Starting phenix.real_space_refine on Mon Jun 23 13:04:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jm0_61595/06_2025/9jm0_61595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jm0_61595/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jm0_61595/06_2025/9jm0_61595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jm0_61595/06_2025/9jm0_61595.map" model { file = "/net/cci-nas-00/data/ceres_data/9jm0_61595/06_2025/9jm0_61595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jm0_61595/06_2025/9jm0_61595.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.40, per 1000 atoms: 0.59 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: 6.82 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 11.79 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: 11.25 Time building geometry restraints manager: 8.15 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: 1.740 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: 1.090 Check model and map are aligned: 0.220 Set scattering table: 0.250 Process input model: 69.120 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:16.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.930 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.001 TRP A 78 HIS 0.005 0.001 HIS K 268 PHE 0.016 0.001 PHE K 92 TYR 0.021 0.001 TYR C 23 ARG 0.014 0.000 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.11822 ( 1322) hydrogen bonds : angle 5.27350 ( 3406) covalent geometry : bond 0.00481 (29609) covalent geometry : angle 0.66437 (42241) 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 : 2.478 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: 0.8177 (p) REVERT: A 250 GLN cc_start: 0.8575 (mm-40) cc_final: 0.7593 (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: 0.5820 (ttm-80) 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: 1.8116 time to fit residues: 654.4094 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 : 2.837 ------------------------------------------------------------------------------- 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 212 optimal weight: 3.9990 chunk 191 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 128 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 197 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 228 optimal weight: 0.5980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 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 = 0.4225 r_free = 0.4225 target = 0.176163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.108996 restraints weight = 38090.677| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.81 r_work: 0.3154 rms_B_bonded: 2.97 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: 0.8045 moved from start: 0.1017 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= 0.162 Angle : 0.600 11.613 42241 Z= 0.324 Chirality : 0.038 0.295 4965 Planarity : 0.004 0.047 3477 Dihedral : 27.433 179.667 9433 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.90 % Allowed : 28.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 2108 helix: 1.35 (0.16), residues: 1132 sheet: 0.91 (0.39), residues: 184 loop : -0.60 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.010 0.001 HIS P 268 PHE 0.014 0.001 PHE K 92 TYR 0.012 0.001 TYR B 179 ARG 0.009 0.001 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 1322) hydrogen bonds : angle 3.81470 ( 3406) covalent geometry : bond 0.00355 (29609) covalent geometry : angle 0.59982 (42241) Misc. bond : bond 0.00224 ( 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 317 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 223 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8911 (mp0) REVERT: A 62 MET cc_start: 0.7720 (pmm) cc_final: 0.7198 (tpp) REVERT: A 168 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8836 (tptm) REVERT: A 250 GLN cc_start: 0.8639 (mm-40) cc_final: 0.7639 (tp-100) REVERT: C 250 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: B 45 ASP cc_start: 0.8632 (m-30) cc_final: 0.8401 (m-30) REVERT: B 207 LYS cc_start: 0.8215 (tmmt) cc_final: 0.7937 (pttt) REVERT: B 308 LYS cc_start: 0.7514 (mmmm) cc_final: 0.7141 (mtmm) REVERT: J 172 LYS cc_start: 0.8830 (ptpp) cc_final: 0.8425 (mppt) REVERT: J 173 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7244 (mp) REVERT: K 45 ASP cc_start: 0.8825 (m-30) cc_final: 0.8598 (m-30) REVERT: K 55 LYS cc_start: 0.5886 (OUTLIER) cc_final: 0.4859 (ttpp) REVERT: K 114 PHE cc_start: 0.7331 (m-80) cc_final: 0.6963 (m-80) REVERT: K 206 MET cc_start: 0.8243 (tpp) cc_final: 0.7919 (tpp) REVERT: K 207 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7965 (tmmt) REVERT: K 278 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7650 (pp) REVERT: K 285 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8225 (mm) REVERT: K 301 THR cc_start: 0.8039 (m) cc_final: 0.7812 (p) REVERT: L 5 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.5719 (t80) REVERT: L 223 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: P 54 GLU cc_start: 0.5178 (tp30) cc_final: 0.4287 (tm-30) REVERT: P 306 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.5611 (mt) REVERT: T 20 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8152 (ttpp) REVERT: T 24 ARG cc_start: 0.8457 (mmt90) cc_final: 0.8148 (mpt90) REVERT: T 69 ASP cc_start: 0.7665 (t70) cc_final: 0.7145 (t0) REVERT: T 81 LEU cc_start: 0.3907 (OUTLIER) cc_final: 0.3653 (pt) REVERT: T 114 GLU cc_start: 0.8590 (tt0) cc_final: 0.8246 (tm-30) REVERT: T 132 ARG cc_start: 0.8417 (mmm160) cc_final: 0.7946 (mpt-90) REVERT: T 190 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7477 (m110) REVERT: T 306 HIS cc_start: 0.5963 (t-170) cc_final: 0.5481 (t-170) outliers start: 94 outliers final: 32 residues processed: 294 average time/residue: 1.4540 time to fit residues: 494.9787 Evaluate side-chains 250 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 205 time to evaluate : 2.380 ------------------------------------------------------------------------------- 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 207 LYS Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 234 VAL Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 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 24 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 249 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 251 optimal weight: 5.9990 chunk 245 optimal weight: 0.9980 chunk 224 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 GLN L 11 GLN L 12 GLN P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.176052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.109238 restraints weight = 38176.056| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.76 r_work: 0.3163 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29610 Z= 0.149 Angle : 0.569 9.958 42241 Z= 0.307 Chirality : 0.037 0.239 4965 Planarity : 0.004 0.041 3477 Dihedral : 27.242 179.036 9409 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.63 % Allowed : 26.69 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.18), residues: 2108 helix: 1.43 (0.15), residues: 1145 sheet: 0.96 (0.39), residues: 184 loop : -0.53 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.006 0.001 HIS J 47 PHE 0.017 0.001 PHE B 92 TYR 0.016 0.001 TYR K 302 ARG 0.009 0.000 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 1322) hydrogen bonds : angle 3.64849 ( 3406) covalent geometry : bond 0.00325 (29609) covalent geometry : angle 0.56906 (42241) Misc. bond : bond 0.00130 ( 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 334 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 226 time to evaluate : 2.327 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: 0.7761 (mm-30) REVERT: A 151 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8588 (mmtm) REVERT: A 168 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8834 (tptm) REVERT: A 250 GLN cc_start: 0.8667 (mm-40) cc_final: 0.7678 (tp-100) REVERT: C 246 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7663 (ttp-170) REVERT: B 45 ASP cc_start: 0.8629 (m-30) cc_final: 0.8427 (m-30) REVERT: B 207 LYS cc_start: 0.8123 (tmmt) cc_final: 0.7887 (pttt) REVERT: B 292 ASP cc_start: 0.8410 (t0) cc_final: 0.8147 (t0) REVERT: B 308 LYS cc_start: 0.7599 (mmmm) cc_final: 0.7252 (mtmm) REVERT: J 8 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8076 (tp30) REVERT: J 172 LYS cc_start: 0.8839 (ptpp) cc_final: 0.8391 (mppt) REVERT: J 173 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6765 (mp) REVERT: K 55 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.4975 (ttpp) REVERT: K 114 PHE cc_start: 0.7255 (m-80) cc_final: 0.6859 (m-80) REVERT: K 119 ASP cc_start: 0.8817 (m-30) cc_final: 0.8194 (m-30) REVERT: K 206 MET cc_start: 0.8203 (tpp) cc_final: 0.7848 (tpp) REVERT: K 207 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7929 (tmmt) REVERT: K 231 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.5602 (tptp) REVERT: K 250 GLN cc_start: 0.6772 (OUTLIER) cc_final: 0.6515 (mp10) REVERT: K 278 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7597 (pp) REVERT: K 285 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8243 (mm) REVERT: L 5 PHE cc_start: 0.6368 (OUTLIER) cc_final: 0.5915 (t80) REVERT: L 223 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7363 (mp0) REVERT: P 54 GLU cc_start: 0.5199 (tp30) cc_final: 0.4384 (tm-30) REVERT: T 20 LYS cc_start: 0.8663 (mtpp) cc_final: 0.8169 (ttpp) REVERT: T 24 ARG cc_start: 0.8450 (mmt90) cc_final: 0.8097 (mpt90) REVERT: T 69 ASP cc_start: 0.7616 (t70) cc_final: 0.7117 (t0) REVERT: T 114 GLU cc_start: 0.8476 (tt0) cc_final: 0.8167 (tm-30) REVERT: T 132 ARG cc_start: 0.8394 (mmm160) cc_final: 0.8036 (mtt90) REVERT: T 306 HIS cc_start: 0.5835 (t-170) cc_final: 0.5368 (t-170) outliers start: 108 outliers final: 45 residues processed: 309 average time/residue: 1.4202 time to fit residues: 510.3339 Evaluate side-chains 266 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 2.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 151 LYS 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 246 ARG 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 315 LEU Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 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 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 64 THR 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 231 LYS Chi-restraints excluded: chain K residue 250 GLN 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 241 ARG Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 162 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 93 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 B 105 ASN ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 ASN P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 306 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.171548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104182 restraints weight = 37966.888| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.77 r_work: 0.3072 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 29610 Z= 0.295 Angle : 0.665 8.782 42241 Z= 0.355 Chirality : 0.043 0.199 4965 Planarity : 0.005 0.047 3477 Dihedral : 27.334 179.970 9403 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 7.25 % Allowed : 25.81 % Favored : 66.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2108 helix: 1.06 (0.15), residues: 1133 sheet: 0.93 (0.38), residues: 176 loop : -0.68 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.005 0.001 HIS B 280 PHE 0.021 0.002 PHE K 10 TYR 0.019 0.002 TYR B 179 ARG 0.013 0.001 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.05545 ( 1322) hydrogen bonds : angle 3.92997 ( 3406) covalent geometry : bond 0.00679 (29609) covalent geometry : angle 0.66496 (42241) Misc. bond : bond 0.00092 ( 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 354 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 215 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.7993 (mm-30) REVERT: A 250 GLN cc_start: 0.8599 (mm-40) cc_final: 0.7570 (tp-100) REVERT: A 257 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7625 (ttp80) REVERT: A 297 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7570 (mtp180) REVERT: B 116 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8958 (tp) REVERT: B 207 LYS cc_start: 0.8249 (tmmt) cc_final: 0.8011 (pttt) REVERT: B 308 LYS cc_start: 0.7630 (mmmm) cc_final: 0.7291 (mtmm) REVERT: J 8 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8211 (tp30) REVERT: J 75 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8431 (pp30) REVERT: J 172 LYS cc_start: 0.8885 (ptpp) cc_final: 0.8341 (mppt) REVERT: K 55 LYS cc_start: 0.5816 (OUTLIER) cc_final: 0.4756 (ttpp) REVERT: K 114 PHE cc_start: 0.7489 (m-80) cc_final: 0.7220 (m-80) REVERT: K 206 MET cc_start: 0.8226 (tpp) cc_final: 0.7859 (tpp) REVERT: K 207 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7908 (tmmt) REVERT: K 213 ARG cc_start: 0.7881 (tmm160) cc_final: 0.7337 (tmm-80) REVERT: K 231 LYS cc_start: 0.7073 (OUTLIER) cc_final: 0.5832 (tptp) REVERT: K 278 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7692 (pp) REVERT: L 5 PHE cc_start: 0.6442 (OUTLIER) cc_final: 0.5972 (t80) REVERT: L 223 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: P 23 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8455 (mm) REVERT: T 20 LYS cc_start: 0.8660 (mtpp) cc_final: 0.8194 (ttpp) REVERT: T 69 ASP cc_start: 0.8010 (t70) cc_final: 0.7481 (t0) REVERT: T 132 ARG cc_start: 0.8441 (mmm160) cc_final: 0.8021 (mtt90) REVERT: T 255 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8416 (tt0) REVERT: T 306 HIS cc_start: 0.6062 (t-90) cc_final: 0.5797 (t-90) outliers start: 139 outliers final: 70 residues processed: 316 average time/residue: 1.6503 time to fit residues: 608.6239 Evaluate side-chains 288 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 204 time to evaluate : 2.620 ------------------------------------------------------------------------------- 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 257 ARG 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 14 ILE Chi-restraints excluded: chain C residue 216 VAL 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 5 PHE Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 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 215 SER Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 235 LEU 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 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 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 244 VAL Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 23 LEU 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 121 GLU 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 30 ILE 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 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 255 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 17 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 173 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 B 105 ASN ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 ASN L 306 HIS P 269 HIS ** P 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.174804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107263 restraints weight = 37886.805| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.85 r_work: 0.3129 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29610 Z= 0.143 Angle : 0.569 8.719 42241 Z= 0.308 Chirality : 0.037 0.201 4965 Planarity : 0.004 0.052 3477 Dihedral : 27.194 179.837 9403 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 4.38 % Allowed : 28.36 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.18), residues: 2108 helix: 1.38 (0.15), residues: 1137 sheet: 1.14 (0.38), residues: 176 loop : -0.64 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 78 HIS 0.019 0.001 HIS K 269 PHE 0.013 0.001 PHE K 92 TYR 0.011 0.001 TYR B 179 ARG 0.011 0.000 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 1322) hydrogen bonds : angle 3.66061 ( 3406) covalent geometry : bond 0.00312 (29609) covalent geometry : angle 0.56858 (42241) Misc. bond : bond 0.00136 ( 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 297 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 213 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: A 151 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8696 (mmtm) REVERT: A 168 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8899 (tptm) REVERT: A 250 GLN cc_start: 0.8641 (mm-40) cc_final: 0.7636 (tp-100) REVERT: B 116 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8964 (tp) REVERT: B 233 CYS cc_start: 0.7573 (p) cc_final: 0.7359 (m) REVERT: K 55 LYS cc_start: 0.5943 (OUTLIER) cc_final: 0.4973 (ttpp) REVERT: K 114 PHE cc_start: 0.7316 (m-80) cc_final: 0.6990 (m-80) REVERT: K 119 ASP cc_start: 0.8915 (m-30) cc_final: 0.8502 (m-30) REVERT: K 206 MET cc_start: 0.8206 (tpp) cc_final: 0.7888 (tpp) REVERT: K 207 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7959 (tmmt) REVERT: K 231 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.5723 (tptp) REVERT: K 278 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7632 (pp) REVERT: L 5 PHE cc_start: 0.6308 (OUTLIER) cc_final: 0.5861 (t80) REVERT: L 223 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: P 23 LEU cc_start: 0.8883 (mm) cc_final: 0.8434 (mm) REVERT: P 54 GLU cc_start: 0.5894 (tp30) cc_final: 0.5010 (tm-30) REVERT: P 121 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: T 20 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8230 (ttpp) REVERT: T 24 ARG cc_start: 0.8538 (mmt90) cc_final: 0.8217 (mpt90) REVERT: T 69 ASP cc_start: 0.7892 (t70) cc_final: 0.7385 (t0) REVERT: T 132 ARG cc_start: 0.8426 (mmm160) cc_final: 0.8110 (mtt90) outliers start: 84 outliers final: 48 residues processed: 282 average time/residue: 1.4437 time to fit residues: 474.1746 Evaluate side-chains 263 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 204 time to evaluate : 2.311 ------------------------------------------------------------------------------- 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 151 LYS 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 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 227 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 300 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 173 LEU 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 72 LEU Chi-restraints excluded: chain K residue 103 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 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 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 239 ILE Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 121 GLU Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 168 ASP Chi-restraints excluded: chain T residue 169 VAL Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE 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 177 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 226 optimal weight: 0.3980 chunk 224 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 27 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 GLN L 288 ASN L 306 HIS P 269 HIS ** P 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.176157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109767 restraints weight = 38252.741| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.74 r_work: 0.3180 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29610 Z= 0.135 Angle : 0.549 9.262 42241 Z= 0.296 Chirality : 0.036 0.198 4965 Planarity : 0.004 0.034 3477 Dihedral : 27.038 178.903 9403 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 4.74 % Allowed : 27.84 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.19), residues: 2108 helix: 1.64 (0.16), residues: 1136 sheet: 1.36 (0.38), residues: 184 loop : -0.62 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 78 HIS 0.006 0.001 HIS A 268 PHE 0.015 0.001 PHE C 205 TYR 0.018 0.001 TYR J 218 ARG 0.011 0.000 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 1322) hydrogen bonds : angle 3.51092 ( 3406) covalent geometry : bond 0.00293 (29609) covalent geometry : angle 0.54935 (42241) Misc. bond : bond 0.00132 ( 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 322 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 231 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.7766 (mm-30) REVERT: A 151 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8625 (mmtm) REVERT: A 168 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8835 (tptm) REVERT: A 250 GLN cc_start: 0.8621 (mm-40) cc_final: 0.7618 (tp-100) REVERT: A 293 SER cc_start: 0.8685 (m) cc_final: 0.8434 (t) REVERT: B 116 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8942 (tp) REVERT: B 292 ASP cc_start: 0.8509 (t0) cc_final: 0.8250 (t0) REVERT: J 1 MET cc_start: 0.3337 (mmt) cc_final: 0.3075 (mpm) REVERT: J 172 LYS cc_start: 0.8765 (ptpp) cc_final: 0.8416 (ptpp) REVERT: K 55 LYS cc_start: 0.5974 (OUTLIER) cc_final: 0.4977 (ttpp) REVERT: K 114 PHE cc_start: 0.7329 (m-80) cc_final: 0.6929 (m-80) REVERT: K 119 ASP cc_start: 0.8913 (m-30) cc_final: 0.8330 (m-30) REVERT: K 206 MET cc_start: 0.8167 (tpp) cc_final: 0.7747 (tpp) REVERT: K 231 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.5614 (tptp) REVERT: K 234 ILE cc_start: 0.7689 (mm) cc_final: 0.7312 (mp) REVERT: K 278 ILE cc_start: 0.7934 (OUTLIER) cc_final: 0.7625 (pp) REVERT: L 5 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.6036 (t80) REVERT: L 12 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: L 223 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: L 261 GLN cc_start: 0.8291 (tt0) cc_final: 0.7539 (tt0) REVERT: P 54 GLU cc_start: 0.5652 (tp30) cc_final: 0.4851 (tm-30) REVERT: P 268 HIS cc_start: 0.6104 (t-170) cc_final: 0.5839 (t-170) REVERT: P 274 LYS cc_start: 0.5161 (OUTLIER) cc_final: 0.4324 (pmtt) REVERT: T 20 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8211 (ttpp) REVERT: T 24 ARG cc_start: 0.8464 (mmt90) cc_final: 0.8033 (mpt90) REVERT: T 69 ASP cc_start: 0.7724 (t70) cc_final: 0.7212 (t0) REVERT: T 114 GLU cc_start: 0.8419 (tt0) cc_final: 0.8087 (tm-30) REVERT: T 132 ARG cc_start: 0.8367 (mmm160) cc_final: 0.8034 (mtt90) REVERT: T 269 TYR cc_start: 0.9304 (t80) cc_final: 0.9101 (t80) outliers start: 91 outliers final: 50 residues processed: 301 average time/residue: 1.4156 time to fit residues: 496.7732 Evaluate side-chains 271 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 210 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 151 LYS Chi-restraints excluded: chain A residue 168 LYS Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL 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 235 SER Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain J residue 5 PHE 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 156 SER Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 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 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 253 VAL 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 L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 GLN 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 239 ILE Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain P residue 121 GLU Chi-restraints excluded: chain P residue 219 ILE 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 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 63 optimal weight: 4.9990 chunk 48 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 179 optimal weight: 30.0000 chunk 69 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 GLN L 288 ASN L 306 HIS P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.173280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107116 restraints weight = 37705.670| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.77 r_work: 0.3120 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29610 Z= 0.189 Angle : 0.583 9.311 42241 Z= 0.313 Chirality : 0.038 0.194 4965 Planarity : 0.004 0.068 3477 Dihedral : 27.031 179.365 9399 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.80 % Allowed : 28.21 % Favored : 67.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2108 helix: 1.46 (0.15), residues: 1141 sheet: 1.23 (0.39), residues: 176 loop : -0.64 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 78 HIS 0.009 0.001 HIS A 268 PHE 0.019 0.002 PHE K 92 TYR 0.019 0.002 TYR A 260 ARG 0.016 0.001 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.04528 ( 1322) hydrogen bonds : angle 3.62382 ( 3406) covalent geometry : bond 0.00430 (29609) covalent geometry : angle 0.58325 (42241) Misc. bond : bond 0.00097 ( 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 306 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 214 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.7767 (mm-30) REVERT: A 62 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.7126 (pmm) REVERT: A 250 GLN cc_start: 0.8627 (mm-40) cc_final: 0.7602 (tp-100) REVERT: A 257 ARG cc_start: 0.7564 (ttt-90) cc_final: 0.7324 (ttt-90) REVERT: A 293 SER cc_start: 0.8662 (m) cc_final: 0.8423 (t) REVERT: B 116 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8946 (tp) REVERT: J 99 GLU cc_start: 0.8835 (pt0) cc_final: 0.8434 (pm20) REVERT: J 172 LYS cc_start: 0.8743 (ptpp) cc_final: 0.8522 (ptpp) REVERT: K 55 LYS cc_start: 0.6026 (OUTLIER) cc_final: 0.4992 (ttpp) REVERT: K 114 PHE cc_start: 0.7393 (m-80) cc_final: 0.7015 (m-80) REVERT: K 119 ASP cc_start: 0.8953 (m-30) cc_final: 0.8539 (m-30) REVERT: K 206 MET cc_start: 0.8202 (tpp) cc_final: 0.7864 (tpp) REVERT: K 213 ARG cc_start: 0.7792 (tmm160) cc_final: 0.7247 (tmm-80) REVERT: K 231 LYS cc_start: 0.6848 (OUTLIER) cc_final: 0.5656 (tptp) REVERT: K 234 ILE cc_start: 0.7770 (mm) cc_final: 0.7393 (mp) REVERT: K 278 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7623 (pp) REVERT: K 285 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8374 (mm) REVERT: L 5 PHE cc_start: 0.6380 (OUTLIER) cc_final: 0.5973 (t80) REVERT: L 223 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: P 261 LYS cc_start: 0.6215 (OUTLIER) cc_final: 0.5588 (mmtm) REVERT: P 269 HIS cc_start: 0.5825 (m170) cc_final: 0.5479 (m90) REVERT: P 274 LYS cc_start: 0.5407 (OUTLIER) cc_final: 0.4407 (pmtt) REVERT: T 20 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8230 (ttpp) REVERT: T 69 ASP cc_start: 0.7870 (t70) cc_final: 0.7346 (t0) REVERT: T 132 ARG cc_start: 0.8402 (mmm160) cc_final: 0.7954 (mtt90) REVERT: T 269 TYR cc_start: 0.9355 (t80) cc_final: 0.9150 (t80) outliers start: 92 outliers final: 60 residues processed: 285 average time/residue: 1.4285 time to fit residues: 473.4632 Evaluate side-chains 285 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 214 time to evaluate : 2.485 ------------------------------------------------------------------------------- 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 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 C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain J residue 5 PHE Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 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 253 VAL 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 17 LEU Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 239 ILE Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 257 THR 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 169 VAL Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain T residue 273 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 20.0000 chunk 119 optimal weight: 0.0170 chunk 89 optimal weight: 10.0000 chunk 131 optimal weight: 20.0000 chunk 28 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 248 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- 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 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 12 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 = 0.4176 r_free = 0.4176 target = 0.172223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105595 restraints weight = 37688.899| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.73 r_work: 0.3112 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 29610 Z= 0.211 Angle : 0.602 9.427 42241 Z= 0.323 Chirality : 0.039 0.188 4965 Planarity : 0.004 0.070 3477 Dihedral : 27.040 179.718 9399 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.43 % Allowed : 28.78 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2108 helix: 1.31 (0.15), residues: 1145 sheet: 0.63 (0.39), residues: 184 loop : -0.68 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.007 0.001 HIS A 268 PHE 0.018 0.002 PHE K 92 TYR 0.019 0.002 TYR A 260 ARG 0.013 0.001 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.04682 ( 1322) hydrogen bonds : angle 3.70684 ( 3406) covalent geometry : bond 0.00483 (29609) covalent geometry : angle 0.60231 (42241) Misc. bond : bond 0.00091 ( 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 295 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 210 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.7832 (mm-30) REVERT: A 62 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7357 (pmm) REVERT: A 250 GLN cc_start: 0.8617 (mm-40) cc_final: 0.7584 (tp-100) REVERT: A 293 SER cc_start: 0.8643 (m) cc_final: 0.8416 (t) REVERT: C 199 ILE cc_start: 0.5601 (tt) cc_final: 0.5262 (tt) REVERT: C 241 ARG cc_start: 0.6531 (mmt-90) cc_final: 0.6325 (mpt90) REVERT: B 116 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8978 (tp) REVERT: J 172 LYS cc_start: 0.8891 (ptpp) cc_final: 0.8445 (mppt) REVERT: K 55 LYS cc_start: 0.6033 (OUTLIER) cc_final: 0.5023 (ttpp) REVERT: K 114 PHE cc_start: 0.7423 (m-80) cc_final: 0.7107 (m-80) REVERT: K 231 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.5665 (tptp) REVERT: K 234 ILE cc_start: 0.7863 (mm) cc_final: 0.7580 (mp) REVERT: K 278 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7655 (pp) REVERT: K 285 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8386 (mm) REVERT: L 5 PHE cc_start: 0.6468 (OUTLIER) cc_final: 0.6066 (t80) REVERT: L 223 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: P 268 HIS cc_start: 0.6321 (t-170) cc_final: 0.5765 (t-170) REVERT: P 274 LYS cc_start: 0.5384 (OUTLIER) cc_final: 0.4638 (pmtt) REVERT: T 20 LYS cc_start: 0.8621 (mtpp) cc_final: 0.8108 (ttpp) REVERT: T 69 ASP cc_start: 0.7840 (t70) cc_final: 0.7336 (t0) REVERT: T 132 ARG cc_start: 0.8396 (mmm160) cc_final: 0.7965 (mtt90) REVERT: T 269 TYR cc_start: 0.9368 (t80) cc_final: 0.9163 (t80) outliers start: 85 outliers final: 61 residues processed: 279 average time/residue: 1.3820 time to fit residues: 452.6140 Evaluate side-chains 273 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 202 time to evaluate : 2.240 ------------------------------------------------------------------------------- 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 62 MET 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 C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL 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 300 ILE 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 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 156 SER Chi-restraints excluded: chain J residue 215 SER Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain J residue 262 VAL Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 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 253 VAL 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 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 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 198 ASP Chi-restraints excluded: chain P residue 219 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 36 optimal weight: 9.9990 chunk 144 optimal weight: 0.0370 chunk 77 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 84 optimal weight: 0.0980 chunk 153 optimal weight: 0.0020 chunk 166 optimal weight: 10.0000 chunk 223 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 overall best weight: 0.3466 ------------------------------------------------------------------------------- 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 ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4218 r_free = 0.4218 target = 0.175979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.111066 restraints weight = 38318.245| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.74 r_work: 0.3179 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29610 Z= 0.126 Angle : 0.551 9.169 42241 Z= 0.298 Chirality : 0.035 0.190 4965 Planarity : 0.004 0.069 3477 Dihedral : 26.936 179.774 9399 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.28 % Allowed : 29.82 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 2108 helix: 1.61 (0.16), residues: 1139 sheet: 0.84 (0.40), residues: 184 loop : -0.59 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 78 HIS 0.007 0.001 HIS A 268 PHE 0.016 0.001 PHE P 92 TYR 0.016 0.001 TYR L 218 ARG 0.012 0.000 ARG L 246 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 1322) hydrogen bonds : angle 3.51774 ( 3406) covalent geometry : bond 0.00267 (29609) covalent geometry : angle 0.55113 (42241) Misc. bond : bond 0.00149 ( 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 280 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.7802 (mm-30) REVERT: A 62 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7134 (pmm) REVERT: A 250 GLN cc_start: 0.8635 (mm-40) cc_final: 0.7623 (tp-100) REVERT: A 257 ARG cc_start: 0.7420 (ttp80) cc_final: 0.7137 (ttt-90) REVERT: A 293 SER cc_start: 0.8576 (m) cc_final: 0.8339 (t) REVERT: C 241 ARG cc_start: 0.6501 (mmt-90) cc_final: 0.6227 (mpt180) REVERT: B 116 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8976 (tp) REVERT: B 233 CYS cc_start: 0.7272 (m) cc_final: 0.6114 (p) REVERT: J 99 GLU cc_start: 0.8765 (pt0) cc_final: 0.8300 (pm20) REVERT: K 114 PHE cc_start: 0.7365 (m-80) cc_final: 0.7036 (m-80) REVERT: K 119 ASP cc_start: 0.8834 (m-30) cc_final: 0.8403 (m-30) REVERT: K 206 MET cc_start: 0.8082 (tpp) cc_final: 0.7673 (tpp) REVERT: K 231 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.5589 (tptp) REVERT: K 234 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7298 (mp) REVERT: K 278 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7698 (pp) REVERT: L 5 PHE cc_start: 0.6272 (OUTLIER) cc_final: 0.5906 (t80) REVERT: L 223 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: L 261 GLN cc_start: 0.8296 (tt0) cc_final: 0.7584 (tt0) REVERT: P 23 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8676 (mm) REVERT: P 54 GLU cc_start: 0.5817 (tp30) cc_final: 0.4862 (tm-30) REVERT: P 261 LYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5500 (mmtm) REVERT: P 268 HIS cc_start: 0.6164 (t-170) cc_final: 0.5794 (t-170) REVERT: P 269 HIS cc_start: 0.5849 (m-70) cc_final: 0.5584 (m90) REVERT: P 274 LYS cc_start: 0.5275 (OUTLIER) cc_final: 0.4576 (pmtt) REVERT: T 20 LYS cc_start: 0.8718 (mtpp) cc_final: 0.8205 (ttpp) REVERT: T 24 ARG cc_start: 0.8488 (mmt90) cc_final: 0.8067 (mpt90) REVERT: T 69 ASP cc_start: 0.7757 (t70) cc_final: 0.7268 (t0) REVERT: T 132 ARG cc_start: 0.8390 (mmm160) cc_final: 0.8040 (mtt90) outliers start: 63 outliers final: 39 residues processed: 265 average time/residue: 1.4367 time to fit residues: 441.9292 Evaluate side-chains 264 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 214 time to evaluate : 2.428 ------------------------------------------------------------------------------- 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 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 C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL 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 235 SER Chi-restraints excluded: chain B residue 306 LEU 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 262 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 53 VAL 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 225 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 253 VAL 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 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 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain P residue 23 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 17 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 251 optimal weight: 0.7980 chunk 88 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.175449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.108472 restraints weight = 38199.415| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.89 r_work: 0.3143 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2781 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= 0.137 Angle : 0.554 8.138 42241 Z= 0.298 Chirality : 0.036 0.187 4965 Planarity : 0.004 0.065 3477 Dihedral : 26.877 179.236 9394 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.71 % Allowed : 30.50 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.19), residues: 2108 helix: 1.66 (0.16), residues: 1140 sheet: 0.91 (0.39), residues: 192 loop : -0.54 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 78 HIS 0.005 0.001 HIS T 78 PHE 0.016 0.001 PHE P 92 TYR 0.042 0.001 TYR K 302 ARG 0.016 0.001 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 1322) hydrogen bonds : angle 3.50633 ( 3406) covalent geometry : bond 0.00302 (29609) covalent geometry : angle 0.55361 (42241) Misc. bond : bond 0.00140 ( 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 272 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 220 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.7752 (mm-30) REVERT: A 62 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7160 (pmm) REVERT: A 250 GLN cc_start: 0.8658 (mm-40) cc_final: 0.7634 (tp-100) REVERT: A 293 SER cc_start: 0.8593 (m) cc_final: 0.8356 (t) REVERT: C 204 ARG cc_start: 0.7688 (mmm-85) cc_final: 0.7458 (tpp80) REVERT: B 116 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8949 (tp) REVERT: J 1 MET cc_start: 0.3249 (mmt) cc_final: 0.2989 (mpm) REVERT: J 172 LYS cc_start: 0.8789 (ptpp) cc_final: 0.8279 (mppt) REVERT: K 114 PHE cc_start: 0.7335 (m-80) cc_final: 0.7010 (m-80) REVERT: K 231 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.5615 (tptp) REVERT: K 234 ILE cc_start: 0.7501 (OUTLIER) cc_final: 0.7172 (mp) REVERT: K 278 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7733 (pp) REVERT: K 294 LYS cc_start: 0.6994 (mmpt) cc_final: 0.6759 (mmmt) REVERT: L 5 PHE cc_start: 0.6289 (OUTLIER) cc_final: 0.5874 (t80) REVERT: L 223 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: L 261 GLN cc_start: 0.8214 (tt0) cc_final: 0.7537 (tt0) REVERT: P 54 GLU cc_start: 0.5834 (tp30) cc_final: 0.4911 (tm-30) REVERT: P 261 LYS cc_start: 0.6054 (OUTLIER) cc_final: 0.5419 (mmtp) REVERT: P 268 HIS cc_start: 0.6253 (t-170) cc_final: 0.5796 (t-170) REVERT: P 274 LYS cc_start: 0.5307 (OUTLIER) cc_final: 0.4496 (pmtt) REVERT: T 20 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8176 (ttpp) REVERT: T 69 ASP cc_start: 0.7729 (t70) cc_final: 0.7213 (t0) REVERT: T 114 GLU cc_start: 0.8429 (tt0) cc_final: 0.8038 (tm-30) REVERT: T 132 ARG cc_start: 0.8418 (mmm160) cc_final: 0.7977 (mtt90) outliers start: 52 outliers final: 37 residues processed: 261 average time/residue: 1.3768 time to fit residues: 420.1285 Evaluate side-chains 258 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 2.455 ------------------------------------------------------------------------------- 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 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 C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL 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 235 SER Chi-restraints excluded: chain B residue 306 LEU 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 262 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 53 VAL 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 231 LYS Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain K residue 253 VAL 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 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 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 234 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 219 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN C 11 GLN C 255 GLN ** J 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4195 r_free = 0.4195 target = 0.173811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107236 restraints weight = 37967.444| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.71 r_work: 0.3140 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2827 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= 0.174 Angle : 0.573 10.107 42241 Z= 0.309 Chirality : 0.037 0.184 4965 Planarity : 0.004 0.071 3477 Dihedral : 26.878 179.824 9394 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.02 % Allowed : 30.29 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.18), residues: 2108 helix: 1.47 (0.15), residues: 1141 sheet: 0.79 (0.40), residues: 184 loop : -0.62 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 78 HIS 0.009 0.001 HIS A 268 PHE 0.019 0.001 PHE P 92 TYR 0.033 0.002 TYR K 302 ARG 0.011 0.001 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 1322) hydrogen bonds : angle 3.59314 ( 3406) covalent geometry : bond 0.00397 (29609) covalent geometry : angle 0.57270 (42241) Misc. bond : bond 0.00101 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28998.46 seconds wall clock time: 501 minutes 27.71 seconds (30087.71 seconds total)