Starting phenix.real_space_refine on Sun Jul 5 10:00:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jm0_61595/07_2026/9jm0_61595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jm0_61595/07_2026/9jm0_61595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jm0_61595/07_2026/9jm0_61595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jm0_61595/07_2026/9jm0_61595.map" model { file = "/net/cci-nas-00/data/ceres_data/9jm0_61595/07_2026/9jm0_61595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jm0_61595/07_2026/9jm0_61595.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 514 5.49 5 S 68 5.16 5 C 15985 2.51 5 N 5039 2.21 5 O 6406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s 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: 28012 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "C" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1096 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 2 Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1752 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "E" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "F" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "B" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "H" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 10, 'rna3p_pur': 20, 'rna3p_pyr': 23} Link IDs: {'rna2p': 15, 'rna3p': 42} Chain breaks: 1 Chain: "I" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "J" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2490 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 6, 'TRANS': 299} Chain: "K" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "L" Number of atoms: 1096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1096 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 2, 'TRANS': 129} Chain breaks: 2 Chain: "M" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1752 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "N" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 10, 'rna3p_pur': 19, 'rna3p_pyr': 23} Link IDs: {'rna2p': 16, 'rna3p': 41} Chain breaks: 1 Chain: "O" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Chain: "P" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2518 Classifications: {'peptide': 314} Link IDs: {'PTRANS': 12, 'TRANS': 301} Chain: "Q" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain breaks: 1 Chain: "R" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1225 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 11, 'rna3p_pur': 20, 'rna3p_pyr': 22} Link IDs: {'rna2p': 16, 'rna3p': 41} Chain breaks: 1 Chain: "S" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "T" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2490 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 6, 'TRANS': 299} Chain: "J" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'AR6': 1, 'NCA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.44, per 1000 atoms: 0.19 Number of scatterers: 28012 At special positions: 0 Unit cell: (109.14, 126.26, 252.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 P 514 15.00 O 6406 8.00 N 5039 7.00 C 15985 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 712.4 milliseconds 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4040 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 19 sheets defined 60.9% alpha, 9.1% beta 159 base pairs and 299 stacking pairs defined. Time for finding SS restraints: 3.83 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.660A pdb=" N LEU A 7 " --> pdb=" O SER A 3 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 15 " --> pdb=" O ARG A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 69 through 83 Processing helix chain 'A' and resid 84 through 87 Processing helix chain 'A' and resid 101 through 107 removed outlier: 3.598A pdb=" N ASN A 105 " --> pdb=" O SER A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 123 through 127 Processing helix chain 'A' and resid 128 through 138 removed outlier: 3.650A pdb=" N VAL A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 154 removed outlier: 3.563A pdb=" N SER A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 174 through 187 removed outlier: 4.669A pdb=" N SER A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 257 through 272 Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.921A pdb=" N VAL A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 removed outlier: 3.502A pdb=" N HIS A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 18 removed outlier: 3.559A pdb=" N HIS C 16 " --> pdb=" O GLN C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 217 through 230 Processing helix chain 'C' and resid 235 through 250 removed outlier: 3.512A pdb=" N ILE C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 274 Processing helix chain 'C' and resid 275 through 292 removed outlier: 3.735A pdb=" N ARG C 292 " --> pdb=" O ASN C 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 14 Processing helix chain 'B' and resid 22 through 31 Processing helix chain 'B' and resid 33 through 43 Processing helix chain 'B' and resid 44 through 46 No H-bonds generated for 'chain 'B' and resid 44 through 46' Processing helix chain 'B' and resid 69 through 83 Processing helix chain 'B' and resid 84 through 87 Processing helix chain 'B' and resid 101 through 107 removed outlier: 3.665A pdb=" N ASN B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.665A pdb=" N LEU B 127 " --> pdb=" O PHE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 139 removed outlier: 3.642A pdb=" N VAL B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU B 139 " --> pdb=" O VAL B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 174 through 188 removed outlier: 4.592A pdb=" N SER B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 188 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.554A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 224 Processing helix chain 'B' and resid 255 through 272 removed outlier: 4.182A pdb=" N LYS B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 292 Processing helix chain 'B' and resid 292 through 311 Processing helix chain 'J' and resid 6 through 14 Processing helix chain 'J' and resid 44 through 56 removed outlier: 3.674A pdb=" N PHE J 56 " --> pdb=" O PHE J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 74 Processing helix chain 'J' and resid 79 through 89 removed outlier: 3.616A pdb=" N GLU J 89 " --> pdb=" O ASN J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 113 removed outlier: 3.551A pdb=" N ASN J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 118 removed outlier: 3.964A pdb=" N ARG J 118 " --> pdb=" O GLU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 132 removed outlier: 3.505A pdb=" N ARG J 132 " --> pdb=" O LYS J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 136 removed outlier: 4.005A pdb=" N ASN J 136 " --> pdb=" O SER J 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 133 through 136' Processing helix chain 'J' and resid 137 through 147 Processing helix chain 'J' and resid 155 through 165 Processing helix chain 'J' and resid 169 through 172 Processing helix chain 'J' and resid 173 through 187 Processing helix chain 'J' and resid 198 through 201 Processing helix chain 'J' and resid 202 through 213 Proline residue: J 208 - end of helix Processing helix chain 'J' and resid 217 through 229 Processing helix chain 'J' and resid 232 through 250 Processing helix chain 'J' and resid 263 through 274 Processing helix chain 'J' and resid 275 through 291 Processing helix chain 'K' and resid 4 through 14 Processing helix chain 'K' and resid 22 through 31 Processing helix chain 'K' and resid 33 through 43 Processing helix chain 'K' and resid 44 through 46 No H-bonds generated for 'chain 'K' and resid 44 through 46' Processing helix chain 'K' and resid 69 through 83 Processing helix chain 'K' and resid 84 through 87 Processing helix chain 'K' and resid 101 through 107 Processing helix chain 'K' and resid 108 through 110 No H-bonds generated for 'chain 'K' and resid 108 through 110' Processing helix chain 'K' and resid 122 through 127 removed outlier: 3.689A pdb=" N LEU K 127 " --> pdb=" O PHE K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 138 removed outlier: 3.588A pdb=" N VAL K 132 " --> pdb=" O THR K 128 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 154 Processing helix chain 'K' and resid 165 through 174 Processing helix chain 'K' and resid 174 through 188 removed outlier: 4.647A pdb=" N SER K 187 " --> pdb=" O GLY K 183 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG K 188 " --> pdb=" O TYR K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 220 Processing helix chain 'K' and resid 221 through 224 Processing helix chain 'K' and resid 256 through 273 Processing helix chain 'K' and resid 277 through 292 removed outlier: 3.924A pdb=" N VAL K 281 " --> pdb=" O GLU K 277 " (cutoff:3.500A) Processing helix chain 'K' and resid 292 through 311 Processing helix chain 'L' and resid 8 through 18 removed outlier: 3.589A pdb=" N GLN L 12 " --> pdb=" O GLU L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 213 removed outlier: 3.555A pdb=" N LEU L 206 " --> pdb=" O ALA L 202 " (cutoff:3.500A) Proline residue: L 208 - end of helix Processing helix chain 'L' and resid 217 through 230 Processing helix chain 'L' and resid 236 through 251 removed outlier: 3.607A pdb=" N VAL L 240 " --> pdb=" O SER L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 274 Processing helix chain 'L' and resid 276 through 291 removed outlier: 3.520A pdb=" N ARG L 281 " --> pdb=" O LYS L 277 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 14 Processing helix chain 'P' and resid 22 through 31 Processing helix chain 'P' and resid 33 through 44 Processing helix chain 'P' and resid 69 through 83 Processing helix chain 'P' and resid 84 through 87 Processing helix chain 'P' and resid 102 through 107 Processing helix chain 'P' and resid 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' Processing helix chain 'P' and resid 122 through 127 removed outlier: 3.626A pdb=" N LEU P 127 " --> pdb=" O PHE P 123 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 139 removed outlier: 4.104A pdb=" N VAL P 132 " --> pdb=" O THR P 128 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU P 139 " --> pdb=" O VAL P 135 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 154 Processing helix chain 'P' and resid 165 through 174 Processing helix chain 'P' and resid 175 through 187 removed outlier: 4.432A pdb=" N SER P 187 " --> pdb=" O GLY P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 205 through 220 Processing helix chain 'P' and resid 221 through 224 Processing helix chain 'P' and resid 256 through 273 Processing helix chain 'P' and resid 277 through 292 Processing helix chain 'P' and resid 292 through 310 Processing helix chain 'T' and resid 6 through 14 Processing helix chain 'T' and resid 44 through 54 Processing helix chain 'T' and resid 66 through 73 removed outlier: 3.584A pdb=" N ASP T 70 " --> pdb=" O ASP T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 89 removed outlier: 3.896A pdb=" N ASN T 85 " --> pdb=" O LEU T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 113 Processing helix chain 'T' and resid 113 through 119 removed outlier: 3.547A pdb=" N ARG T 118 " --> pdb=" O GLU T 114 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS T 119 " --> pdb=" O ASN T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 129 No H-bonds generated for 'chain 'T' and resid 127 through 129' Processing helix chain 'T' and resid 133 through 138 Processing helix chain 'T' and resid 138 through 147 Processing helix chain 'T' and resid 155 through 164 Processing helix chain 'T' and resid 169 through 172 Processing helix chain 'T' and resid 173 through 188 Processing helix chain 'T' and resid 198 through 201 Processing helix chain 'T' and resid 202 through 213 Proline residue: T 208 - end of helix Processing helix chain 'T' and resid 217 through 229 Processing helix chain 'T' and resid 232 through 250 Processing helix chain 'T' and resid 263 through 272 Processing helix chain 'T' and resid 275 through 292 removed outlier: 3.865A pdb=" N ARG T 292 " --> pdb=" O ASN T 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 53 Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 195 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA4, first strand: chain 'C' and resid 253 through 255 Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 53 removed outlier: 3.874A pdb=" N ARG B 63 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 94 Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AA8, first strand: chain 'J' and resid 59 through 62 removed outlier: 6.453A pdb=" N THR J 31 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ILE J 95 " --> pdb=" O THR J 31 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE J 33 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N LEU J 152 " --> pdb=" O LEU J 120 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N CYS J 122 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N CYS J 154 " --> pdb=" O CYS J 122 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N GLN J 124 " --> pdb=" O CYS J 154 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 253 through 256 removed outlier: 3.621A pdb=" N GLY J 259 " --> pdb=" O MET J 256 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 48 through 52 Processing sheet with id=AB2, first strand: chain 'K' and resid 191 through 195 removed outlier: 4.466A pdb=" N VAL K 226 " --> pdb=" O GLU K 121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 247 through 248 Processing sheet with id=AB4, first strand: chain 'L' and resid 253 through 256 Processing sheet with id=AB5, first strand: chain 'P' and resid 48 through 52 Processing sheet with id=AB6, first strand: chain 'P' and resid 191 through 195 removed outlier: 4.668A pdb=" N VAL P 226 " --> pdb=" O GLU P 121 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 191 through 195 Processing sheet with id=AB8, first strand: chain 'P' and resid 242 through 243 Processing sheet with id=AB9, first strand: chain 'T' and resid 59 through 62 Processing sheet with id=AC1, first strand: chain 'T' and resid 253 through 255 934 hydrogen bonds defined for protein. 2682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 400 hydrogen bonds 724 hydrogen bond angles 0 basepair planarities 159 basepair parallelities 299 stacking parallelities Total time for adding SS restraints: 5.50 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5690 1.33 - 1.45: 9083 1.45 - 1.57: 13721 1.57 - 1.69: 1015 1.69 - 1.81: 100 Bond restraints: 29609 Sorted by residual: bond pdb=" C1' AR6 J 402 " pdb=" O4' AR6 J 402 " ideal model delta sigma weight residual 1.396 1.645 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C1' AR6 J 402 " pdb=" C2' AR6 J 402 " ideal model delta sigma weight residual 1.529 1.324 0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C1D AR6 J 402 " pdb=" O4D AR6 J 402 " ideal model delta sigma weight residual 1.417 1.605 -0.188 2.00e-02 2.50e+03 8.87e+01 bond pdb=" N9 A N 13 " pdb=" C4 A N 13 " ideal model delta sigma weight residual 1.374 1.425 -0.051 6.00e-03 2.78e+04 7.29e+01 bond pdb=" C2D AR6 J 402 " pdb=" C3D AR6 J 402 " ideal model delta sigma weight residual 1.525 1.355 0.170 2.00e-02 2.50e+03 7.23e+01 ... (remaining 29604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 42026 3.40 - 6.80: 191 6.80 - 10.19: 12 10.19 - 13.59: 8 13.59 - 16.99: 4 Bond angle restraints: 42241 Sorted by residual: angle pdb=" C6 A N 13 " pdb=" N1 A N 13 " pdb=" C2 A N 13 " ideal model delta sigma weight residual 118.60 109.64 8.96 6.00e-01 2.78e+00 2.23e+02 angle pdb=" C5 A N 13 " pdb=" C6 A N 13 " pdb=" N6 A N 13 " ideal model delta sigma weight residual 123.70 111.78 11.92 8.00e-01 1.56e+00 2.22e+02 angle pdb=" C5 A N 13 " pdb=" C6 A N 13 " pdb=" N1 A N 13 " ideal model delta sigma weight residual 117.70 124.85 -7.15 5.00e-01 4.00e+00 2.04e+02 angle pdb=" C2 U O 2 " pdb=" N3 U O 2 " pdb=" C4 U O 2 " ideal model delta sigma weight residual 127.00 118.61 8.39 6.00e-01 2.78e+00 1.96e+02 angle pdb=" N9 A N 13 " pdb=" C4 A N 13 " pdb=" N3 A N 13 " ideal model delta sigma weight residual 127.40 138.08 -10.68 8.00e-01 1.56e+00 1.78e+02 ... (remaining 42236 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 15489 35.87 - 71.74: 2128 71.74 - 107.62: 116 107.62 - 143.49: 13 143.49 - 179.36: 32 Dihedral angle restraints: 17778 sinusoidal: 11524 harmonic: 6254 Sorted by residual: dihedral pdb=" O4' U R 68 " pdb=" C1' U R 68 " pdb=" N1 U R 68 " pdb=" C2 U R 68 " ideal model delta sinusoidal sigma weight residual 200.00 33.41 166.59 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' U N 68 " pdb=" C1' U N 68 " pdb=" N1 U N 68 " pdb=" C2 U N 68 " ideal model delta sinusoidal sigma weight residual 200.00 55.59 144.41 1 1.50e+01 4.44e-03 7.74e+01 dihedral pdb=" O4' C E 65 " pdb=" C1' C E 65 " pdb=" N1 C E 65 " pdb=" C2 C E 65 " ideal model delta sinusoidal sigma weight residual 200.00 65.56 134.44 1 1.50e+01 4.44e-03 7.25e+01 ... (remaining 17775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4357 0.063 - 0.126: 554 0.126 - 0.189: 44 0.189 - 0.251: 8 0.251 - 0.314: 2 Chirality restraints: 4965 Sorted by residual: chirality pdb=" C1' C N 10 " pdb=" O4' C N 10 " pdb=" C2' C N 10 " pdb=" N1 C N 10 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C1' C R 10 " pdb=" O4' C R 10 " pdb=" C2' C R 10 " pdb=" N1 C R 10 " both_signs ideal model delta sigma weight residual False 2.47 2.18 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C1' G N 45 " pdb=" O4' G N 45 " pdb=" C2' G N 45 " pdb=" N9 G N 45 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4962 not shown) Planarity restraints: 3477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU J 106 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.52e+01 pdb=" CD GLU J 106 " -0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU J 106 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU J 106 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C H 10 " 0.030 2.00e-02 2.50e+03 1.63e-02 5.99e+00 pdb=" N1 C H 10 " -0.030 2.00e-02 2.50e+03 pdb=" C2 C H 10 " 0.013 2.00e-02 2.50e+03 pdb=" O2 C H 10 " -0.015 2.00e-02 2.50e+03 pdb=" N3 C H 10 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C H 10 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C H 10 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C H 10 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C H 10 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A O 3 " 0.030 2.00e-02 2.50e+03 1.44e-02 5.74e+00 pdb=" N9 A O 3 " -0.037 2.00e-02 2.50e+03 pdb=" C8 A O 3 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A O 3 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A O 3 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A O 3 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A O 3 " 0.006 2.00e-02 2.50e+03 pdb=" N1 A O 3 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A O 3 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A O 3 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A O 3 " -0.003 2.00e-02 2.50e+03 ... (remaining 3474 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 254 2.57 - 3.15: 21034 3.15 - 3.74: 50125 3.74 - 4.32: 68677 4.32 - 4.90: 103249 Nonbonded interactions: 243339 Sorted by model distance: nonbonded pdb=" O2' C S 0 " pdb=" N3 U S 2 " model vdw 1.990 3.120 nonbonded pdb=" OD2 ASP L 280 " pdb=" OG SER P 33 " model vdw 2.119 3.040 nonbonded pdb=" OG SER K 33 " pdb=" OD2 ASP T 280 " model vdw 2.137 3.040 nonbonded pdb=" OG SER A 33 " pdb=" OD2 ASP J 280 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR A 128 " pdb=" OD1 ASN A 130 " model vdw 2.159 3.040 ... (remaining 243334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'K' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'G' selection = chain 'Q' } ncs_group { reference = (chain 'J' and resid 1 through 306) selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 26.300 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 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 : 0.005 0.249 29610 Z= 0.410 Angle : 0.723 16.990 42241 Z= 0.627 Chirality : 0.043 0.314 4965 Planarity : 0.004 0.087 3477 Dihedral : 26.161 179.362 13738 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.87 % Allowed : 31.75 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 2108 helix: 1.19 (0.16), residues: 1125 sheet: 0.84 (0.38), residues: 184 loop : -0.67 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG K 257 TYR 0.021 0.001 TYR C 23 PHE 0.016 0.001 PHE K 92 TRP 0.004 0.001 TRP A 78 HIS 0.005 0.001 HIS K 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.41 (29609) covalent geometry : angle 0.72331 / 0.63 (42241) hydrogen bonds : bond 0.11822 / 7.87 ( 1322) hydrogen bonds : angle 5.27350 / 3.67 ( 3406) Misc. bond : bond 0.05691 / 3.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 270 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8570 (mp0) REVERT: A 249 SER cc_start: 0.8609 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 250 GLN cc_start: 0.8575 (mm-40) cc_final: 0.7594 (tp-100) REVERT: A 294 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7874 (mmtt) REVERT: B 25 ASP cc_start: 0.8863 (m-30) cc_final: 0.8624 (m-30) REVERT: B 45 ASP cc_start: 0.8629 (m-30) cc_final: 0.8406 (m-30) REVERT: B 292 ASP cc_start: 0.8197 (t0) cc_final: 0.7961 (t0) REVERT: B 308 LYS cc_start: 0.7408 (mmmm) cc_final: 0.7075 (mtmm) REVERT: J 172 LYS cc_start: 0.8536 (ptpp) cc_final: 0.7992 (mppt) REVERT: J 173 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7300 (mp) REVERT: J 174 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6669 (ptm160) REVERT: K 114 PHE cc_start: 0.7452 (m-80) cc_final: 0.6911 (m-80) REVERT: K 119 ASP cc_start: 0.8637 (m-30) cc_final: 0.8361 (m-30) REVERT: K 206 MET cc_start: 0.8451 (tpp) cc_final: 0.7925 (tpp) REVERT: K 231 LYS cc_start: 0.6901 (tttm) cc_final: 0.5697 (tptp) REVERT: K 235 SER cc_start: 0.8158 (OUTLIER) cc_final: 0.7844 (t) REVERT: K 264 ARG cc_start: 0.6469 (ttt180) cc_final: 0.5854 (ttt-90) REVERT: K 278 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7649 (pp) REVERT: K 294 LYS cc_start: 0.7384 (tptp) cc_final: 0.7148 (mmpt) REVERT: K 301 THR cc_start: 0.7995 (m) cc_final: 0.7786 (p) REVERT: L 5 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.6097 (t80) REVERT: L 260 TYR cc_start: 0.7401 (m-80) cc_final: 0.6677 (m-80) REVERT: P 306 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.6098 (mt) REVERT: T 20 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8102 (ttpp) REVERT: T 24 ARG cc_start: 0.8395 (mmt90) cc_final: 0.8131 (mpt90) REVERT: T 69 ASP cc_start: 0.7869 (t70) cc_final: 0.7425 (t0) REVERT: T 114 GLU cc_start: 0.8697 (tt0) cc_final: 0.8440 (tm-30) REVERT: T 132 ARG cc_start: 0.8426 (mmm160) cc_final: 0.8222 (mtt90) REVERT: T 190 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7530 (m110) REVERT: T 306 HIS cc_start: 0.5396 (t-170) cc_final: 0.5003 (t-170) outliers start: 55 outliers final: 25 residues processed: 314 average time/residue: 0.7409 time to fit residues: 265.9644 Evaluate side-chains 249 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 174 ARG Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 143 ARG Chi-restraints excluded: chain K residue 175 SER Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 235 SER Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 50.0000 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 ASN C 9 GLN C 10 GLN C 11 GLN C 255 GLN ** K 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 GLN P 204 GLN P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.176357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109362 restraints weight = 38390.785| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.85 r_work: 0.3153 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29610 Z= 0.161 Angle : 0.597 9.472 42241 Z= 0.352 Chirality : 0.045 0.470 4965 Planarity : 0.005 0.056 3477 Dihedral : 27.621 179.941 9433 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.37 % Allowed : 27.11 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.18), residues: 2108 helix: 1.25 (0.15), residues: 1137 sheet: 0.87 (0.39), residues: 184 loop : -0.59 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 257 TYR 0.012 0.001 TYR B 179 PHE 0.014 0.001 PHE K 92 TRP 0.006 0.001 TRP B 78 HIS 0.010 0.001 HIS P 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (29609) covalent geometry : angle 0.59714 / 0.35 (42241) hydrogen bonds : bond 0.05840 / 3.98 ( 1322) hydrogen bonds : angle 3.92871 / 2.80 ( 3406) Misc. bond : bond 0.00128 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 224 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8846 (mp0) REVERT: A 62 MET cc_start: 0.7670 (pmm) cc_final: 0.7167 (tpp) REVERT: A 250 GLN cc_start: 0.8676 (mm-40) cc_final: 0.7651 (tp-100) REVERT: A 257 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7304 (mtp85) REVERT: C 250 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: B 31 ARG cc_start: 0.8680 (mtm-85) cc_final: 0.8365 (mtm180) REVERT: B 45 ASP cc_start: 0.8616 (m-30) cc_final: 0.8394 (m-30) REVERT: B 207 LYS cc_start: 0.8253 (tmmt) cc_final: 0.7964 (pttt) REVERT: B 308 LYS cc_start: 0.7524 (mmmm) cc_final: 0.7173 (mtmm) REVERT: J 172 LYS cc_start: 0.8838 (ptpp) cc_final: 0.8445 (mppt) REVERT: J 173 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7151 (mp) REVERT: K 45 ASP cc_start: 0.8867 (m-30) cc_final: 0.8626 (m-30) REVERT: K 55 LYS cc_start: 0.5675 (OUTLIER) cc_final: 0.4667 (ttpp) REVERT: K 114 PHE cc_start: 0.7381 (m-80) cc_final: 0.6691 (m-80) REVERT: K 206 MET cc_start: 0.8299 (tpp) cc_final: 0.7892 (tpp) REVERT: K 207 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7981 (tmmt) REVERT: K 278 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7712 (pp) REVERT: K 285 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8229 (mm) REVERT: K 301 THR cc_start: 0.8017 (m) cc_final: 0.7790 (p) REVERT: L 5 PHE cc_start: 0.6183 (OUTLIER) cc_final: 0.5700 (t80) REVERT: L 223 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: P 54 GLU cc_start: 0.5369 (tp30) cc_final: 0.4267 (tm-30) REVERT: P 306 LEU cc_start: 0.5861 (OUTLIER) cc_final: 0.5631 (mt) REVERT: T 20 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8151 (ttpp) REVERT: T 24 ARG cc_start: 0.8478 (mmt90) cc_final: 0.8193 (mpt90) REVERT: T 69 ASP cc_start: 0.7702 (t70) cc_final: 0.7205 (t0) REVERT: T 81 LEU cc_start: 0.3978 (OUTLIER) cc_final: 0.3602 (pt) REVERT: T 114 GLU cc_start: 0.8634 (tt0) cc_final: 0.8290 (tm-30) REVERT: T 132 ARG cc_start: 0.8420 (mmm160) cc_final: 0.7954 (mtt90) REVERT: T 190 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7409 (m110) REVERT: T 306 HIS cc_start: 0.5962 (t-170) cc_final: 0.5485 (t-170) outliers start: 103 outliers final: 38 residues processed: 305 average time/residue: 0.7125 time to fit residues: 251.8079 Evaluate side-chains 258 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain T residue 273 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 105 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 190 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 172 optimal weight: 50.0000 chunk 50 optimal weight: 50.0000 chunk 107 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 296 HIS C 9 GLN C 10 GLN C 11 GLN C 255 GLN B 105 ASN J 51 GLN K 76 GLN K 240 GLN L 12 GLN P 104 ASN P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.172638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104776 restraints weight = 37933.632| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.80 r_work: 0.3090 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 29610 Z= 0.260 Angle : 0.643 12.151 42241 Z= 0.371 Chirality : 0.047 0.454 4965 Planarity : 0.005 0.063 3477 Dihedral : 27.567 179.543 9408 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 6.62 % Allowed : 26.07 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.18), residues: 2108 helix: 0.99 (0.15), residues: 1134 sheet: 0.97 (0.38), residues: 176 loop : -0.70 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 257 TYR 0.019 0.002 TYR B 179 PHE 0.022 0.002 PHE A 10 TRP 0.005 0.001 TRP K 78 HIS 0.009 0.002 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.26 (29609) covalent geometry : angle 0.64278 / 0.37 (42241) hydrogen bonds : bond 0.06139 / 4.12 ( 1322) hydrogen bonds : angle 4.00260 / 2.85 ( 3406) Misc. bond : bond 0.00486 / 0.26 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 220 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.7995 (mm-30) REVERT: A 250 GLN cc_start: 0.8719 (mm-40) cc_final: 0.7716 (tp-100) REVERT: A 297 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7583 (mtp180) REVERT: C 201 TYR cc_start: 0.6766 (m-80) cc_final: 0.6533 (m-80) REVERT: C 246 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7728 (ttp-170) REVERT: C 250 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: B 31 ARG cc_start: 0.8750 (mtm-85) cc_final: 0.8425 (mtm180) REVERT: B 116 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8923 (tp) REVERT: B 207 LYS cc_start: 0.8238 (tmmt) cc_final: 0.7982 (pttt) REVERT: B 308 LYS cc_start: 0.7532 (mmmm) cc_final: 0.7252 (mtmm) REVERT: J 8 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8143 (tp30) REVERT: J 172 LYS cc_start: 0.8835 (ptpp) cc_final: 0.8408 (mppt) REVERT: J 173 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.6930 (mp) REVERT: J 174 ARG cc_start: 0.7486 (OUTLIER) cc_final: 0.7044 (ptm160) REVERT: K 55 LYS cc_start: 0.5910 (OUTLIER) cc_final: 0.4930 (ttpp) REVERT: K 119 ASP cc_start: 0.8929 (m-30) cc_final: 0.8539 (m-30) REVERT: K 122 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8774 (m-30) REVERT: K 206 MET cc_start: 0.8269 (tpp) cc_final: 0.7909 (tpp) REVERT: K 207 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7956 (tmmt) REVERT: K 231 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.5682 (tptp) REVERT: K 278 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7693 (pp) REVERT: K 285 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8342 (mm) REVERT: K 301 THR cc_start: 0.8051 (m) cc_final: 0.7783 (p) REVERT: L 5 PHE cc_start: 0.6357 (OUTLIER) cc_final: 0.5779 (t80) REVERT: L 223 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: T 20 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8114 (ttpp) REVERT: T 69 ASP cc_start: 0.7939 (t70) cc_final: 0.7449 (t0) REVERT: T 81 LEU cc_start: 0.3912 (OUTLIER) cc_final: 0.3707 (pt) REVERT: T 114 GLU cc_start: 0.8562 (tt0) cc_final: 0.8266 (tm-30) REVERT: T 132 ARG cc_start: 0.8385 (mmm160) cc_final: 0.7987 (mtt90) REVERT: T 190 ASN cc_start: 0.7847 (OUTLIER) cc_final: 0.7500 (m110) REVERT: T 306 HIS cc_start: 0.6019 (t-170) cc_final: 0.5540 (t-170) outliers start: 127 outliers final: 58 residues processed: 315 average time/residue: 0.6635 time to fit residues: 244.2529 Evaluate side-chains 286 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 210 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 174 ARG Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 215 SER Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 177 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 9 GLN C 10 GLN C 11 GLN C 255 GLN L 12 GLN L 288 ASN L 306 HIS P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.174390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106278 restraints weight = 37981.376| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.84 r_work: 0.3112 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 29610 Z= 0.171 Angle : 0.568 9.779 42241 Z= 0.335 Chirality : 0.043 0.384 4965 Planarity : 0.004 0.058 3477 Dihedral : 27.530 179.517 9406 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 6.20 % Allowed : 26.38 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 2108 helix: 1.26 (0.15), residues: 1128 sheet: 0.60 (0.38), residues: 184 loop : -0.62 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 257 TYR 0.014 0.001 TYR A 260 PHE 0.015 0.001 PHE A 10 TRP 0.007 0.001 TRP B 78 HIS 0.007 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (29609) covalent geometry : angle 0.56807 / 0.34 (42241) hydrogen bonds : bond 0.05327 / 3.56 ( 1322) hydrogen bonds : angle 3.82899 / 2.73 ( 3406) Misc. bond : bond 0.00402 / 0.21 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 217 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: A 62 MET cc_start: 0.7390 (ppp) cc_final: 0.7172 (pmm) REVERT: A 250 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8120 (mm-40) REVERT: A 297 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7621 (mtp180) REVERT: C 201 TYR cc_start: 0.6775 (m-80) cc_final: 0.6539 (m-80) REVERT: C 246 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7626 (ttp-170) REVERT: C 250 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: B 31 ARG cc_start: 0.8779 (mtm-85) cc_final: 0.8443 (mtm180) REVERT: B 116 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8933 (tp) REVERT: B 207 LYS cc_start: 0.8214 (tmmt) cc_final: 0.7999 (pttt) REVERT: B 308 LYS cc_start: 0.7535 (mmmm) cc_final: 0.7244 (mtmm) REVERT: J 8 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8136 (tp30) REVERT: J 172 LYS cc_start: 0.8869 (ptpp) cc_final: 0.8368 (mppt) REVERT: J 174 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.6906 (ttp-110) REVERT: K 55 LYS cc_start: 0.5965 (OUTLIER) cc_final: 0.5008 (ttpp) REVERT: K 206 MET cc_start: 0.8298 (tpp) cc_final: 0.7941 (tpp) REVERT: K 207 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7961 (tmmt) REVERT: K 231 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.5636 (tptp) REVERT: K 278 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7658 (pp) REVERT: K 285 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8321 (mm) REVERT: K 294 LYS cc_start: 0.7027 (mmmt) cc_final: 0.6805 (mmmt) REVERT: L 5 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.5838 (t80) REVERT: L 223 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: T 20 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8123 (ttpp) REVERT: T 24 ARG cc_start: 0.8526 (mmt90) cc_final: 0.8226 (mpt90) REVERT: T 69 ASP cc_start: 0.7910 (t70) cc_final: 0.7412 (t0) REVERT: T 81 LEU cc_start: 0.3195 (OUTLIER) cc_final: 0.2985 (pt) REVERT: T 132 ARG cc_start: 0.8440 (mmm160) cc_final: 0.8046 (mtt90) REVERT: T 190 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7341 (m110) REVERT: T 255 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8336 (tt0) REVERT: T 306 HIS cc_start: 0.5901 (t-170) cc_final: 0.5472 (t-170) outliers start: 119 outliers final: 64 residues processed: 305 average time/residue: 0.6103 time to fit residues: 217.7262 Evaluate side-chains 287 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 206 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 174 ARG Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 219 ILE Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 215 SER Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 64 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 162 MET Chi-restraints excluded: chain T residue 168 ASP Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain T residue 255 GLN Chi-restraints excluded: chain T residue 273 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 193 optimal weight: 0.0470 chunk 73 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 1 optimal weight: 0.0270 chunk 192 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 chunk 174 optimal weight: 50.0000 chunk 28 optimal weight: 2.9990 chunk 172 optimal weight: 50.0000 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 10 GLN C 11 GLN C 255 GLN B 105 ASN L 11 GLN L 288 ASN L 306 HIS P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.174458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.107264 restraints weight = 37926.340| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.83 r_work: 0.3113 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29610 Z= 0.166 Angle : 0.560 10.286 42241 Z= 0.331 Chirality : 0.043 0.323 4965 Planarity : 0.004 0.046 3477 Dihedral : 27.481 179.946 9406 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 6.52 % Allowed : 26.64 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.18), residues: 2108 helix: 1.32 (0.15), residues: 1132 sheet: 1.07 (0.38), residues: 176 loop : -0.58 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 257 TYR 0.018 0.001 TYR A 260 PHE 0.015 0.001 PHE A 10 TRP 0.006 0.001 TRP B 78 HIS 0.009 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.17 (29609) covalent geometry : angle 0.56045 / 0.33 (42241) hydrogen bonds : bond 0.05186 / 3.44 ( 1322) hydrogen bonds : angle 3.75266 / 2.67 ( 3406) Misc. bond : bond 0.00148 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 211 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.7845 (mm-30) REVERT: A 250 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8481 (mm-40) REVERT: C 201 TYR cc_start: 0.6773 (m-80) cc_final: 0.6537 (m-80) REVERT: B 31 ARG cc_start: 0.8781 (mtm-85) cc_final: 0.8434 (mtm180) REVERT: B 116 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8959 (tp) REVERT: B 308 LYS cc_start: 0.7665 (mmmm) cc_final: 0.7318 (mtmm) REVERT: J 8 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8184 (tp30) REVERT: J 172 LYS cc_start: 0.8872 (ptpp) cc_final: 0.8372 (mppt) REVERT: K 55 LYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5000 (ttpp) REVERT: K 206 MET cc_start: 0.8262 (tpp) cc_final: 0.7896 (tpp) REVERT: K 207 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7951 (tmmt) REVERT: K 231 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.5651 (tptp) REVERT: K 278 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7644 (pp) REVERT: K 285 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8302 (mm) REVERT: L 5 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.5800 (t80) REVERT: L 223 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: P 23 LEU cc_start: 0.8876 (mm) cc_final: 0.8391 (mm) REVERT: P 62 MET cc_start: 0.6785 (mmp) cc_final: 0.6324 (ptp) REVERT: P 261 LYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5482 (mmtm) REVERT: T 20 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8187 (ttpp) REVERT: T 69 ASP cc_start: 0.7913 (t70) cc_final: 0.7425 (t0) REVERT: T 132 ARG cc_start: 0.8435 (mmm160) cc_final: 0.8057 (mtt90) REVERT: T 306 HIS cc_start: 0.5924 (t-170) cc_final: 0.5481 (t-170) outliers start: 125 outliers final: 67 residues processed: 300 average time/residue: 0.6339 time to fit residues: 222.3774 Evaluate side-chains 283 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 205 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 60 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 215 SER Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 254 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 261 LYS Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 162 MET Chi-restraints excluded: chain T residue 168 ASP Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain T residue 273 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 143 optimal weight: 4.9990 chunk 147 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 244 optimal weight: 0.6980 chunk 210 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 191 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 10 GLN C 11 GLN C 255 GLN L 288 ASN L 306 HIS P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.174463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.106350 restraints weight = 37872.497| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.85 r_work: 0.3112 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29610 Z= 0.168 Angle : 0.561 10.178 42241 Z= 0.329 Chirality : 0.042 0.301 4965 Planarity : 0.004 0.068 3477 Dihedral : 27.459 179.838 9403 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.58 % Allowed : 27.74 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2108 helix: 1.35 (0.15), residues: 1132 sheet: 1.07 (0.38), residues: 176 loop : -0.58 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 257 TYR 0.014 0.001 TYR C 260 PHE 0.014 0.001 PHE A 10 TRP 0.005 0.001 TRP B 78 HIS 0.008 0.001 HIS K 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (29609) covalent geometry : angle 0.56100 / 0.33 (42241) hydrogen bonds : bond 0.05090 / 3.36 ( 1322) hydrogen bonds : angle 3.73604 / 2.66 ( 3406) Misc. bond : bond 0.00147 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 213 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.7842 (mm-30) REVERT: A 250 GLN cc_start: 0.8675 (mm-40) cc_final: 0.7887 (tm-30) REVERT: C 201 TYR cc_start: 0.6785 (m-80) cc_final: 0.6559 (m-80) REVERT: B 116 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8968 (tp) REVERT: B 305 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7674 (tttt) REVERT: B 308 LYS cc_start: 0.7664 (mmmm) cc_final: 0.7308 (mtmm) REVERT: J 172 LYS cc_start: 0.8844 (ptpp) cc_final: 0.8329 (mppt) REVERT: J 187 ARG cc_start: 0.7815 (mmm-85) cc_final: 0.7579 (mmm160) REVERT: K 55 LYS cc_start: 0.5980 (OUTLIER) cc_final: 0.4994 (ttpp) REVERT: K 206 MET cc_start: 0.8261 (tpp) cc_final: 0.7890 (tpp) REVERT: K 207 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7970 (tmmt) REVERT: K 226 VAL cc_start: 0.9326 (m) cc_final: 0.9092 (m) REVERT: K 231 LYS cc_start: 0.6887 (OUTLIER) cc_final: 0.5639 (tptp) REVERT: K 278 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7686 (pp) REVERT: K 285 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8290 (mm) REVERT: K 294 LYS cc_start: 0.7074 (mmmt) cc_final: 0.6855 (mmmt) REVERT: L 5 PHE cc_start: 0.6294 (OUTLIER) cc_final: 0.5810 (t80) REVERT: L 223 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: P 62 MET cc_start: 0.6807 (mmp) cc_final: 0.6299 (ptp) REVERT: T 20 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8202 (ttpp) REVERT: T 69 ASP cc_start: 0.7889 (t70) cc_final: 0.7388 (t0) REVERT: T 114 GLU cc_start: 0.8486 (tt0) cc_final: 0.8193 (tm-30) REVERT: T 132 ARG cc_start: 0.8428 (mmm160) cc_final: 0.8042 (mtt90) REVERT: T 306 HIS cc_start: 0.5921 (t-170) cc_final: 0.5576 (t-90) outliers start: 107 outliers final: 73 residues processed: 295 average time/residue: 0.6548 time to fit residues: 226.0251 Evaluate side-chains 288 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 205 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 60 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 215 SER Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 92 PHE Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 162 MET Chi-restraints excluded: chain T residue 168 ASP Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain T residue 273 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 219 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 243 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 145 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 10 GLN C 11 GLN C 255 GLN K 240 GLN L 288 ASN L 306 HIS P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.174835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106987 restraints weight = 37862.510| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.83 r_work: 0.3121 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29610 Z= 0.157 Angle : 0.552 9.797 42241 Z= 0.324 Chirality : 0.042 0.282 4965 Planarity : 0.004 0.043 3477 Dihedral : 27.425 179.507 9403 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.74 % Allowed : 27.58 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2108 helix: 1.42 (0.15), residues: 1134 sheet: 1.09 (0.38), residues: 176 loop : -0.64 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 257 TYR 0.013 0.001 TYR B 179 PHE 0.019 0.001 PHE K 92 TRP 0.005 0.001 TRP B 78 HIS 0.011 0.001 HIS P 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (29609) covalent geometry : angle 0.55163 / 0.32 (42241) hydrogen bonds : bond 0.04909 / 3.23 ( 1322) hydrogen bonds : angle 3.69129 / 2.63 ( 3406) Misc. bond : bond 0.00126 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 227 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.7814 (mm-30) REVERT: A 168 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8932 (tptm) REVERT: A 250 GLN cc_start: 0.8690 (mm-40) cc_final: 0.8442 (mm-40) REVERT: A 251 GLU cc_start: 0.8236 (pt0) cc_final: 0.7997 (pm20) REVERT: C 201 TYR cc_start: 0.6778 (m-80) cc_final: 0.6550 (m-80) REVERT: B 116 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8961 (tp) REVERT: B 308 LYS cc_start: 0.7662 (mmmm) cc_final: 0.7303 (mtmm) REVERT: J 172 LYS cc_start: 0.8812 (ptpp) cc_final: 0.8240 (mppt) REVERT: J 187 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7539 (mmm160) REVERT: K 55 LYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5008 (ttpp) REVERT: K 206 MET cc_start: 0.8259 (tpp) cc_final: 0.7882 (tpp) REVERT: K 207 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7979 (tmmt) REVERT: K 226 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.9092 (m) REVERT: K 231 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.5707 (tptp) REVERT: K 278 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7696 (pp) REVERT: K 285 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8274 (mm) REVERT: L 5 PHE cc_start: 0.6271 (OUTLIER) cc_final: 0.5876 (t80) REVERT: L 223 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: P 62 MET cc_start: 0.6908 (mmp) cc_final: 0.6446 (ptp) REVERT: P 153 CYS cc_start: 0.8432 (m) cc_final: 0.7931 (m) REVERT: P 261 LYS cc_start: 0.6240 (OUTLIER) cc_final: 0.5565 (mmtt) REVERT: P 268 HIS cc_start: 0.6189 (t-170) cc_final: 0.5750 (t-170) REVERT: P 269 HIS cc_start: 0.5606 (m170) cc_final: 0.5371 (m90) REVERT: P 274 LYS cc_start: 0.5219 (OUTLIER) cc_final: 0.4415 (pmtt) REVERT: T 20 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8176 (ttpp) REVERT: T 69 ASP cc_start: 0.7958 (t70) cc_final: 0.7447 (t0) REVERT: T 114 GLU cc_start: 0.8475 (tt0) cc_final: 0.8176 (tm-30) REVERT: T 132 ARG cc_start: 0.8414 (mmm160) cc_final: 0.8008 (mtt90) outliers start: 110 outliers final: 72 residues processed: 312 average time/residue: 0.6215 time to fit residues: 226.4077 Evaluate side-chains 294 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 209 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 60 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 215 SER Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 92 PHE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 261 LYS Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 162 MET Chi-restraints excluded: chain T residue 168 ASP Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain T residue 273 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 201 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 136 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 93 optimal weight: 10.0000 chunk 231 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN C 10 GLN C 11 GLN C 255 GLN L 288 ASN L 306 HIS ** P 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.175031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.107156 restraints weight = 37910.653| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.83 r_work: 0.3131 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29610 Z= 0.146 Angle : 0.547 9.594 42241 Z= 0.322 Chirality : 0.041 0.273 4965 Planarity : 0.004 0.067 3477 Dihedral : 27.406 179.456 9402 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.16 % Allowed : 28.52 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.18), residues: 2108 helix: 1.46 (0.16), residues: 1136 sheet: 1.15 (0.38), residues: 176 loop : -0.62 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 257 TYR 0.020 0.001 TYR T 269 PHE 0.017 0.001 PHE K 92 TRP 0.005 0.001 TRP B 78 HIS 0.008 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (29609) covalent geometry : angle 0.54674 / 0.32 (42241) hydrogen bonds : bond 0.04825 / 3.17 ( 1322) hydrogen bonds : angle 3.67580 / 2.62 ( 3406) Misc. bond : bond 0.00137 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 209 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.7797 (mm-30) REVERT: A 168 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8918 (tptm) REVERT: A 250 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8465 (mm-40) REVERT: A 251 GLU cc_start: 0.8274 (pt0) cc_final: 0.8028 (pm20) REVERT: C 201 TYR cc_start: 0.6777 (m-80) cc_final: 0.6548 (m-80) REVERT: B 116 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8957 (tp) REVERT: B 305 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7655 (tttt) REVERT: J 172 LYS cc_start: 0.8803 (ptpp) cc_final: 0.8583 (ptpp) REVERT: J 187 ARG cc_start: 0.7862 (mmm-85) cc_final: 0.7578 (mmm160) REVERT: K 55 LYS cc_start: 0.6004 (OUTLIER) cc_final: 0.4989 (ttpp) REVERT: K 206 MET cc_start: 0.8265 (tpp) cc_final: 0.7887 (tpp) REVERT: K 207 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7975 (tmmt) REVERT: K 226 VAL cc_start: 0.9308 (OUTLIER) cc_final: 0.9082 (m) REVERT: K 231 LYS cc_start: 0.6915 (OUTLIER) cc_final: 0.5694 (tptp) REVERT: K 278 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7635 (pp) REVERT: K 285 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8271 (mm) REVERT: L 5 PHE cc_start: 0.6265 (OUTLIER) cc_final: 0.5870 (t80) REVERT: L 223 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: P 62 MET cc_start: 0.6893 (mmp) cc_final: 0.6459 (ptp) REVERT: P 261 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5577 (mmtt) REVERT: P 269 HIS cc_start: 0.5775 (m170) cc_final: 0.5473 (m90) REVERT: P 274 LYS cc_start: 0.5228 (OUTLIER) cc_final: 0.4391 (pmtt) REVERT: T 20 LYS cc_start: 0.8636 (mtpp) cc_final: 0.8155 (ttpp) REVERT: T 24 ARG cc_start: 0.8499 (mmt90) cc_final: 0.8187 (mpt90) REVERT: T 69 ASP cc_start: 0.7895 (t70) cc_final: 0.7387 (t0) REVERT: T 114 GLU cc_start: 0.8471 (tt0) cc_final: 0.8190 (tm-30) REVERT: T 132 ARG cc_start: 0.8412 (mmm160) cc_final: 0.8006 (mtt90) REVERT: T 187 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.8221 (mtp85) outliers start: 99 outliers final: 73 residues processed: 285 average time/residue: 0.6651 time to fit residues: 222.0081 Evaluate side-chains 292 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 204 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 60 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 215 SER Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 92 PHE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 261 LYS Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 162 MET Chi-restraints excluded: chain T residue 168 ASP Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 187 ARG Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain T residue 273 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 197 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 181 optimal weight: 50.0000 chunk 36 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN C 10 GLN C 11 GLN B 105 ASN ** J 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 ASN L 306 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.171865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.104263 restraints weight = 37818.628| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.74 r_work: 0.3080 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 29610 Z= 0.260 Angle : 0.628 12.747 42241 Z= 0.359 Chirality : 0.046 0.392 4965 Planarity : 0.005 0.075 3477 Dihedral : 27.420 179.889 9400 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 5.11 % Allowed : 28.62 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.18), residues: 2108 helix: 1.10 (0.15), residues: 1138 sheet: 0.83 (0.38), residues: 176 loop : -0.68 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 297 TYR 0.020 0.002 TYR B 179 PHE 0.024 0.002 PHE A 10 TRP 0.006 0.002 TRP K 78 HIS 0.010 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.26 (29609) covalent geometry : angle 0.62779 / 0.36 (42241) hydrogen bonds : bond 0.05611 / 3.67 ( 1322) hydrogen bonds : angle 3.87741 / 2.76 ( 3406) Misc. bond : bond 0.00105 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 216 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.7926 (mm-30) REVERT: A 250 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8473 (mm-40) REVERT: A 251 GLU cc_start: 0.8354 (pt0) cc_final: 0.8114 (pm20) REVERT: C 201 TYR cc_start: 0.6847 (m-80) cc_final: 0.6640 (m-80) REVERT: B 116 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8932 (tp) REVERT: B 305 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7652 (tttt) REVERT: B 308 LYS cc_start: 0.7653 (mmmm) cc_final: 0.7353 (mtmm) REVERT: J 187 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7584 (mmm160) REVERT: K 55 LYS cc_start: 0.6026 (OUTLIER) cc_final: 0.4928 (ttpp) REVERT: K 119 ASP cc_start: 0.8972 (m-30) cc_final: 0.8590 (m-30) REVERT: K 207 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7902 (tmmt) REVERT: K 213 ARG cc_start: 0.7842 (tmm160) cc_final: 0.7293 (tmm-80) REVERT: K 226 VAL cc_start: 0.9319 (OUTLIER) cc_final: 0.9095 (m) REVERT: K 231 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.5794 (tptp) REVERT: K 234 ILE cc_start: 0.7875 (mm) cc_final: 0.7575 (mp) REVERT: K 278 ILE cc_start: 0.7946 (OUTLIER) cc_final: 0.7652 (pp) REVERT: K 285 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8351 (mm) REVERT: K 294 LYS cc_start: 0.7167 (mmpt) cc_final: 0.6901 (mmmt) REVERT: L 5 PHE cc_start: 0.6429 (OUTLIER) cc_final: 0.5935 (t80) REVERT: L 223 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: P 62 MET cc_start: 0.6848 (mmp) cc_final: 0.6399 (ptp) REVERT: P 261 LYS cc_start: 0.6308 (OUTLIER) cc_final: 0.5607 (mmtm) REVERT: P 274 LYS cc_start: 0.5446 (OUTLIER) cc_final: 0.4050 (pttt) REVERT: T 20 LYS cc_start: 0.8658 (mtpp) cc_final: 0.8172 (ttpp) REVERT: T 69 ASP cc_start: 0.7918 (t70) cc_final: 0.7401 (t0) REVERT: T 132 ARG cc_start: 0.8398 (mmm160) cc_final: 0.7974 (mtt90) outliers start: 98 outliers final: 68 residues processed: 292 average time/residue: 0.6958 time to fit residues: 236.7143 Evaluate side-chains 287 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 206 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 SER Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 60 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 215 SER Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 92 PHE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 121 GLU Chi-restraints excluded: chain P residue 128 THR Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 261 LYS Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 168 ASP Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 210 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 240 optimal weight: 5.9990 chunk 141 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 223 optimal weight: 0.7980 chunk 214 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 10 GLN C 11 GLN C 255 GLN B 105 ASN L 288 ASN L 306 HIS P 269 HIS ** P 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.175319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.108607 restraints weight = 37913.106| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.81 r_work: 0.3139 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29610 Z= 0.130 Angle : 0.547 8.596 42241 Z= 0.321 Chirality : 0.041 0.253 4965 Planarity : 0.004 0.062 3477 Dihedral : 27.394 179.559 9400 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.65 % Allowed : 30.24 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2108 helix: 1.45 (0.16), residues: 1134 sheet: 1.00 (0.38), residues: 176 loop : -0.60 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 257 TYR 0.013 0.001 TYR A 260 PHE 0.016 0.001 PHE K 92 TRP 0.009 0.001 TRP A 78 HIS 0.008 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (29609) covalent geometry : angle 0.54732 / 0.32 (42241) hydrogen bonds : bond 0.04681 / 3.06 ( 1322) hydrogen bonds : angle 3.68257 / 2.62 ( 3406) Misc. bond : bond 0.00131 / 0.07 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 218 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.7775 (mm-30) REVERT: A 168 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8854 (tptm) REVERT: A 250 GLN cc_start: 0.8752 (mm-40) cc_final: 0.8478 (mm-40) REVERT: A 251 GLU cc_start: 0.8365 (pt0) cc_final: 0.8093 (pm20) REVERT: C 204 ARG cc_start: 0.7766 (mmm-85) cc_final: 0.7544 (tpp80) REVERT: B 305 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7599 (tttt) REVERT: K 55 LYS cc_start: 0.6019 (OUTLIER) cc_final: 0.4976 (ttpp) REVERT: K 207 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7952 (tmmt) REVERT: K 226 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.9079 (m) REVERT: K 231 LYS cc_start: 0.6919 (OUTLIER) cc_final: 0.5721 (tptp) REVERT: K 234 ILE cc_start: 0.7798 (mm) cc_final: 0.7486 (mp) REVERT: K 278 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7643 (pp) REVERT: K 285 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8339 (mm) REVERT: L 5 PHE cc_start: 0.6268 (OUTLIER) cc_final: 0.5822 (t80) REVERT: L 223 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: P 62 MET cc_start: 0.6947 (mmp) cc_final: 0.6468 (ptp) REVERT: P 121 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7046 (mm-30) REVERT: P 261 LYS cc_start: 0.6225 (OUTLIER) cc_final: 0.5563 (mmmm) REVERT: P 268 HIS cc_start: 0.6225 (t-170) cc_final: 0.5672 (t-170) REVERT: P 269 HIS cc_start: 0.5826 (m-70) cc_final: 0.5515 (m90) REVERT: P 274 LYS cc_start: 0.5327 (OUTLIER) cc_final: 0.4554 (pmtt) REVERT: T 20 LYS cc_start: 0.8654 (mtpp) cc_final: 0.8172 (ttpp) REVERT: T 24 ARG cc_start: 0.8540 (mmt90) cc_final: 0.8163 (mpt90) REVERT: T 69 ASP cc_start: 0.7853 (t70) cc_final: 0.7336 (t0) REVERT: T 132 ARG cc_start: 0.8395 (mmm160) cc_final: 0.7953 (mtt90) outliers start: 70 outliers final: 42 residues processed: 274 average time/residue: 0.7042 time to fit residues: 224.1985 Evaluate side-chains 261 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 205 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 305 LYS Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 207 LYS Chi-restraints excluded: chain K residue 226 VAL Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 215 SER Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 92 PHE Chi-restraints excluded: chain P residue 121 GLU Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 261 LYS Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 168 ASP Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 227 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 179 optimal weight: 50.0000 chunk 250 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN C 10 GLN C 11 GLN ** J 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 ASN L 306 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.173727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.107240 restraints weight = 37868.401| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.84 r_work: 0.3108 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29610 Z= 0.182 Angle : 0.567 10.548 42241 Z= 0.330 Chirality : 0.042 0.293 4965 Planarity : 0.004 0.065 3477 Dihedral : 27.366 179.735 9400 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.70 % Allowed : 30.14 % Favored : 66.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.18), residues: 2108 helix: 1.40 (0.16), residues: 1132 sheet: 1.08 (0.38), residues: 176 loop : -0.60 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 257 TYR 0.019 0.002 TYR J 218 PHE 0.017 0.002 PHE K 92 TRP 0.005 0.001 TRP B 78 HIS 0.008 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (29609) covalent geometry : angle 0.56657 / 0.33 (42241) hydrogen bonds : bond 0.04920 / 3.22 ( 1322) hydrogen bonds : angle 3.71272 / 2.64 ( 3406) Misc. bond : bond 0.00121 / 0.06 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13167.87 seconds wall clock time: 224 minutes 17.97 seconds (13457.97 seconds total)