Starting phenix.real_space_refine on Mon Aug 25 10:07:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jm0_61595/08_2025/9jm0_61595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jm0_61595/08_2025/9jm0_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jm0_61595/08_2025/9jm0_61595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jm0_61595/08_2025/9jm0_61595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jm0_61595/08_2025/9jm0_61595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jm0_61595/08_2025/9jm0_61595.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.25, 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: 2.28 Conformation dependent library (CDL) restraints added in 777.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 3.33 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: 4.65 Time building geometry restraints manager: 3.07 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=" 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 bond pdb=" C4' AR6 J 402 " pdb=" O4' AR6 J 402 " ideal model delta sigma weight residual 1.431 1.297 0.134 2.00e-02 2.50e+03 4.48e+01 ... (remaining 29604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 42039 3.40 - 6.80: 178 6.80 - 10.19: 12 10.19 - 13.59: 8 13.59 - 16.99: 4 Bond angle restraints: 42241 Sorted by residual: angle pdb=" O3A AR6 J 402 " pdb=" PA AR6 J 402 " pdb=" O5' AR6 J 402 " ideal model delta sigma weight residual 93.19 110.18 -16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" C1' A N 13 " pdb=" N9 A N 13 " pdb=" C4 A N 13 " ideal model delta sigma weight residual 126.30 142.54 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" C1' A N 13 " pdb=" N9 A N 13 " pdb=" C8 A N 13 " ideal model delta sigma weight residual 127.70 112.37 15.33 3.00e+00 1.11e-01 2.61e+01 angle pdb=" N1 AR6 J 402 " pdb=" C6 AR6 J 402 " pdb=" N6 AR6 J 402 " ideal model delta sigma weight residual 119.27 104.32 14.95 3.00e+00 1.11e-01 2.48e+01 angle pdb=" O3A AR6 J 402 " pdb=" PB AR6 J 402 " pdb=" O5D AR6 J 402 " ideal model delta sigma weight residual 94.44 107.72 -13.28 3.00e+00 1.11e-01 1.96e+01 ... (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: 4510 0.063 - 0.126: 410 0.126 - 0.189: 35 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: 1.180 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: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.380 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 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= 0.231 Angle : 0.664 16.990 42241 Z= 0.342 Chirality : 0.039 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 aren 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 covalent geometry : bond 0.00481 (29609) covalent geometry : angle 0.66437 (42241) hydrogen bonds : bond 0.11822 ( 1322) hydrogen bonds : angle 5.27350 ( 3406) Misc. bond : bond 0.05691 ( 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 : 0.780 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: 0.6345 time to fit residues: 227.4594 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 : 0.862 ------------------------------------------------------------------------------- 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: 20.0000 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: 5.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 GLN P 104 ASN P 204 GLN P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.176244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109134 restraints weight = 38244.473| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.81 r_work: 0.3155 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29610 Z= 0.161 Angle : 0.599 11.564 42241 Z= 0.323 Chirality : 0.038 0.295 4965 Planarity : 0.004 0.047 3477 Dihedral : 27.426 179.657 9433 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.74 % Allowed : 28.10 % Favored : 67.15 % 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 aren not related in a simple way. whole: 0.84 (0.18), residues: 2108 helix: 1.32 (0.16), residues: 1138 sheet: 0.91 (0.39), residues: 184 loop : -0.60 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 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 covalent geometry : bond 0.00353 (29609) covalent geometry : angle 0.59892 (42241) hydrogen bonds : bond 0.05041 ( 1322) hydrogen bonds : angle 3.79965 ( 3406) Misc. bond : bond 0.00298 ( 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 314 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 223 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8907 (mp0) REVERT: A 62 MET cc_start: 0.7709 (pmm) cc_final: 0.7191 (tpp) REVERT: A 168 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8838 (tptm) REVERT: A 250 GLN cc_start: 0.8635 (mm-40) cc_final: 0.7633 (tp-100) REVERT: A 302 TYR cc_start: 0.6994 (t80) cc_final: 0.6727 (t80) REVERT: C 250 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: B 45 ASP cc_start: 0.8633 (m-30) cc_final: 0.8408 (m-30) REVERT: B 207 LYS cc_start: 0.8219 (tmmt) cc_final: 0.7941 (pttt) REVERT: B 308 LYS cc_start: 0.7514 (mmmm) cc_final: 0.7137 (mtmm) REVERT: J 172 LYS cc_start: 0.8831 (ptpp) cc_final: 0.8421 (mppt) REVERT: J 173 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7254 (mp) REVERT: K 45 ASP cc_start: 0.8823 (m-30) cc_final: 0.8594 (m-30) REVERT: K 55 LYS cc_start: 0.5882 (OUTLIER) cc_final: 0.4853 (ttpp) REVERT: K 114 PHE cc_start: 0.7327 (m-80) cc_final: 0.6966 (m-80) REVERT: K 206 MET cc_start: 0.8236 (tpp) cc_final: 0.7913 (tpp) REVERT: K 278 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7653 (pp) REVERT: K 285 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8210 (mm) REVERT: K 301 THR cc_start: 0.8030 (m) cc_final: 0.7804 (p) REVERT: L 5 PHE cc_start: 0.6180 (OUTLIER) cc_final: 0.5718 (t80) REVERT: L 223 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: P 54 GLU cc_start: 0.5157 (tp30) cc_final: 0.4296 (tm-30) REVERT: P 306 LEU cc_start: 0.5819 (OUTLIER) cc_final: 0.5607 (mt) REVERT: T 20 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8144 (ttpp) REVERT: T 24 ARG cc_start: 0.8462 (mmt90) cc_final: 0.8150 (mpt90) REVERT: T 69 ASP cc_start: 0.7612 (t70) cc_final: 0.7100 (t0) REVERT: T 81 LEU cc_start: 0.3920 (OUTLIER) cc_final: 0.3665 (pt) REVERT: T 114 GLU cc_start: 0.8591 (tt0) cc_final: 0.8246 (tm-30) REVERT: T 132 ARG cc_start: 0.8388 (mmm160) cc_final: 0.7954 (mpt-90) REVERT: T 190 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7482 (m110) REVERT: T 306 HIS cc_start: 0.5951 (t-170) cc_final: 0.5471 (t-170) outliers start: 91 outliers final: 33 residues processed: 293 average time/residue: 0.5794 time to fit residues: 195.7145 Evaluate side-chains 248 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 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 250 GLU 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 130 SER 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 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 62 MET Chi-restraints excluded: chain P residue 116 LEU 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 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: 4.9990 chunk 21 optimal weight: 5.9990 chunk 164 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 190 optimal weight: 5.9990 chunk 147 optimal weight: 7.9990 chunk 172 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 HIS C 10 GLN C 11 GLN C 255 GLN B 105 ASN J 51 GLN K 76 GLN K 240 GLN L 11 GLN L 12 GLN L 288 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 = 0.4179 r_free = 0.4179 target = 0.172137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.105472 restraints weight = 37820.542| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.85 r_work: 0.3075 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 29610 Z= 0.257 Angle : 0.647 9.790 42241 Z= 0.347 Chirality : 0.041 0.234 4965 Planarity : 0.005 0.054 3477 Dihedral : 27.368 179.981 9409 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 6.88 % Allowed : 26.02 % Favored : 67.10 % 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 aren not related in a simple way. whole: 0.63 (0.18), residues: 2108 helix: 1.09 (0.15), residues: 1132 sheet: 1.01 (0.38), residues: 176 loop : -0.61 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 257 TYR 0.018 0.002 TYR B 179 PHE 0.021 0.002 PHE A 10 TRP 0.006 0.001 TRP B 78 HIS 0.006 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00587 (29609) covalent geometry : angle 0.64703 (42241) hydrogen bonds : bond 0.05473 ( 1322) hydrogen bonds : angle 3.91038 ( 3406) Misc. bond : bond 0.00089 ( 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 350 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 218 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: A 250 GLN cc_start: 0.8634 (mm-40) cc_final: 0.7623 (tp-100) REVERT: A 297 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7580 (mtp180) REVERT: A 302 TYR cc_start: 0.7244 (t80) cc_final: 0.6970 (t80) REVERT: C 204 ARG cc_start: 0.7996 (mmm-85) cc_final: 0.7737 (tpp80) REVERT: C 246 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7815 (ttp-170) REVERT: C 250 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: B 25 ASP cc_start: 0.8933 (m-30) cc_final: 0.8726 (m-30) REVERT: B 116 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8937 (tp) REVERT: B 207 LYS cc_start: 0.8214 (tmmt) cc_final: 0.8005 (pttt) REVERT: B 308 LYS cc_start: 0.7639 (mmmm) cc_final: 0.7343 (mtmm) REVERT: J 75 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8415 (pp30) REVERT: J 172 LYS cc_start: 0.8845 (ptpp) cc_final: 0.8417 (mppt) REVERT: J 173 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6902 (mp) REVERT: J 174 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7063 (ptm160) REVERT: K 55 LYS cc_start: 0.5873 (OUTLIER) cc_final: 0.4806 (ttpp) REVERT: K 206 MET cc_start: 0.8237 (tpp) cc_final: 0.7859 (tpp) REVERT: K 207 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7964 (tmmt) REVERT: K 213 ARG cc_start: 0.7848 (tmm160) cc_final: 0.7271 (tmm-80) REVERT: K 231 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.5774 (tptp) REVERT: K 278 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7642 (pp) REVERT: K 285 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8357 (mm) REVERT: L 5 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.5967 (t80) REVERT: L 223 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: P 54 GLU cc_start: 0.5289 (tp30) cc_final: 0.4628 (tm-30) REVERT: P 139 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8812 (mp) REVERT: P 269 HIS cc_start: 0.6130 (m170) cc_final: 0.5927 (m90) REVERT: T 20 LYS cc_start: 0.8580 (mtpp) cc_final: 0.8132 (ttpp) REVERT: T 69 ASP cc_start: 0.7986 (t70) cc_final: 0.7490 (t0) REVERT: T 114 GLU cc_start: 0.8519 (tt0) cc_final: 0.8219 (tm-30) REVERT: T 132 ARG cc_start: 0.8452 (mmm160) cc_final: 0.8169 (mtt90) REVERT: T 255 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: T 306 HIS cc_start: 0.6020 (t-170) cc_final: 0.5601 (t-170) outliers start: 132 outliers final: 58 residues processed: 316 average time/residue: 0.6448 time to fit residues: 236.2086 Evaluate side-chains 280 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 205 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 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 28 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 75 GLN 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 156 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 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 72 LEU 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 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 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 92 PHE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 219 ILE 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 168 ASP 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 158 optimal weight: 6.9990 chunk 177 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN C 11 GLN C 255 GLN 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 = 0.4191 r_free = 0.4191 target = 0.173198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106509 restraints weight = 37741.774| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.74 r_work: 0.3099 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 29610 Z= 0.199 Angle : 0.599 8.977 42241 Z= 0.323 Chirality : 0.039 0.206 4965 Planarity : 0.004 0.053 3477 Dihedral : 27.300 179.888 9405 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 6.20 % Allowed : 27.06 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.18), residues: 2108 helix: 1.23 (0.15), residues: 1132 sheet: 0.97 (0.38), residues: 176 loop : -0.61 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 257 TYR 0.016 0.001 TYR J 218 PHE 0.019 0.002 PHE B 92 TRP 0.007 0.001 TRP B 78 HIS 0.006 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00451 (29609) covalent geometry : angle 0.59900 (42241) hydrogen bonds : bond 0.04855 ( 1322) hydrogen bonds : angle 3.77643 ( 3406) Misc. bond : bond 0.00109 ( 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 : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: A 250 GLN cc_start: 0.8623 (mm-40) cc_final: 0.7609 (tp-100) REVERT: A 297 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7604 (mtp180) REVERT: A 302 TYR cc_start: 0.7098 (t80) cc_final: 0.6770 (t80) REVERT: C 250 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: B 25 ASP cc_start: 0.8913 (m-30) cc_final: 0.8696 (m-30) REVERT: B 116 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8943 (tp) REVERT: B 233 CYS cc_start: 0.7508 (p) cc_final: 0.7293 (m) REVERT: B 308 LYS cc_start: 0.7628 (mmmm) cc_final: 0.7312 (mtmm) REVERT: J 172 LYS cc_start: 0.8887 (ptpp) cc_final: 0.8342 (mppt) REVERT: J 174 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.7090 (ptm160) REVERT: K 55 LYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5007 (ttpp) REVERT: K 119 ASP cc_start: 0.8887 (m-30) cc_final: 0.8537 (m-30) REVERT: K 206 MET cc_start: 0.8201 (tpp) cc_final: 0.7863 (tpp) REVERT: K 207 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7962 (tmmt) REVERT: K 213 ARG cc_start: 0.7853 (tmm160) cc_final: 0.7206 (tmm-80) REVERT: K 217 PHE cc_start: 0.8868 (m-80) cc_final: 0.8636 (m-80) REVERT: K 231 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.5724 (tptp) REVERT: K 278 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7697 (pp) REVERT: K 285 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8361 (mm) REVERT: L 5 PHE cc_start: 0.6363 (OUTLIER) cc_final: 0.5896 (t80) REVERT: L 223 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: P 54 GLU cc_start: 0.5166 (tp30) cc_final: 0.4633 (tm-30) REVERT: P 139 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8735 (mp) REVERT: P 268 HIS cc_start: 0.6077 (t-170) cc_final: 0.5828 (t-170) REVERT: T 20 LYS cc_start: 0.8656 (mtpp) cc_final: 0.8191 (ttpp) REVERT: T 67 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8496 (tp) REVERT: T 69 ASP cc_start: 0.7832 (t70) cc_final: 0.7348 (t0) REVERT: T 114 GLU cc_start: 0.8457 (tt0) cc_final: 0.8160 (tm-30) REVERT: T 132 ARG cc_start: 0.8457 (mmm160) cc_final: 0.8051 (mtt90) REVERT: T 306 HIS cc_start: 0.5968 (t-170) cc_final: 0.5588 (t-90) outliers start: 119 outliers final: 65 residues processed: 305 average time/residue: 0.6120 time to fit residues: 217.2448 Evaluate side-chains 285 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 206 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 116 LEU 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 244 VAL Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 40 LEU 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 235 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 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 169 VAL 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 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 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 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 216 VAL Chi-restraints excluded: chain L residue 223 GLU 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 139 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 67 LEU Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 162 MET Chi-restraints excluded: chain T residue 167 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 193 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN C 10 GLN C 11 GLN C 255 GLN B 105 ASN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.173899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.105897 restraints weight = 37872.739| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.85 r_work: 0.3106 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29610 Z= 0.175 Angle : 0.582 10.597 42241 Z= 0.315 Chirality : 0.038 0.200 4965 Planarity : 0.004 0.044 3477 Dihedral : 27.203 179.928 9404 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.13 % Favored : 95.83 % Rotamer: Outliers : 5.94 % Allowed : 27.22 % 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 aren not related in a simple way. whole: 0.81 (0.18), residues: 2108 helix: 1.32 (0.15), residues: 1137 sheet: 1.03 (0.38), residues: 176 loop : -0.68 (0.22), residues: 795 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 0.016 0.001 PHE B 92 TRP 0.005 0.001 TRP B 78 HIS 0.010 0.001 HIS K 269 Details of bonding type rmsd covalent geometry : bond 0.00393 (29609) covalent geometry : angle 0.58231 (42241) hydrogen bonds : bond 0.04586 ( 1322) hydrogen bonds : angle 3.67942 ( 3406) Misc. bond : bond 0.00114 ( 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 331 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 217 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.7826 (mm-30) REVERT: A 168 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8939 (tptm) REVERT: A 250 GLN cc_start: 0.8632 (mm-40) cc_final: 0.7620 (tp-100) REVERT: A 302 TYR cc_start: 0.7121 (t80) cc_final: 0.6778 (t80) REVERT: C 261 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: B 116 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8977 (tp) REVERT: J 172 LYS cc_start: 0.8863 (ptpp) cc_final: 0.8500 (ptpp) REVERT: J 174 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.7154 (ptm160) REVERT: J 187 ARG cc_start: 0.7899 (mmm-85) cc_final: 0.7593 (mmm160) REVERT: K 55 LYS cc_start: 0.5942 (OUTLIER) cc_final: 0.4980 (ttpp) REVERT: K 119 ASP cc_start: 0.8929 (m-30) cc_final: 0.8501 (m-30) REVERT: K 206 MET cc_start: 0.8208 (tpp) cc_final: 0.7866 (tpp) REVERT: K 207 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7922 (tmmt) REVERT: K 213 ARG cc_start: 0.7883 (tmm160) cc_final: 0.7258 (tmm-80) REVERT: K 231 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.5787 (tptp) REVERT: K 278 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7598 (pp) REVERT: K 285 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8366 (mm) REVERT: L 5 PHE cc_start: 0.6318 (OUTLIER) cc_final: 0.5887 (t80) REVERT: L 223 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: P 139 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8765 (mp) REVERT: P 268 HIS cc_start: 0.6159 (t-170) cc_final: 0.5940 (t-170) REVERT: T 20 LYS cc_start: 0.8700 (mtpp) cc_final: 0.8238 (ttpp) REVERT: T 69 ASP cc_start: 0.7880 (t70) cc_final: 0.7379 (t0) REVERT: T 114 GLU cc_start: 0.8456 (tt0) cc_final: 0.8160 (tm-30) REVERT: T 132 ARG cc_start: 0.8448 (mmm160) cc_final: 0.8109 (mtt90) REVERT: T 187 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8252 (mtp85) outliers start: 114 outliers final: 67 residues processed: 303 average time/residue: 0.5793 time to fit residues: 203.8828 Evaluate side-chains 280 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 199 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 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 293 SER 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 244 VAL Chi-restraints excluded: chain C residue 261 GLN 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 235 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 28 ILE 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 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 60 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 97 GLU 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 255 ILE 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 262 VAL Chi-restraints excluded: chain P residue 92 PHE Chi-restraints excluded: chain P residue 121 GLU Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain P residue 198 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 143 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 191 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN C 10 GLN C 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.173608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.106944 restraints weight = 37803.854| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.70 r_work: 0.3114 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29610 Z= 0.179 Angle : 0.583 8.956 42241 Z= 0.314 Chirality : 0.038 0.194 4965 Planarity : 0.004 0.069 3477 Dihedral : 27.162 179.820 9402 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.17 % Favored : 95.78 % Rotamer: Outliers : 5.74 % Allowed : 27.63 % Favored : 66.63 % 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 aren not related in a simple way. whole: 0.89 (0.18), residues: 2108 helix: 1.38 (0.15), residues: 1130 sheet: 1.06 (0.38), residues: 176 loop : -0.62 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 257 TYR 0.019 0.001 TYR A 260 PHE 0.020 0.001 PHE B 92 TRP 0.005 0.001 TRP B 78 HIS 0.008 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00405 (29609) covalent geometry : angle 0.58293 (42241) hydrogen bonds : bond 0.04556 ( 1322) hydrogen bonds : angle 3.66136 ( 3406) Misc. bond : bond 0.00116 ( 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 319 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 209 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.7823 (mm-30) REVERT: A 250 GLN cc_start: 0.8626 (mm-40) cc_final: 0.7596 (tp-100) REVERT: A 257 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7273 (ttp80) REVERT: A 302 TYR cc_start: 0.7294 (t80) cc_final: 0.6934 (t80) REVERT: C 261 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: B 116 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8980 (tp) REVERT: B 305 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7650 (tttt) REVERT: J 75 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8298 (pp30) REVERT: J 172 LYS cc_start: 0.8902 (ptpp) cc_final: 0.8701 (ptpp) REVERT: J 174 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7213 (ptm160) REVERT: J 187 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7587 (mmm160) REVERT: K 55 LYS cc_start: 0.6012 (OUTLIER) cc_final: 0.4986 (ttpp) REVERT: K 206 MET cc_start: 0.8201 (tpp) cc_final: 0.7848 (tpp) REVERT: K 207 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7925 (tmmt) REVERT: K 213 ARG cc_start: 0.7889 (tmm160) cc_final: 0.7279 (tmm-80) REVERT: K 231 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.5760 (tptp) REVERT: K 278 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7632 (pp) REVERT: K 285 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8393 (mm) REVERT: L 5 PHE cc_start: 0.6346 (OUTLIER) cc_final: 0.5891 (t80) REVERT: L 223 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: P 54 GLU cc_start: 0.5895 (tp30) cc_final: 0.5116 (tm-30) REVERT: P 261 LYS cc_start: 0.6191 (OUTLIER) cc_final: 0.5592 (mmtm) REVERT: P 268 HIS cc_start: 0.6099 (t-170) cc_final: 0.5829 (t-170) REVERT: P 269 HIS cc_start: 0.5802 (m170) cc_final: 0.5560 (m90) REVERT: P 274 LYS cc_start: 0.5419 (OUTLIER) cc_final: 0.4533 (pmtt) REVERT: T 20 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8226 (ttpp) REVERT: T 69 ASP cc_start: 0.7906 (t70) cc_final: 0.7389 (t0) REVERT: T 114 GLU cc_start: 0.8465 (tt0) cc_final: 0.8169 (tm-30) REVERT: T 132 ARG cc_start: 0.8446 (mmm160) cc_final: 0.8015 (mtt90) outliers start: 110 outliers final: 73 residues processed: 294 average time/residue: 0.6171 time to fit residues: 209.8950 Evaluate side-chains 298 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 209 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 110 ILE 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 257 ARG Chi-restraints excluded: chain A residue 301 THR 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 244 VAL Chi-restraints excluded: chain C residue 261 GLN 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 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 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 60 ASP Chi-restraints excluded: chain J residue 75 GLN 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 174 ARG 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 231 LYS Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 255 ILE 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 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 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 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: 10.0000 chunk 177 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 243 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 227 optimal weight: 0.0770 chunk 145 optimal weight: 7.9990 chunk 248 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 244 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN C 11 GLN C 255 GLN 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 = 0.4204 r_free = 0.4204 target = 0.174648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.107849 restraints weight = 38040.536| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.77 r_work: 0.3142 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29610 Z= 0.146 Angle : 0.559 9.160 42241 Z= 0.302 Chirality : 0.036 0.198 4965 Planarity : 0.004 0.059 3477 Dihedral : 27.075 179.174 9402 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 4.95 % Allowed : 28.31 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.18), residues: 2108 helix: 1.53 (0.16), residues: 1134 sheet: 1.20 (0.38), residues: 176 loop : -0.64 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 257 TYR 0.017 0.001 TYR A 260 PHE 0.018 0.001 PHE B 92 TRP 0.005 0.001 TRP P 78 HIS 0.007 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00321 (29609) covalent geometry : angle 0.55878 (42241) hydrogen bonds : bond 0.04227 ( 1322) hydrogen bonds : angle 3.56365 ( 3406) Misc. bond : bond 0.00116 ( 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 329 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 234 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: A 62 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7092 (pmm) REVERT: A 168 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8857 (tptm) REVERT: A 250 GLN cc_start: 0.8648 (mm-40) cc_final: 0.7619 (tp-100) REVERT: A 257 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.7191 (ttp80) REVERT: A 302 TYR cc_start: 0.7206 (t80) cc_final: 0.6866 (t80) REVERT: B 71 GLU cc_start: 0.8719 (mp0) cc_final: 0.8461 (mp0) REVERT: B 292 ASP cc_start: 0.8511 (t0) cc_final: 0.8261 (t0) REVERT: B 305 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7513 (tttt) REVERT: J 99 GLU cc_start: 0.8799 (pt0) cc_final: 0.8397 (pm20) REVERT: J 187 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7553 (mmm160) REVERT: K 55 LYS cc_start: 0.5995 (OUTLIER) cc_final: 0.4985 (ttpp) REVERT: K 207 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7901 (tmmt) REVERT: K 231 LYS cc_start: 0.6832 (OUTLIER) cc_final: 0.5679 (tptp) REVERT: K 234 ILE cc_start: 0.7768 (mm) cc_final: 0.7393 (mp) REVERT: K 278 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7619 (pp) REVERT: K 285 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8345 (mm) REVERT: L 5 PHE cc_start: 0.6249 (OUTLIER) cc_final: 0.5886 (t80) REVERT: L 223 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: L 261 GLN cc_start: 0.8294 (tt0) cc_final: 0.7481 (tt0) REVERT: P 54 GLU cc_start: 0.5877 (tp30) cc_final: 0.5066 (tm-30) REVERT: P 261 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5475 (mmmm) REVERT: P 268 HIS cc_start: 0.5978 (t-170) cc_final: 0.5759 (t-170) REVERT: P 274 LYS cc_start: 0.5455 (OUTLIER) cc_final: 0.4638 (pmtt) REVERT: T 20 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8205 (ttpp) REVERT: T 69 ASP cc_start: 0.7799 (t70) cc_final: 0.7276 (t0) REVERT: T 114 GLU cc_start: 0.8408 (tt0) cc_final: 0.8091 (tm-30) REVERT: T 132 ARG cc_start: 0.8395 (mmm160) cc_final: 0.8028 (mtt90) REVERT: T 269 TYR cc_start: 0.9308 (t80) cc_final: 0.9100 (t80) outliers start: 95 outliers final: 57 residues processed: 307 average time/residue: 0.6376 time to fit residues: 225.0438 Evaluate side-chains 283 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 212 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 62 MET 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 257 ARG Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain B residue 23 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 227 ILE Chi-restraints excluded: chain B residue 235 SER 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 20 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 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 207 LYS 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 257 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 116 LEU 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 148 SER Chi-restraints excluded: chain T residue 162 MET 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 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: 10.0000 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 157 optimal weight: 0.0970 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 93 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4208 r_free = 0.4208 target = 0.175065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108713 restraints weight = 38081.471| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.76 r_work: 0.3144 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29610 Z= 0.142 Angle : 0.562 9.347 42241 Z= 0.302 Chirality : 0.036 0.191 4965 Planarity : 0.004 0.078 3477 Dihedral : 27.004 178.896 9399 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.38 % Allowed : 29.20 % Favored : 66.42 % 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 aren not related in a simple way. whole: 1.07 (0.19), residues: 2108 helix: 1.59 (0.16), residues: 1136 sheet: 0.85 (0.40), residues: 184 loop : -0.59 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 257 TYR 0.020 0.001 TYR J 218 PHE 0.017 0.001 PHE B 92 TRP 0.004 0.001 TRP P 78 HIS 0.007 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00313 (29609) covalent geometry : angle 0.56217 (42241) hydrogen bonds : bond 0.04152 ( 1322) hydrogen bonds : angle 3.53128 ( 3406) Misc. bond : bond 0.00130 ( 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 307 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 223 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: A 62 MET cc_start: 0.7495 (ppp) cc_final: 0.7155 (pmm) REVERT: A 168 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8847 (tptm) REVERT: A 250 GLN cc_start: 0.8662 (mm-40) cc_final: 0.7647 (tp-100) REVERT: A 293 SER cc_start: 0.8619 (m) cc_final: 0.8372 (t) REVERT: A 302 TYR cc_start: 0.7229 (t80) cc_final: 0.6878 (t80) REVERT: B 71 GLU cc_start: 0.8707 (mp0) cc_final: 0.8447 (mp0) REVERT: B 116 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8944 (tp) REVERT: B 292 ASP cc_start: 0.8502 (t0) cc_final: 0.8247 (t0) REVERT: B 305 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7496 (tttt) REVERT: J 99 GLU cc_start: 0.8781 (pt0) cc_final: 0.8334 (pm20) REVERT: J 172 LYS cc_start: 0.8797 (ptpp) cc_final: 0.8483 (ptpp) REVERT: J 187 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7546 (mmm160) REVERT: K 55 LYS cc_start: 0.5992 (OUTLIER) cc_final: 0.4984 (ttpp) REVERT: K 231 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.5632 (tptp) REVERT: K 234 ILE cc_start: 0.7734 (mm) cc_final: 0.7342 (mp) REVERT: K 278 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7664 (pp) REVERT: K 285 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8352 (mm) REVERT: L 5 PHE cc_start: 0.6243 (OUTLIER) cc_final: 0.5864 (t80) REVERT: L 223 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: L 256 MET cc_start: 0.7385 (mpp) cc_final: 0.7125 (mpp) REVERT: L 261 GLN cc_start: 0.8232 (tt0) cc_final: 0.7517 (tt0) REVERT: P 54 GLU cc_start: 0.5773 (tp30) cc_final: 0.4988 (tm-30) REVERT: P 62 MET cc_start: 0.6740 (mmp) cc_final: 0.6484 (ptp) REVERT: P 261 LYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5502 (mmmm) REVERT: P 268 HIS cc_start: 0.5974 (t-170) cc_final: 0.5774 (t-170) REVERT: P 269 HIS cc_start: 0.5791 (m-70) cc_final: 0.5406 (m90) REVERT: P 274 LYS cc_start: 0.5479 (OUTLIER) cc_final: 0.4703 (pmtt) REVERT: T 20 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8197 (ttpp) REVERT: T 24 ARG cc_start: 0.8492 (mmt90) cc_final: 0.8102 (mpt90) REVERT: T 69 ASP cc_start: 0.7804 (t70) cc_final: 0.7283 (t0) REVERT: T 132 ARG cc_start: 0.8402 (mmm160) cc_final: 0.8023 (mtt90) outliers start: 84 outliers final: 58 residues processed: 289 average time/residue: 0.6208 time to fit residues: 207.3189 Evaluate side-chains 282 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 212 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 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 C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain B residue 23 LEU 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 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 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 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 34 VAL 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 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 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 257 THR 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 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 57 SER Chi-restraints excluded: chain T residue 162 MET 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 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: 0.7980 chunk 177 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 126 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 chunk 224 optimal weight: 0.1980 chunk 181 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 72 optimal weight: 0.9990 chunk 157 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.173241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.106001 restraints weight = 37940.833| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.79 r_work: 0.3123 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29610 Z= 0.178 Angle : 0.583 9.403 42241 Z= 0.313 Chirality : 0.037 0.186 4965 Planarity : 0.004 0.086 3477 Dihedral : 26.988 179.634 9399 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.54 % Allowed : 29.04 % Favored : 66.42 % 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 aren not related in a simple way. whole: 1.01 (0.19), residues: 2108 helix: 1.52 (0.16), residues: 1128 sheet: 0.72 (0.39), residues: 184 loop : -0.54 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 257 TYR 0.026 0.001 TYR T 269 PHE 0.016 0.001 PHE K 92 TRP 0.004 0.001 TRP K 78 HIS 0.005 0.001 HIS T 78 Details of bonding type rmsd covalent geometry : bond 0.00403 (29609) covalent geometry : angle 0.58317 (42241) hydrogen bonds : bond 0.04453 ( 1322) hydrogen bonds : angle 3.62412 ( 3406) Misc. bond : bond 0.00107 ( 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 299 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 212 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.7712 (mm-30) REVERT: A 250 GLN cc_start: 0.8660 (mm-40) cc_final: 0.7635 (tp-100) REVERT: A 293 SER cc_start: 0.8581 (m) cc_final: 0.8362 (t) REVERT: A 302 TYR cc_start: 0.7262 (t80) cc_final: 0.6898 (t80) REVERT: B 71 GLU cc_start: 0.8704 (mp0) cc_final: 0.8449 (mp0) REVERT: B 116 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8954 (tp) REVERT: B 305 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7461 (tttt) REVERT: J 99 GLU cc_start: 0.8810 (pt0) cc_final: 0.8351 (pm20) REVERT: J 187 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7559 (mmm160) REVERT: K 55 LYS cc_start: 0.5910 (OUTLIER) cc_final: 0.4986 (ttpp) REVERT: K 206 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.7068 (mmm) REVERT: K 231 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.5636 (tptp) REVERT: K 234 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7481 (mp) REVERT: K 278 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7657 (pp) REVERT: K 285 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8372 (mm) REVERT: L 5 PHE cc_start: 0.6299 (OUTLIER) cc_final: 0.5847 (t80) REVERT: L 223 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: L 256 MET cc_start: 0.7466 (mpp) cc_final: 0.7221 (mpp) REVERT: P 62 MET cc_start: 0.6799 (mmp) cc_final: 0.6512 (ptp) REVERT: P 261 LYS cc_start: 0.6159 (OUTLIER) cc_final: 0.5553 (mmtm) REVERT: P 274 LYS cc_start: 0.5410 (OUTLIER) cc_final: 0.4612 (pmtt) REVERT: T 20 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8191 (ttpp) REVERT: T 69 ASP cc_start: 0.7844 (t70) cc_final: 0.7293 (t0) REVERT: T 114 GLU cc_start: 0.8432 (tt0) cc_final: 0.8019 (tm-30) REVERT: T 132 ARG cc_start: 0.8385 (mmm160) cc_final: 0.7883 (mtt90) REVERT: T 188 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8194 (tmtm) outliers start: 87 outliers final: 59 residues processed: 278 average time/residue: 0.6106 time to fit residues: 196.2289 Evaluate side-chains 281 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 209 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 244 VAL Chi-restraints excluded: chain B residue 23 LEU 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 303 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 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 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 26 MET Chi-restraints excluded: chain K residue 34 VAL 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 206 MET Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 255 ILE 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 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 234 VAL 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 219 ILE Chi-restraints excluded: chain P residue 261 LYS Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 162 MET 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 253 ILE Chi-restraints excluded: chain T residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 210 optimal weight: 1.9990 chunk 131 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 240 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 142 optimal weight: 0.2980 chunk 223 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN C 11 GLN L 288 ASN L 306 HIS ** P 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.175005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108303 restraints weight = 37966.936| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.70 r_work: 0.3166 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29610 Z= 0.141 Angle : 0.565 10.590 42241 Z= 0.303 Chirality : 0.036 0.186 4965 Planarity : 0.004 0.077 3477 Dihedral : 26.936 179.220 9399 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.75 % Allowed : 29.82 % Favored : 66.42 % 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 aren not related in a simple way. whole: 1.11 (0.19), residues: 2108 helix: 1.60 (0.16), residues: 1135 sheet: 1.30 (0.39), residues: 176 loop : -0.63 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 246 TYR 0.019 0.001 TYR J 218 PHE 0.016 0.001 PHE B 114 TRP 0.005 0.001 TRP B 78 HIS 0.007 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00310 (29609) covalent geometry : angle 0.56463 (42241) hydrogen bonds : bond 0.04112 ( 1322) hydrogen bonds : angle 3.53247 ( 3406) Misc. bond : bond 0.00130 ( 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 287 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 215 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.7720 (mm-30) REVERT: A 62 MET cc_start: 0.7583 (pmm) cc_final: 0.6864 (tpp) REVERT: A 168 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8810 (tptm) REVERT: A 250 GLN cc_start: 0.8617 (mm-40) cc_final: 0.7577 (tp-100) REVERT: A 257 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6659 (ttp80) REVERT: A 293 SER cc_start: 0.8579 (m) cc_final: 0.8331 (t) REVERT: A 302 TYR cc_start: 0.7360 (t80) cc_final: 0.7004 (t80) REVERT: B 116 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8985 (tp) REVERT: B 292 ASP cc_start: 0.8427 (t0) cc_final: 0.8214 (t0) REVERT: J 99 GLU cc_start: 0.8767 (pt0) cc_final: 0.8302 (pm20) REVERT: J 187 ARG cc_start: 0.7778 (mmm-85) cc_final: 0.7542 (mmm160) REVERT: K 55 LYS cc_start: 0.5898 (OUTLIER) cc_final: 0.4976 (ttpp) REVERT: K 119 ASP cc_start: 0.8814 (m-30) cc_final: 0.8377 (m-30) REVERT: K 206 MET cc_start: 0.7490 (tpp) cc_final: 0.6962 (tmm) REVERT: K 231 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.5634 (tptp) REVERT: K 234 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7315 (mp) REVERT: K 278 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7699 (pp) REVERT: K 285 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8364 (mm) REVERT: L 5 PHE cc_start: 0.6267 (OUTLIER) cc_final: 0.5955 (t80) REVERT: L 223 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: L 256 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7097 (mpp) REVERT: L 261 GLN cc_start: 0.8242 (tt0) cc_final: 0.7586 (tt0) REVERT: P 54 GLU cc_start: 0.5879 (tp30) cc_final: 0.4985 (tm-30) REVERT: P 62 MET cc_start: 0.6594 (mmp) cc_final: 0.6357 (ptp) REVERT: P 261 LYS cc_start: 0.6149 (OUTLIER) cc_final: 0.5571 (mmtm) REVERT: P 274 LYS cc_start: 0.5459 (OUTLIER) cc_final: 0.4597 (pmtt) REVERT: T 20 LYS cc_start: 0.8684 (mtpp) cc_final: 0.8165 (ttpp) REVERT: T 24 ARG cc_start: 0.8472 (mmt90) cc_final: 0.8102 (mpt90) REVERT: T 69 ASP cc_start: 0.7792 (t70) cc_final: 0.7282 (t0) REVERT: T 114 GLU cc_start: 0.8413 (tt0) cc_final: 0.8067 (tm-30) REVERT: T 132 ARG cc_start: 0.8388 (mmm160) cc_final: 0.8031 (mtt90) REVERT: T 188 LYS cc_start: 0.8576 (ttmm) cc_final: 0.8194 (tmtm) outliers start: 72 outliers final: 48 residues processed: 270 average time/residue: 0.6318 time to fit residues: 198.0587 Evaluate side-chains 271 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 209 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 216 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain B residue 23 LEU 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 306 LEU Chi-restraints excluded: chain J residue 20 LYS 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 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 34 VAL 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 116 LEU Chi-restraints excluded: chain K residue 231 LYS Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 234 ILE 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 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 256 MET 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 219 ILE Chi-restraints excluded: chain P residue 261 LYS Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain T residue 5 PHE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 162 MET 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 253 ILE Chi-restraints excluded: chain T residue 273 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 227 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 179 optimal weight: 30.0000 chunk 250 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 153 optimal weight: 0.0270 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN C 10 GLN C 11 GLN L 288 ASN L 306 HIS ** P 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4215 r_free = 0.4215 target = 0.175642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108605 restraints weight = 38279.497| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.80 r_work: 0.3159 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29610 Z= 0.133 Angle : 0.549 8.235 42241 Z= 0.296 Chirality : 0.036 0.184 4965 Planarity : 0.004 0.075 3477 Dihedral : 26.867 179.136 9397 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.60 % Allowed : 30.03 % Favored : 66.37 % 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 aren not related in a simple way. whole: 1.19 (0.19), residues: 2108 helix: 1.67 (0.16), residues: 1127 sheet: 1.39 (0.38), residues: 184 loop : -0.62 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 257 TYR 0.024 0.001 TYR T 269 PHE 0.015 0.001 PHE K 92 TRP 0.004 0.001 TRP P 78 HIS 0.007 0.001 HIS A 268 Details of bonding type rmsd covalent geometry : bond 0.00293 (29609) covalent geometry : angle 0.54915 (42241) hydrogen bonds : bond 0.04022 ( 1322) hydrogen bonds : angle 3.48843 ( 3406) Misc. bond : bond 0.00133 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12280.84 seconds wall clock time: 209 minutes 10.88 seconds (12550.88 seconds total)