0.8546 (ptmm) cc_final: 0.8057 (ptpp) REVERT: d 178 LYS cc_start: 0.8910 (tmmm) cc_final: 0.8631 (tmmt) REVERT: d 179 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8364 (tm-30) REVERT: d 182 LEU cc_start: 0.9334 (tm) cc_final: 0.8995 (pp) REVERT: d 183 GLU cc_start: 0.8977 (tp30) cc_final: 0.8484 (tm-30) REVERT: d 187 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8101 (pp20) REVERT: d 188 PHE cc_start: 0.7732 (t80) cc_final: 0.7493 (t80) REVERT: d 189 LYS cc_start: 0.8397 (mppt) cc_final: 0.8069 (mppt) REVERT: d 191 ASP cc_start: 0.8185 (t0) cc_final: 0.7843 (p0) REVERT: d 270 ARG cc_start: 0.8850 (ttm-80) cc_final: 0.8370 (ptp-110) REVERT: e 24 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8671 (mmmm) REVERT: e 59 GLU cc_start: 0.8512 (pp20) cc_final: 0.8140 (pp20) REVERT: e 61 MET cc_start: 0.8357 (tpt) cc_final: 0.7968 (tpt) REVERT: e 98 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7665 (p) REVERT: e 99 LYS cc_start: 0.9144 (ptpp) cc_final: 0.8813 (ptmm) REVERT: e 102 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8843 (mm-40) REVERT: e 111 GLU cc_start: 0.8801 (tp30) cc_final: 0.8375 (tp30) REVERT: e 114 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8006 (mtpp) REVERT: e 125 ARG cc_start: 0.8400 (ttm-80) cc_final: 0.7600 (ttp-170) REVERT: e 127 ASP cc_start: 0.8456 (m-30) cc_final: 0.8188 (t0) REVERT: e 169 GLU cc_start: 0.8084 (tp30) cc_final: 0.7626 (tp30) REVERT: e 174 LYS cc_start: 0.8619 (pttp) cc_final: 0.8313 (tppt) REVERT: e 178 LYS cc_start: 0.9167 (ptmm) cc_final: 0.8537 (tptp) REVERT: e 189 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8516 (ptmm) REVERT: e 191 ASP cc_start: 0.8199 (t0) cc_final: 0.7861 (t0) REVERT: e 200 LYS cc_start: 0.9106 (pptt) cc_final: 0.8769 (pptt) REVERT: e 261 GLN cc_start: 0.8719 (mp10) cc_final: 0.8077 (mp10) REVERT: e 278 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8830 (mtpp) REVERT: A 64 ASP cc_start: 0.8629 (p0) cc_final: 0.8142 (p0) REVERT: A 65 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8454 (pmtt) REVERT: A 172 ASP cc_start: 0.8282 (p0) cc_final: 0.7858 (p0) REVERT: A 225 ASP cc_start: 0.8553 (m-30) cc_final: 0.8095 (p0) REVERT: A 241 LYS cc_start: 0.9088 (mmmm) cc_final: 0.8753 (mmmm) REVERT: A 248 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8777 (mmmt) REVERT: A 282 ASN cc_start: 0.8950 (t0) cc_final: 0.8630 (t0) REVERT: A 305 LEU cc_start: 0.8961 (tp) cc_final: 0.8650 (tp) REVERT: A 322 LYS cc_start: 0.9042 (mtmm) cc_final: 0.8626 (mtmm) REVERT: A 331 LYS cc_start: 0.9287 (tppp) cc_final: 0.9018 (mmmm) REVERT: A 445 VAL cc_start: 0.8636 (t) cc_final: 0.8295 (p) REVERT: A 568 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8685 (mp10) REVERT: A 591 ASP cc_start: 0.8362 (t0) cc_final: 0.7967 (t0) REVERT: A 622 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8334 (mt0) REVERT: A 627 GLU cc_start: 0.8669 (pp20) cc_final: 0.8199 (pp20) REVERT: A 631 GLN cc_start: 0.8925 (tp40) cc_final: 0.8588 (tp40) REVERT: A 675 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9072 (mmmm) REVERT: A 693 GLU cc_start: 0.8332 (pp20) cc_final: 0.8033 (pp20) REVERT: A 807 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8693 (tppp) REVERT: A 850 PHE cc_start: 0.8181 (OUTLIER) cc_final: 0.7845 (m-10) REVERT: A 870 THR cc_start: 0.8174 (m) cc_final: 0.7903 (p) REVERT: A 881 LYS cc_start: 0.5466 (mttt) cc_final: 0.5093 (tttt) REVERT: A 913 LEU cc_start: 0.8843 (mt) cc_final: 0.8551 (tt) REVERT: A 922 ASP cc_start: 0.7900 (t70) cc_final: 0.7246 (t0) outliers start: 123 outliers final: 68 residues processed: 821 average time/residue: 0.7233 time to fit residues: 712.4969 Evaluate side-chains 819 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 726 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 60 ARG Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 270 ARG Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 1 TYR Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 191 MET Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 284 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 63 GLN Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 188 GLU Chi-restraints excluded: chain M residue 197 SER Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain a residue 13 ILE Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain a residue 37 ILE Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 25 ASN Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 123 LYS Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 17 SER Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 52 GLU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 189 LYS Chi-restraints excluded: chain e residue 294 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 675 LYS Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 850 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 341 optimal weight: 8.9990 chunk 360 optimal weight: 2.9990 chunk 433 optimal weight: 4.9990 chunk 185 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 443 optimal weight: 1.9990 chunk 350 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 445 optimal weight: 3.9990 chunk 386 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 228 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 HIS I 55 ASN I 63 GLN ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 ASN K 208 ASN K 219 ASN L 288 GLN a 46 GLN d 25 ASN ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 150 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.114071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100828 restraints weight = 182661.845| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 4.09 r_work: 0.3336 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 40402 Z= 0.175 Angle : 0.704 14.529 55513 Z= 0.374 Chirality : 0.044 0.368 6335 Planarity : 0.004 0.061 6513 Dihedral : 19.519 179.995 7147 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.72 % Favored : 95.08 % Rotamer: Outliers : 3.11 % Allowed : 30.80 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.88 (0.12), residues: 4559 helix: 0.66 (0.12), residues: 1724 sheet: -1.11 (0.20), residues: 691 loop : -1.42 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 133 TYR 0.023 0.002 TYR J 99 PHE 0.023 0.001 PHE C 4 TRP 0.040 0.001 TRP d 218 HIS 0.006 0.001 HIS e 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (40402) covalent geometry : angle 0.70422 / 0.37 (55513) hydrogen bonds : bond 0.04019 / 2.68 ( 1438) hydrogen bonds : angle 4.37980 / 3.11 ( 4034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 731 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8507 (mm-30) REVERT: B 35 LYS cc_start: 0.8768 (mppt) cc_final: 0.8422 (mppt) REVERT: B 46 MET cc_start: 0.8928 (mtm) cc_final: 0.8697 (mtm) REVERT: B 126 SER cc_start: 0.8949 (t) cc_final: 0.8569 (m) REVERT: B 173 VAL cc_start: 0.8421 (t) cc_final: 0.8083 (m) REVERT: C 1 MET cc_start: 0.7587 (tpp) cc_final: 0.7120 (tpp) REVERT: C 37 GLU cc_start: 0.6678 (pp20) cc_final: 0.6335 (pp20) REVERT: C 48 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8582 (mtmt) REVERT: C 75 ASP cc_start: 0.8676 (m-30) cc_final: 0.8362 (t0) REVERT: C 89 GLN cc_start: 0.9300 (mm-40) cc_final: 0.8953 (mm-40) REVERT: C 115 ASP cc_start: 0.8661 (t0) cc_final: 0.8395 (t0) REVERT: C 172 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: C 201 LYS cc_start: 0.9079 (ptpp) cc_final: 0.8683 (pptt) REVERT: C 214 MET cc_start: 0.8731 (tpp) cc_final: 0.8130 (mpp) REVERT: D 4 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8088 (tm-30) REVERT: D 18 ARG cc_start: 0.9106 (ttm110) cc_final: 0.8861 (ttm-80) REVERT: D 113 LYS cc_start: 0.9314 (ttmm) cc_final: 0.9089 (ttmm) REVERT: D 120 GLU cc_start: 0.8819 (tt0) cc_final: 0.8490 (tm-30) REVERT: D 123 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8321 (mmpt) REVERT: D 139 ASP cc_start: 0.8536 (p0) cc_final: 0.8109 (p0) REVERT: D 174 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8813 (mmmm) REVERT: D 186 ILE cc_start: 0.9085 (tp) cc_final: 0.8536 (pp) REVERT: D 191 ASP cc_start: 0.7921 (t0) cc_final: 0.7381 (t0) REVERT: D 224 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8187 (t0) REVERT: D 225 SER cc_start: 0.9189 (m) cc_final: 0.8782 (p) REVERT: D 241 ASP cc_start: 0.9294 (t0) cc_final: 0.9026 (t0) REVERT: D 260 ASP cc_start: 0.8564 (t70) cc_final: 0.8311 (p0) REVERT: D 278 LYS cc_start: 0.9272 (ttpp) cc_final: 0.8915 (ttpp) REVERT: D 280 ASP cc_start: 0.8894 (t0) cc_final: 0.8418 (t0) REVERT: E 75 LYS cc_start: 0.4483 (tptp) cc_final: 0.2669 (tptp) REVERT: E 120 GLU cc_start: 0.8691 (tp30) cc_final: 0.8290 (tp30) REVERT: E 124 MET cc_start: 0.8679 (ptp) cc_final: 0.8425 (ptm) REVERT: E 127 ASP cc_start: 0.8587 (t70) cc_final: 0.8283 (t0) REVERT: E 139 ASP cc_start: 0.8038 (t0) cc_final: 0.7640 (t0) REVERT: E 150 ASN cc_start: 0.8862 (m110) cc_final: 0.8413 (m-40) REVERT: E 154 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8612 (mttt) REVERT: E 183 GLU cc_start: 0.8537 (tp30) cc_final: 0.8236 (tp30) REVERT: E 189 LYS cc_start: 0.8824 (ptmm) cc_final: 0.8565 (ttpp) REVERT: E 261 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8431 (mp10) REVERT: E 278 LYS cc_start: 0.9116 (mtpp) cc_final: 0.8648 (mtmm) REVERT: G 9 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8568 (t) REVERT: G 100 SER cc_start: 0.7906 (m) cc_final: 0.7372 (p) REVERT: G 111 ASP cc_start: 0.8245 (t70) cc_final: 0.7767 (p0) REVERT: G 140 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7710 (tp30) REVERT: G 159 GLU cc_start: 0.8428 (pm20) cc_final: 0.7940 (pm20) REVERT: G 161 ASP cc_start: 0.8457 (m-30) cc_final: 0.7837 (m-30) REVERT: G 217 ASP cc_start: 0.8439 (p0) cc_final: 0.8023 (p0) REVERT: G 289 MET cc_start: 0.8665 (mtm) cc_final: 0.8255 (mtp) REVERT: H 117 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8561 (mm-30) REVERT: I 42 LYS cc_start: 0.9145 (pttm) cc_final: 0.8937 (pttm) REVERT: I 108 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7675 (mm-30) REVERT: I 138 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8571 (p) REVERT: I 156 LEU cc_start: 0.8959 (mm) cc_final: 0.8121 (mt) REVERT: I 159 GLU cc_start: 0.8007 (pm20) cc_final: 0.7505 (pm20) REVERT: I 171 ASP cc_start: 0.8254 (m-30) cc_final: 0.7947 (m-30) REVERT: I 193 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8791 (mm) REVERT: I 195 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7906 (mm-30) REVERT: I 217 ASP cc_start: 0.7870 (p0) cc_final: 0.7461 (p0) REVERT: I 241 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8253 (mp0) REVERT: I 250 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8132 (mm-30) REVERT: I 281 LYS cc_start: 0.8619 (tmmt) cc_final: 0.8264 (tmmt) REVERT: J 30 ASP cc_start: 0.8785 (t0) cc_final: 0.7890 (t0) REVERT: J 63 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7585 (mm110) REVERT: J 80 LYS cc_start: 0.9209 (mtpm) cc_final: 0.8941 (mtmm) REVERT: J 84 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8640 (tppp) REVERT: J 88 ASP cc_start: 0.8570 (t0) cc_final: 0.8104 (t0) REVERT: K 30 ASP cc_start: 0.8302 (p0) cc_final: 0.8013 (p0) REVERT: K 59 LYS cc_start: 0.8930 (ptpt) cc_final: 0.8710 (ptpp) REVERT: K 108 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7917 (mm-30) REVERT: K 153 SER cc_start: 0.8695 (p) cc_final: 0.8448 (p) REVERT: K 159 GLU cc_start: 0.7999 (pp20) cc_final: 0.7712 (pp20) REVERT: K 186 LYS cc_start: 0.9167 (mmmm) cc_final: 0.8733 (mmmm) REVERT: K 250 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8170 (mp0) REVERT: K 285 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7617 (tm-30) REVERT: K 289 MET cc_start: 0.8567 (mtp) cc_final: 0.8243 (mtp) REVERT: L 12 TYR cc_start: 0.8955 (m-80) cc_final: 0.8559 (m-80) REVERT: L 100 SER cc_start: 0.8830 (m) cc_final: 0.8590 (p) REVERT: L 111 ASP cc_start: 0.7885 (p0) cc_final: 0.7662 (p0) REVERT: L 156 LEU cc_start: 0.8815 (mt) cc_final: 0.8570 (mm) REVERT: L 203 GLN cc_start: 0.8947 (mp10) cc_final: 0.8686 (mt0) REVERT: L 213 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8183 (ttmt) REVERT: L 214 GLN cc_start: 0.8786 (mm110) cc_final: 0.8434 (mm-40) REVERT: L 245 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8881 (p) REVERT: L 274 MET cc_start: 0.8891 (mtm) cc_final: 0.8254 (ptp) REVERT: L 289 MET cc_start: 0.8896 (ttm) cc_final: 0.8626 (ttm) REVERT: M 63 GLN cc_start: 0.6385 (OUTLIER) cc_final: 0.5543 (pt0) REVERT: M 74 LYS cc_start: 0.8207 (mttp) cc_final: 0.7970 (mtpp) REVERT: M 81 TYR cc_start: 0.8581 (p90) cc_final: 0.8308 (p90) REVERT: M 156 LEU cc_start: 0.8231 (mt) cc_final: 0.7748 (pp) REVERT: M 195 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7497 (tp30) REVERT: M 262 TYR cc_start: 0.9392 (m-80) cc_final: 0.9190 (m-10) REVERT: a 28 THR cc_start: 0.5813 (OUTLIER) cc_final: 0.5415 (t) REVERT: d 14 TYR cc_start: 0.8030 (m-80) cc_final: 0.7778 (m-10) REVERT: d 123 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.7966 (mmpt) REVERT: d 138 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7516 (m) REVERT: d 154 LYS cc_start: 0.8534 (ptmm) cc_final: 0.8085 (ptpp) REVERT: d 178 LYS cc_start: 0.8899 (tmmm) cc_final: 0.8633 (tmmt) REVERT: d 179 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8265 (pp20) REVERT: d 182 LEU cc_start: 0.9325 (tm) cc_final: 0.8980 (pp) REVERT: d 183 GLU cc_start: 0.9033 (tp30) cc_final: 0.8555 (tm-30) REVERT: d 187 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8196 (pp20) REVERT: d 189 LYS cc_start: 0.8384 (mppt) cc_final: 0.8117 (mppt) REVERT: d 240 PHE cc_start: 0.7283 (m-10) cc_final: 0.7033 (m-10) REVERT: e 24 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8692 (mmmm) REVERT: e 59 GLU cc_start: 0.8522 (pp20) cc_final: 0.8147 (pp20) REVERT: e 61 MET cc_start: 0.8364 (tpt) cc_final: 0.8005 (tpt) REVERT: e 98 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7644 (p) REVERT: e 99 LYS cc_start: 0.9136 (ptpp) cc_final: 0.8803 (ptmm) REVERT: e 102 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8827 (mm-40) REVERT: e 111 GLU cc_start: 0.8760 (tp30) cc_final: 0.8373 (tp30) REVERT: e 114 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8008 (mtpp) REVERT: e 125 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.7969 (ttp-170) REVERT: e 127 ASP cc_start: 0.8455 (m-30) cc_final: 0.8211 (t0) REVERT: e 174 LYS cc_start: 0.8639 (pttp) cc_final: 0.8365 (tppt) REVERT: e 178 LYS cc_start: 0.9171 (ptmm) cc_final: 0.8556 (tptp) REVERT: e 189 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8516 (ptmm) REVERT: e 191 ASP cc_start: 0.8174 (t0) cc_final: 0.7841 (t0) REVERT: e 200 LYS cc_start: 0.9083 (pptt) cc_final: 0.8755 (pptt) REVERT: e 261 GLN cc_start: 0.8718 (mp10) cc_final: 0.8075 (mp10) REVERT: e 278 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8856 (mtpp) REVERT: A 64 ASP cc_start: 0.8667 (p0) cc_final: 0.8333 (p0) REVERT: A 65 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8461 (pmtt) REVERT: A 172 ASP cc_start: 0.8309 (p0) cc_final: 0.7862 (p0) REVERT: A 225 ASP cc_start: 0.8587 (m-30) cc_final: 0.8130 (p0) REVERT: A 241 LYS cc_start: 0.9105 (mmmm) cc_final: 0.8769 (mmmm) REVERT: A 248 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8794 (mmmt) REVERT: A 282 ASN cc_start: 0.8968 (t0) cc_final: 0.8667 (t0) REVERT: A 305 LEU cc_start: 0.8975 (tp) cc_final: 0.8663 (tp) REVERT: A 322 LYS cc_start: 0.9030 (mtmm) cc_final: 0.8638 (mtmm) REVERT: A 331 LYS cc_start: 0.9325 (tppp) cc_final: 0.9028 (mmmm) REVERT: A 445 VAL cc_start: 0.8623 (t) cc_final: 0.8302 (p) REVERT: A 491 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7738 (tppt) REVERT: A 568 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8693 (mp10) REVERT: A 622 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8350 (mt0) REVERT: A 627 GLU cc_start: 0.8680 (pp20) cc_final: 0.8210 (pp20) REVERT: A 631 GLN cc_start: 0.8978 (tp40) cc_final: 0.8645 (tp40) REVERT: A 675 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9083 (mmmm) REVERT: A 693 GLU cc_start: 0.8324 (pp20) cc_final: 0.8044 (pp20) REVERT: A 850 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7887 (m-10) REVERT: A 870 THR cc_start: 0.8228 (m) cc_final: 0.7997 (p) REVERT: A 881 LYS cc_start: 0.5533 (mttt) cc_final: 0.5128 (tttt) REVERT: A 913 LEU cc_start: 0.8840 (mt) cc_final: 0.8516 (tt) outliers start: 119 outliers final: 71 residues processed: 806 average time/residue: 0.7195 time to fit residues: 694.2389 Evaluate side-chains 831 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 736 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 270 ARG Chi-restraints excluded: chain E residue 294 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 1 TYR Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 84 LYS Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 284 THR Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 191 MET Chi-restraints excluded: chain J residue 252 TYR Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 129 LEU Chi-restraints excluded: chain K residue 146 ASN Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 219 ASN Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain K residue 284 THR Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 245 THR Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 63 GLN Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 188 GLU Chi-restraints excluded: chain M residue 197 SER Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain a residue 13 ILE Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 123 LYS Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 17 SER Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 52 GLU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 189 LYS Chi-restraints excluded: chain e residue 294 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 675 LYS Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 850 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 331 optimal weight: 0.0270 chunk 71 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 chunk 227 optimal weight: 0.9980 chunk 325 optimal weight: 0.9990 chunk 250 optimal weight: 0.9990 chunk 217 optimal weight: 0.6980 chunk 426 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 159 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 228 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 ASN I 55 ASN ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN K 208 ASN K 219 ASN L 288 GLN M 33 ASN a 46 GLN d 25 ASN ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.114930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.102062 restraints weight = 165815.957| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.93 r_work: 0.3360 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40402 Z= 0.150 Angle : 0.709 14.750 55513 Z= 0.375 Chirality : 0.044 0.359 6335 Planarity : 0.004 0.063 6513 Dihedral : 19.500 179.849 7147 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 2.59 % Allowed : 31.48 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % 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: -0.86 (0.12), residues: 4559 helix: 0.66 (0.12), residues: 1724 sheet: -1.06 (0.20), residues: 671 loop : -1.40 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 133 TYR 0.029 0.001 TYR L 190 PHE 0.038 0.001 PHE d 188 TRP 0.046 0.001 TRP d 218 HIS 0.006 0.001 HIS e 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (40402) covalent geometry : angle 0.70943 / 0.38 (55513) hydrogen bonds : bond 0.03898 / 2.61 ( 1438) hydrogen bonds : angle 4.35160 / 3.09 ( 4034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9118 Ramachandran restraints generated. 4559 Oldfield, 0 Emsley, 4559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 751 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8464 (mm-30) REVERT: B 35 LYS cc_start: 0.8760 (mppt) cc_final: 0.8401 (mppt) REVERT: B 46 MET cc_start: 0.8916 (mtm) cc_final: 0.8649 (mtm) REVERT: B 82 GLU cc_start: 0.7992 (mp0) cc_final: 0.7509 (mt-10) REVERT: B 84 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7419 (mp) REVERT: B 126 SER cc_start: 0.8889 (t) cc_final: 0.8520 (m) REVERT: B 173 VAL cc_start: 0.8423 (t) cc_final: 0.8114 (m) REVERT: C 1 MET cc_start: 0.7576 (tpp) cc_final: 0.7113 (tpp) REVERT: C 37 GLU cc_start: 0.6634 (pp20) cc_final: 0.5986 (pp20) REVERT: C 39 MET cc_start: 0.9040 (ttp) cc_final: 0.8752 (ttm) REVERT: C 48 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8522 (mtmt) REVERT: C 75 ASP cc_start: 0.8702 (m-30) cc_final: 0.8408 (t0) REVERT: C 89 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8881 (mm-40) REVERT: C 108 ASP cc_start: 0.8310 (m-30) cc_final: 0.8011 (m-30) REVERT: C 115 ASP cc_start: 0.8664 (t0) cc_final: 0.8372 (t0) REVERT: C 163 ASP cc_start: 0.8732 (t0) cc_final: 0.8440 (t0) REVERT: C 172 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7377 (mm-30) REVERT: C 173 ASP cc_start: 0.7581 (p0) cc_final: 0.7039 (p0) REVERT: C 201 LYS cc_start: 0.9029 (ptpp) cc_final: 0.8643 (pptt) REVERT: C 214 MET cc_start: 0.8716 (tpp) cc_final: 0.8178 (mpp) REVERT: D 4 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8154 (tm-30) REVERT: D 18 ARG cc_start: 0.9028 (ttm110) cc_final: 0.8728 (ttm-80) REVERT: D 113 LYS cc_start: 0.9259 (ttmm) cc_final: 0.9042 (ttmm) REVERT: D 120 GLU cc_start: 0.8775 (tt0) cc_final: 0.8440 (tm-30) REVERT: D 123 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8326 (mmpt) REVERT: D 139 ASP cc_start: 0.8530 (p0) cc_final: 0.8101 (p0) REVERT: D 174 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8797 (mmmm) REVERT: D 186 ILE cc_start: 0.9055 (tp) cc_final: 0.8533 (pp) REVERT: D 191 ASP cc_start: 0.7931 (t0) cc_final: 0.7394 (t0) REVERT: D 224 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8138 (t0) REVERT: D 225 SER cc_start: 0.9200 (m) cc_final: 0.8819 (p) REVERT: D 241 ASP cc_start: 0.9284 (t0) cc_final: 0.9025 (t0) REVERT: D 257 HIS cc_start: 0.8546 (t70) cc_final: 0.7800 (t70) REVERT: D 260 ASP cc_start: 0.8552 (t70) cc_final: 0.8320 (p0) REVERT: D 278 LYS cc_start: 0.9255 (ttpp) cc_final: 0.8890 (ttpp) REVERT: D 280 ASP cc_start: 0.8912 (t0) cc_final: 0.8576 (t0) REVERT: E 59 GLU cc_start: 0.8364 (pm20) cc_final: 0.8157 (pm20) REVERT: E 63 MET cc_start: 0.8458 (ttm) cc_final: 0.8219 (ttm) REVERT: E 75 LYS cc_start: 0.4624 (tptp) cc_final: 0.2035 (tmtm) REVERT: E 120 GLU cc_start: 0.8685 (tp30) cc_final: 0.8265 (tp30) REVERT: E 124 MET cc_start: 0.8666 (ptp) cc_final: 0.8403 (ptm) REVERT: E 127 ASP cc_start: 0.8549 (t70) cc_final: 0.8238 (t0) REVERT: E 139 ASP cc_start: 0.8038 (t0) cc_final: 0.7631 (t0) REVERT: E 150 ASN cc_start: 0.8856 (m110) cc_final: 0.8425 (m-40) REVERT: E 154 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8618 (mttt) REVERT: E 183 GLU cc_start: 0.8480 (tp30) cc_final: 0.8164 (tp30) REVERT: E 189 LYS cc_start: 0.8865 (ptmm) cc_final: 0.8471 (ttpp) REVERT: E 261 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8347 (mp10) REVERT: E 278 LYS cc_start: 0.9083 (mtpp) cc_final: 0.8599 (mtmm) REVERT: G 9 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8531 (t) REVERT: G 100 SER cc_start: 0.7839 (m) cc_final: 0.7310 (p) REVERT: G 111 ASP cc_start: 0.8239 (t70) cc_final: 0.7703 (p0) REVERT: G 117 TYR cc_start: 0.8498 (t80) cc_final: 0.8252 (t80) REVERT: G 140 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7709 (tp30) REVERT: G 159 GLU cc_start: 0.8444 (pm20) cc_final: 0.7989 (pm20) REVERT: G 161 ASP cc_start: 0.8370 (m-30) cc_final: 0.7717 (m-30) REVERT: G 217 ASP cc_start: 0.8401 (p0) cc_final: 0.7994 (p0) REVERT: G 289 MET cc_start: 0.8645 (mtm) cc_final: 0.8062 (mtp) REVERT: H 90 TYR cc_start: 0.7803 (m-80) cc_final: 0.7581 (m-10) REVERT: H 117 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8542 (mm-30) REVERT: I 42 LYS cc_start: 0.9143 (pttm) cc_final: 0.8833 (pttm) REVERT: I 138 SER cc_start: 0.8719 (OUTLIER) cc_final: 0.8497 (p) REVERT: I 156 LEU cc_start: 0.8975 (mm) cc_final: 0.8126 (mt) REVERT: I 159 GLU cc_start: 0.7955 (pm20) cc_final: 0.7463 (pm20) REVERT: I 171 ASP cc_start: 0.8231 (m-30) cc_final: 0.7939 (m-30) REVERT: I 193 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8759 (mm) REVERT: I 195 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7814 (mm-30) REVERT: I 217 ASP cc_start: 0.7834 (p0) cc_final: 0.7430 (p0) REVERT: I 241 GLU cc_start: 0.8444 (mt-10) cc_final: 0.8198 (mp0) REVERT: I 250 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8182 (mm-30) REVERT: I 281 LYS cc_start: 0.8582 (tmmt) cc_final: 0.8254 (tmmt) REVERT: I 285 GLU cc_start: 0.8214 (tp30) cc_final: 0.7989 (tm-30) REVERT: J 30 ASP cc_start: 0.8761 (t0) cc_final: 0.7896 (t0) REVERT: J 63 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7562 (mm110) REVERT: J 80 LYS cc_start: 0.9182 (mtpm) cc_final: 0.8916 (mtmm) REVERT: J 88 ASP cc_start: 0.8544 (t0) cc_final: 0.8072 (t0) REVERT: J 191 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7747 (ptm) REVERT: K 30 ASP cc_start: 0.8257 (p0) cc_final: 0.7995 (p0) REVERT: K 59 LYS cc_start: 0.8921 (ptpt) cc_final: 0.8704 (ptpp) REVERT: K 108 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7851 (mm-30) REVERT: K 153 SER cc_start: 0.8738 (p) cc_final: 0.8480 (p) REVERT: K 159 GLU cc_start: 0.8018 (pp20) cc_final: 0.7697 (pp20) REVERT: K 186 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8712 (mmmm) REVERT: K 217 ASP cc_start: 0.8666 (p0) cc_final: 0.8354 (p0) REVERT: K 250 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8121 (mp0) REVERT: K 285 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7608 (tm-30) REVERT: K 289 MET cc_start: 0.8523 (mtp) cc_final: 0.8199 (mtp) REVERT: L 12 TYR cc_start: 0.8963 (m-80) cc_final: 0.8563 (m-80) REVERT: L 100 SER cc_start: 0.8816 (m) cc_final: 0.8565 (p) REVERT: L 111 ASP cc_start: 0.7900 (p0) cc_final: 0.7625 (p0) REVERT: L 156 LEU cc_start: 0.8797 (mt) cc_final: 0.8555 (mm) REVERT: L 203 GLN cc_start: 0.8956 (mp10) cc_final: 0.8717 (mt0) REVERT: L 207 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8492 (pp20) REVERT: L 213 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8126 (ttmt) REVERT: L 214 GLN cc_start: 0.8737 (mm110) cc_final: 0.8356 (mm-40) REVERT: L 289 MET cc_start: 0.8911 (ttm) cc_final: 0.8654 (ttm) REVERT: M 33 ASN cc_start: 0.8847 (t0) cc_final: 0.8630 (t0) REVERT: M 81 TYR cc_start: 0.8498 (p90) cc_final: 0.8237 (p90) REVERT: M 156 LEU cc_start: 0.8215 (mt) cc_final: 0.7794 (pp) REVERT: M 195 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7438 (tp30) REVERT: a 28 THR cc_start: 0.5801 (OUTLIER) cc_final: 0.5401 (t) REVERT: a 51 ASN cc_start: 0.8617 (t0) cc_final: 0.8145 (t0) REVERT: d 14 TYR cc_start: 0.8029 (m-80) cc_final: 0.7789 (m-10) REVERT: d 34 ASP cc_start: 0.8920 (p0) cc_final: 0.8658 (p0) REVERT: d 102 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: d 106 ARG cc_start: 0.8928 (tpp80) cc_final: 0.8370 (mpt-90) REVERT: d 123 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8046 (mmmt) REVERT: d 138 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7522 (m) REVERT: d 154 LYS cc_start: 0.8528 (ptmm) cc_final: 0.8086 (ptpp) REVERT: d 178 LYS cc_start: 0.8897 (tmmm) cc_final: 0.8576 (tmmt) REVERT: d 179 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8258 (pp20) REVERT: d 182 LEU cc_start: 0.9303 (tm) cc_final: 0.8991 (pp) REVERT: d 183 GLU cc_start: 0.9017 (tp30) cc_final: 0.8522 (tm-30) REVERT: d 191 ASP cc_start: 0.8073 (t0) cc_final: 0.7826 (p0) REVERT: d 240 PHE cc_start: 0.7348 (m-10) cc_final: 0.7064 (m-10) REVERT: d 270 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.8048 (mtm-85) REVERT: e 22 LEU cc_start: 0.8904 (pp) cc_final: 0.8438 (pt) REVERT: e 59 GLU cc_start: 0.8526 (pp20) cc_final: 0.8168 (pp20) REVERT: e 61 MET cc_start: 0.8339 (tpt) cc_final: 0.7977 (tpt) REVERT: e 98 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7629 (p) REVERT: e 99 LYS cc_start: 0.9132 (ptpp) cc_final: 0.8796 (ptmm) REVERT: e 102 GLN cc_start: 0.9057 (mm-40) cc_final: 0.8834 (mm-40) REVERT: e 111 GLU cc_start: 0.8787 (tp30) cc_final: 0.8376 (tp30) REVERT: e 114 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8010 (mtpp) REVERT: e 125 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.7927 (ttp-170) REVERT: e 127 ASP cc_start: 0.8441 (m-30) cc_final: 0.8220 (t0) REVERT: e 141 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8794 (mm-30) REVERT: e 174 LYS cc_start: 0.8642 (pttp) cc_final: 0.8376 (tppt) REVERT: e 178 LYS cc_start: 0.9134 (ptmm) cc_final: 0.8657 (tmtt) REVERT: e 179 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8327 (pp20) REVERT: e 191 ASP cc_start: 0.8188 (t0) cc_final: 0.7728 (t0) REVERT: e 200 LYS cc_start: 0.9069 (pptt) cc_final: 0.8728 (pptt) REVERT: e 261 GLN cc_start: 0.8708 (mp10) cc_final: 0.8065 (mp10) REVERT: e 278 LYS cc_start: 0.9051 (ttmt) cc_final: 0.8839 (mtpp) REVERT: A 64 ASP cc_start: 0.8702 (p0) cc_final: 0.7411 (p0) REVERT: A 65 LYS cc_start: 0.8779 (pmmt) cc_final: 0.8478 (pmtt) REVERT: A 172 ASP cc_start: 0.8295 (p0) cc_final: 0.7821 (p0) REVERT: A 225 ASP cc_start: 0.8539 (m-30) cc_final: 0.8088 (p0) REVERT: A 241 LYS cc_start: 0.9074 (mmmm) cc_final: 0.8734 (mmmm) REVERT: A 245 ARG cc_start: 0.8744 (ppp80) cc_final: 0.8372 (ppt-90) REVERT: A 248 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.8816 (mmmt) REVERT: A 282 ASN cc_start: 0.8934 (t0) cc_final: 0.8602 (t0) REVERT: A 305 LEU cc_start: 0.8970 (tp) cc_final: 0.8665 (tp) REVERT: A 322 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8747 (mtmm) REVERT: A 331 LYS cc_start: 0.9286 (tppp) cc_final: 0.8996 (mmmm) REVERT: A 445 VAL cc_start: 0.8586 (t) cc_final: 0.8321 (p) REVERT: A 568 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8701 (mp10) REVERT: A 591 ASP cc_start: 0.8370 (t0) cc_final: 0.7948 (t0) REVERT: A 622 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8333 (mt0) REVERT: A 627 GLU cc_start: 0.8685 (pp20) cc_final: 0.8189 (pp20) REVERT: A 631 GLN cc_start: 0.8938 (tp40) cc_final: 0.8601 (tp40) REVERT: A 693 GLU cc_start: 0.8368 (pp20) cc_final: 0.8086 (pp20) REVERT: A 807 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8690 (tppp) REVERT: A 850 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7896 (m-10) REVERT: A 881 LYS cc_start: 0.5442 (mttt) cc_final: 0.5234 (tttt) REVERT: A 913 LEU cc_start: 0.8842 (mt) cc_final: 0.8522 (tt) outliers start: 99 outliers final: 63 residues processed: 819 average time/residue: 0.7235 time to fit residues: 711.4200 Evaluate side-chains 809 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 725 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 91 CYS Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain D residue 87 ILE Chi-restraints excluded: chain D residue 123 LYS Chi-restraints excluded: chain D residue 224 ASN Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 270 ARG Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain H residue 1 TYR Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain I residue 59 LYS Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain I residue 193 LEU Chi-restraints excluded: chain I residue 284 THR Chi-restraints excluded: chain I residue 296 ILE Chi-restraints excluded: chain J residue 13 SER Chi-restraints excluded: chain J residue 157 VAL Chi-restraints excluded: chain J residue 191 MET Chi-restraints excluded: chain J residue 252 TYR Chi-restraints excluded: chain J residue 300 VAL Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 199 VAL Chi-restraints excluded: chain K residue 260 VAL Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 47 THR Chi-restraints excluded: chain L residue 123 ILE Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 197 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 244 THR Chi-restraints excluded: chain L residue 300 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 29 SER Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 197 SER Chi-restraints excluded: chain M residue 212 SER Chi-restraints excluded: chain M residue 245 THR Chi-restraints excluded: chain M residue 300 VAL Chi-restraints excluded: chain a residue 13 ILE Chi-restraints excluded: chain a residue 28 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 52 GLU Chi-restraints excluded: chain d residue 87 ILE Chi-restraints excluded: chain d residue 102 GLN Chi-restraints excluded: chain d residue 123 LYS Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain d residue 187 GLU Chi-restraints excluded: chain e residue 17 SER Chi-restraints excluded: chain e residue 30 HIS Chi-restraints excluded: chain e residue 52 GLU Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 98 THR Chi-restraints excluded: chain e residue 114 LYS Chi-restraints excluded: chain e residue 126 VAL Chi-restraints excluded: chain e residue 189 LYS Chi-restraints excluded: chain e residue 294 MET Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 568 GLN Chi-restraints excluded: chain A residue 622 GLN Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 850 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 296 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 377 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 chunk 70 optimal weight: 0.0470 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 228 GLN E 192 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 55 ASN I 63 GLN ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 146 ASN L 288 GLN M 63 GLN ** a 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 ASN ** d 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 168 HIS d 199 ASN e 150 ASN ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 HIS A 901 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.112928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100262 restraints weight = 149274.474| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.62 r_work: 0.3333 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 40402 Z= 0.216 Angle : 0.741 14.816 55513 Z= 0.390 Chirality : 0.046 0.532 6335 Planarity : 0.004 0.063 6513 Dihedral : 19.506 179.876 7147 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.76 % Favored : 95.04 % Rotamer: Outliers : 2.93 % Allowed : 31.17 % Favored : 65.91 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.92 % 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: -0.89 (0.12), residues: 4559 helix: 0.64 (0.12), residues: 1724 sheet: -1.17 (0.19), residues: 699 loop : -1.38 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 133 TYR 0.021 0.002 TYR J 99 PHE 0.027 0.001 PHE d 188 TRP 0.042 0.001 TRP d 218 HIS 0.005 0.001 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (40402) covalent geometry : angle 0.74074 / 0.39 (55513) hydrogen bonds : bond 0.04212 / 2.80 ( 1438) hydrogen bonds : angle 4.40628 / 3.13 ( 4034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17282.42 seconds wall clock time: 294 minutes 20.13 seconds (17660.13 seconds total)