Starting phenix.real_space_refine on Sun May 25 18:44:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jm0_61595/05_2025/9jm0_61595.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jm0_61595/05_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_61595/05_2025/9jm0_61595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jm0_61595/05_2025/9jm0_61595.map" model { file = "/net/cci-nas-00/data/ceres_data/9jm0_61595/05_2025/9jm0_61595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jm0_61595/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 14.77, per 1000 atoms: 0.53 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: 6.34 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: 12.49 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: 12.37 Time building geometry restraints manager: 7.62 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.930 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 67.050 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.630 ------------------------------------------------------------------------------- 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 : 2.535 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: 1.5689 time to fit residues: 562.9351 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 : 2.278 ------------------------------------------------------------------------------- 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 = 38090.676| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.81 r_work: 0.3155 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 2.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8909 (mp0) REVERT: A 62 MET cc_start: 0.7705 (pmm) cc_final: 0.7186 (tpp) REVERT: A 168 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8837 (tptm) REVERT: A 250 GLN cc_start: 0.8644 (mm-40) cc_final: 0.7643 (tp-100) REVERT: C 250 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: B 45 ASP cc_start: 0.8632 (m-30) cc_final: 0.8400 (m-30) REVERT: B 207 LYS cc_start: 0.8217 (tmmt) cc_final: 0.7940 (pttt) REVERT: B 308 LYS cc_start: 0.7515 (mmmm) cc_final: 0.7140 (mtmm) REVERT: J 172 LYS cc_start: 0.8830 (ptpp) cc_final: 0.8424 (mppt) REVERT: J 173 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7252 (mp) REVERT: K 45 ASP cc_start: 0.8828 (m-30) cc_final: 0.8597 (m-30) REVERT: K 55 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.4861 (ttpp) REVERT: K 114 PHE cc_start: 0.7328 (m-80) cc_final: 0.6962 (m-80) REVERT: K 206 MET cc_start: 0.8238 (tpp) cc_final: 0.7915 (tpp) REVERT: K 207 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7966 (tmmt) REVERT: K 278 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7650 (pp) REVERT: K 285 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8227 (mm) REVERT: K 301 THR cc_start: 0.8033 (m) cc_final: 0.7808 (p) REVERT: L 5 PHE cc_start: 0.6179 (OUTLIER) cc_final: 0.5718 (t80) REVERT: L 223 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: P 54 GLU cc_start: 0.5186 (tp30) cc_final: 0.4294 (tm-30) REVERT: P 306 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5596 (mt) REVERT: T 20 LYS cc_start: 0.8605 (mtpp) cc_final: 0.8145 (ttpp) REVERT: T 24 ARG cc_start: 0.8457 (mmt90) cc_final: 0.8147 (mpt90) REVERT: T 69 ASP cc_start: 0.7668 (t70) cc_final: 0.7149 (t0) REVERT: T 81 LEU cc_start: 0.3918 (OUTLIER) cc_final: 0.3661 (pt) REVERT: T 114 GLU cc_start: 0.8592 (tt0) cc_final: 0.8245 (tm-30) REVERT: T 132 ARG cc_start: 0.8424 (mmm160) cc_final: 0.7949 (mpt-90) REVERT: T 190 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7480 (m110) REVERT: T 306 HIS cc_start: 0.5956 (t-170) cc_final: 0.5474 (t-170) outliers start: 94 outliers final: 32 residues processed: 294 average time/residue: 1.4731 time to fit residues: 500.6498 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 : 2.384 ------------------------------------------------------------------------------- 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: 0.0470 chunk 158 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 249 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 245 optimal weight: 0.0970 chunk 224 optimal weight: 0.4980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 GLN C 11 GLN C 255 GLN J 51 GLN K 76 GLN L 11 GLN L 12 GLN ** 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 = 0.4251 r_free = 0.4251 target = 0.178998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.112970 restraints weight = 38560.663| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.75 r_work: 0.3231 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1653 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= 0.125 Angle : 0.554 9.723 42241 Z= 0.298 Chirality : 0.036 0.233 4965 Planarity : 0.003 0.047 3477 Dihedral : 27.192 179.945 9409 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.06 % Allowed : 27.06 % Favored : 67.88 % 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: 1.19 (0.19), residues: 2108 helix: 1.63 (0.16), residues: 1139 sheet: 1.14 (0.38), residues: 192 loop : -0.53 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 78 HIS 0.007 0.001 HIS A 268 PHE 0.016 0.001 PHE B 92 TYR 0.018 0.001 TYR K 302 ARG 0.010 0.001 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 1322) hydrogen bonds : angle 3.54725 ( 3406) covalent geometry : bond 0.00261 (29609) covalent geometry : angle 0.55431 (42241) Misc. bond : bond 0.00150 ( 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: 97 poor density : 237 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8808 (mp0) REVERT: A 250 GLN cc_start: 0.8630 (mm-40) cc_final: 0.7646 (tp-100) REVERT: A 268 HIS cc_start: 0.6515 (t-170) cc_final: 0.6274 (t-170) REVERT: C 268 SER cc_start: 0.8135 (m) cc_final: 0.7869 (p) REVERT: B 28 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8643 (mppt) REVERT: B 45 ASP cc_start: 0.8618 (m-30) cc_final: 0.8382 (m-30) REVERT: B 207 LYS cc_start: 0.8132 (tmmt) cc_final: 0.7869 (pttm) REVERT: B 308 LYS cc_start: 0.7639 (mmmm) cc_final: 0.7307 (mtmm) REVERT: J 1 MET cc_start: 0.3149 (OUTLIER) cc_final: 0.2941 (mpm) REVERT: J 8 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8090 (tp30) REVERT: J 172 LYS cc_start: 0.8761 (ptpp) cc_final: 0.8297 (mppt) REVERT: J 173 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6739 (mp) REVERT: K 200 THR cc_start: 0.8323 (m) cc_final: 0.8088 (m) REVERT: K 206 MET cc_start: 0.8229 (tpp) cc_final: 0.7846 (tpp) REVERT: K 207 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7970 (tmmt) REVERT: K 278 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7611 (pp) REVERT: K 285 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8279 (mm) REVERT: L 5 PHE cc_start: 0.6308 (OUTLIER) cc_final: 0.5999 (t80) REVERT: L 223 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: P 54 GLU cc_start: 0.5026 (tp30) cc_final: 0.4221 (tm-30) REVERT: P 62 MET cc_start: 0.6637 (mmp) cc_final: 0.6409 (ptp) REVERT: T 20 LYS cc_start: 0.8719 (mtpp) cc_final: 0.8237 (ttpp) REVERT: T 24 ARG cc_start: 0.8434 (mmt90) cc_final: 0.8127 (mpt90) REVERT: T 69 ASP cc_start: 0.7461 (t70) cc_final: 0.7032 (t0) REVERT: T 114 GLU cc_start: 0.8514 (tt0) cc_final: 0.8257 (tm-30) REVERT: T 132 ARG cc_start: 0.8375 (mmm160) cc_final: 0.7982 (mpt-90) REVERT: T 306 HIS cc_start: 0.5833 (t-170) cc_final: 0.5240 (t-170) outliers start: 97 outliers final: 33 residues processed: 309 average time/residue: 1.3869 time to fit residues: 499.3316 Evaluate side-chains 248 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 206 time to evaluate : 2.604 ------------------------------------------------------------------------------- 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 116 LEU Chi-restraints excluded: chain A residue 271 PHE 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 205 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 8 GLU Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 130 SER Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain K residue 53 VAL 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 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 241 ARG Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 31 THR 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: 4.9990 chunk 69 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 ** L 12 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 = 0.4183 r_free = 0.4183 target = 0.172443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.105248 restraints weight = 37998.787| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.80 r_work: 0.3081 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 29610 Z= 0.277 Angle : 0.647 8.768 42241 Z= 0.346 Chirality : 0.041 0.202 4965 Planarity : 0.005 0.071 3477 Dihedral : 27.266 179.841 9398 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 6.47 % Allowed : 26.64 % 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: 0.78 (0.18), residues: 2108 helix: 1.24 (0.15), residues: 1134 sheet: 1.17 (0.38), residues: 176 loop : -0.63 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.017 0.001 HIS P 268 PHE 0.023 0.002 PHE B 92 TYR 0.017 0.002 TYR B 179 ARG 0.011 0.001 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.05289 ( 1322) hydrogen bonds : angle 3.83409 ( 3406) covalent geometry : bond 0.00637 (29609) covalent geometry : angle 0.64706 (42241) Misc. bond : bond 0.00065 ( 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 337 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 213 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8010 (mm-30) REVERT: A 249 SER cc_start: 0.8366 (t) cc_final: 0.7921 (p) REVERT: A 250 GLN cc_start: 0.8616 (mm-40) cc_final: 0.7577 (tp-100) REVERT: A 297 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7580 (mtp180) REVERT: B 116 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8953 (tp) REVERT: B 207 LYS cc_start: 0.8243 (tmmt) cc_final: 0.8002 (pttt) REVERT: B 308 LYS cc_start: 0.7650 (mmmm) cc_final: 0.7309 (mtmm) REVERT: J 8 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8190 (tp30) REVERT: J 172 LYS cc_start: 0.8852 (ptpp) cc_final: 0.8342 (mppt) REVERT: J 173 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7127 (mp) REVERT: K 55 LYS cc_start: 0.5984 (OUTLIER) cc_final: 0.4979 (ttpp) REVERT: K 114 PHE cc_start: 0.7441 (m-80) cc_final: 0.7230 (m-80) REVERT: K 206 MET cc_start: 0.8189 (tpp) cc_final: 0.7820 (tpp) REVERT: K 207 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7922 (tmmt) REVERT: K 213 ARG cc_start: 0.7839 (tmm160) cc_final: 0.7189 (tmm-80) REVERT: K 217 PHE cc_start: 0.8891 (m-80) cc_final: 0.8655 (m-80) REVERT: K 226 VAL cc_start: 0.9318 (OUTLIER) cc_final: 0.9096 (m) REVERT: K 278 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7701 (pp) REVERT: K 285 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8329 (mm) REVERT: L 5 PHE cc_start: 0.6396 (OUTLIER) cc_final: 0.5867 (t80) REVERT: L 12 GLN cc_start: 0.7861 (pt0) cc_final: 0.7206 (pm20) REVERT: L 223 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: P 139 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8780 (mp) REVERT: T 20 LYS cc_start: 0.8650 (mtpp) cc_final: 0.8186 (ttpp) REVERT: T 69 ASP cc_start: 0.7942 (t70) cc_final: 0.7397 (t0) REVERT: T 114 GLU cc_start: 0.8524 (tt0) cc_final: 0.8183 (tm-30) REVERT: T 132 ARG cc_start: 0.8436 (mmm160) cc_final: 0.8019 (mtt90) REVERT: T 255 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8444 (tt0) REVERT: T 306 HIS cc_start: 0.6016 (t-90) cc_final: 0.5705 (t-170) outliers start: 124 outliers final: 61 residues processed: 301 average time/residue: 1.2660 time to fit residues: 448.6514 Evaluate side-chains 284 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 209 time to evaluate : 2.503 ------------------------------------------------------------------------------- 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 219 ILE Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 122 ASP 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 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 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 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 226 VAL Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain K residue 285 LEU Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 244 VAL Chi-restraints excluded: chain P residue 9 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 139 LEU Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 281 VAL 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 167 ILE Chi-restraints excluded: chain T residue 168 ASP Chi-restraints excluded: chain T residue 220 THR Chi-restraints excluded: chain T residue 229 ILE Chi-restraints excluded: chain T residue 234 VAL Chi-restraints excluded: chain T residue 253 ILE Chi-restraints excluded: chain T residue 255 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 17 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 184 optimal weight: 1.9990 chunk 173 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN C 11 GLN C 255 GLN L 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.173348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106696 restraints weight = 37746.252| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.71 r_work: 0.3129 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29610 Z= 0.186 Angle : 0.586 8.988 42241 Z= 0.317 Chirality : 0.038 0.199 4965 Planarity : 0.004 0.067 3477 Dihedral : 27.195 179.555 9398 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 5.47 % Allowed : 27.32 % Favored : 67.21 % 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: 0.88 (0.18), residues: 2108 helix: 1.36 (0.15), residues: 1130 sheet: 1.17 (0.38), residues: 176 loop : -0.62 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 78 HIS 0.006 0.001 HIS A 268 PHE 0.020 0.002 PHE B 92 TYR 0.014 0.001 TYR A 260 ARG 0.013 0.001 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.04625 ( 1322) hydrogen bonds : angle 3.70243 ( 3406) covalent geometry : bond 0.00419 (29609) covalent geometry : angle 0.58638 (42241) Misc. bond : bond 0.00098 ( 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 326 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 221 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: A 250 GLN cc_start: 0.8651 (mm-40) cc_final: 0.7606 (tp-100) REVERT: A 302 TYR cc_start: 0.7033 (t80) cc_final: 0.6826 (t80) REVERT: B 116 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8963 (tp) REVERT: B 308 LYS cc_start: 0.7579 (mmmm) cc_final: 0.7257 (mtmm) REVERT: J 172 LYS cc_start: 0.8901 (ptpp) cc_final: 0.8504 (ptpp) REVERT: K 55 LYS cc_start: 0.5930 (OUTLIER) cc_final: 0.4966 (ttpp) REVERT: K 206 MET cc_start: 0.8176 (tpp) cc_final: 0.7812 (tpp) REVERT: K 207 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7923 (tmmt) REVERT: K 213 ARG cc_start: 0.7855 (tmm160) cc_final: 0.7203 (tmm-80) REVERT: K 278 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7650 (pp) REVERT: K 285 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8378 (mm) REVERT: K 294 LYS cc_start: 0.7191 (mmmt) cc_final: 0.6967 (mmmt) REVERT: K 297 ARG cc_start: 0.7447 (ptp-110) cc_final: 0.7104 (ptm-80) REVERT: L 5 PHE cc_start: 0.6343 (OUTLIER) cc_final: 0.5873 (t80) REVERT: L 12 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7137 (pm20) REVERT: L 223 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: P 54 GLU cc_start: 0.5864 (tp30) cc_final: 0.4940 (tm-30) REVERT: T 20 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8179 (ttpp) REVERT: T 69 ASP cc_start: 0.7868 (t70) cc_final: 0.7361 (t0) REVERT: T 114 GLU cc_start: 0.8446 (tt0) cc_final: 0.8154 (tm-30) REVERT: T 132 ARG cc_start: 0.8420 (mmm160) cc_final: 0.8089 (mtt90) outliers start: 105 outliers final: 65 residues processed: 295 average time/residue: 1.3623 time to fit residues: 468.0224 Evaluate side-chains 282 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 208 time to evaluate : 2.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 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 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 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 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 12 GLN Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 121 GLU Chi-restraints excluded: chain P residue 198 ASP Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 281 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 57 SER Chi-restraints excluded: chain T residue 148 SER Chi-restraints excluded: chain T residue 162 MET Chi-restraints excluded: chain T residue 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 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: 0.8980 chunk 66 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 216 optimal weight: 20.0000 chunk 27 optimal weight: 0.0670 chunk 68 optimal weight: 0.8980 overall best weight: 0.7718 ------------------------------------------------------------------------------- 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 L 288 ASN L 306 HIS P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.175604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108879 restraints weight = 38210.081| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.74 r_work: 0.3170 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2235 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= 0.134 Angle : 0.555 8.952 42241 Z= 0.300 Chirality : 0.036 0.200 4965 Planarity : 0.004 0.055 3477 Dihedral : 27.092 179.446 9398 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.94 % Favored : 96.02 % Rotamer: Outliers : 4.01 % Allowed : 28.68 % Favored : 67.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.18), residues: 2108 helix: 1.59 (0.16), residues: 1135 sheet: 1.32 (0.38), residues: 176 loop : -0.66 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 78 HIS 0.008 0.001 HIS A 268 PHE 0.016 0.001 PHE B 92 TYR 0.015 0.001 TYR C 260 ARG 0.010 0.000 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 1322) hydrogen bonds : angle 3.56095 ( 3406) covalent geometry : bond 0.00289 (29609) covalent geometry : angle 0.55533 (42241) Misc. bond : bond 0.00138 ( 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 300 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 223 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.7723 (mm-30) REVERT: A 151 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8632 (mmtm) REVERT: A 250 GLN cc_start: 0.8664 (mm-40) cc_final: 0.7565 (tp-100) REVERT: A 257 ARG cc_start: 0.7412 (OUTLIER) cc_final: 0.7194 (ttt-90) REVERT: A 302 TYR cc_start: 0.7007 (t80) cc_final: 0.6743 (t80) REVERT: B 71 GLU cc_start: 0.8705 (mp0) cc_final: 0.8442 (mp0) REVERT: B 116 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8956 (tp) REVERT: J 99 GLU cc_start: 0.8779 (pt0) cc_final: 0.8363 (pm20) REVERT: K 213 ARG cc_start: 0.7824 (tmm160) cc_final: 0.7217 (tmm-80) REVERT: K 278 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7658 (pp) REVERT: L 5 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.5990 (t80) REVERT: L 12 GLN cc_start: 0.7874 (pt0) cc_final: 0.7424 (pm20) REVERT: L 13 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7106 (tt) REVERT: L 223 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7539 (mp0) REVERT: P 54 GLU cc_start: 0.5783 (tp30) cc_final: 0.4889 (tm-30) REVERT: P 268 HIS cc_start: 0.6196 (t-170) cc_final: 0.5870 (t-170) REVERT: T 20 LYS cc_start: 0.8721 (mtpp) cc_final: 0.8225 (ttpp) REVERT: T 24 ARG cc_start: 0.8459 (mmt90) cc_final: 0.8108 (mpt90) REVERT: T 69 ASP cc_start: 0.7745 (t70) cc_final: 0.7251 (t0) REVERT: T 114 GLU cc_start: 0.8411 (tt0) cc_final: 0.8097 (tm-30) REVERT: T 132 ARG cc_start: 0.8355 (mmm160) cc_final: 0.8036 (mtt90) outliers start: 77 outliers final: 42 residues processed: 278 average time/residue: 1.3284 time to fit residues: 432.4285 Evaluate side-chains 262 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 212 time to evaluate : 2.308 ------------------------------------------------------------------------------- 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 151 LYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain 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 233 CYS Chi-restraints excluded: chain J residue 5 PHE 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 216 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 72 LEU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain L residue 5 PHE Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 17 LEU Chi-restraints excluded: chain L residue 216 VAL Chi-restraints excluded: chain L residue 223 GLU Chi-restraints excluded: chain L residue 241 ARG Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 121 GLU Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain 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: 5.9990 chunk 48 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 144 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 179 optimal weight: 30.0000 chunk 69 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 ** J 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4190 r_free = 0.4190 target = 0.173265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.107139 restraints weight = 37758.870| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.77 r_work: 0.3121 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 29610 Z= 0.191 Angle : 0.586 9.208 42241 Z= 0.315 Chirality : 0.038 0.194 4965 Planarity : 0.004 0.063 3477 Dihedral : 27.069 179.550 9394 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.01 % Allowed : 28.10 % 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: 1.01 (0.18), residues: 2108 helix: 1.49 (0.16), residues: 1132 sheet: 1.23 (0.38), residues: 176 loop : -0.61 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 78 HIS 0.007 0.001 HIS A 268 PHE 0.018 0.002 PHE P 92 TYR 0.017 0.001 TYR J 218 ARG 0.013 0.000 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 1322) hydrogen bonds : angle 3.65055 ( 3406) covalent geometry : bond 0.00433 (29609) covalent geometry : angle 0.58574 (42241) Misc. bond : bond 0.00094 ( 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 312 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 216 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: A 62 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7130 (pmm) REVERT: A 249 SER cc_start: 0.8215 (t) cc_final: 0.7751 (p) REVERT: A 250 GLN cc_start: 0.8712 (mm-40) cc_final: 0.7556 (tp-100) REVERT: A 257 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7252 (ttp80) REVERT: A 293 SER cc_start: 0.8694 (m) cc_final: 0.8459 (t) REVERT: A 302 TYR cc_start: 0.7091 (t80) cc_final: 0.6773 (t80) REVERT: B 116 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.8950 (tp) REVERT: J 99 GLU cc_start: 0.8817 (pt0) cc_final: 0.8384 (pm20) REVERT: J 171 ARG cc_start: 0.6756 (mpt180) cc_final: 0.6274 (mtm-85) REVERT: K 55 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.4992 (ttpp) REVERT: K 234 ILE cc_start: 0.7857 (mm) cc_final: 0.7507 (mp) REVERT: K 278 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7709 (pp) REVERT: K 294 LYS cc_start: 0.7527 (tppt) cc_final: 0.7289 (mmmt) REVERT: L 5 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.5923 (t80) REVERT: L 12 GLN cc_start: 0.7892 (pt0) cc_final: 0.7206 (pm20) REVERT: L 223 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: P 261 LYS cc_start: 0.6207 (OUTLIER) cc_final: 0.5493 (mmtt) REVERT: P 268 HIS cc_start: 0.6269 (t-170) cc_final: 0.5883 (t-170) REVERT: P 269 HIS cc_start: 0.5818 (m170) cc_final: 0.5583 (m90) REVERT: P 274 LYS cc_start: 0.5334 (OUTLIER) cc_final: 0.4375 (pmtt) REVERT: T 20 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8235 (ttpp) REVERT: T 69 ASP cc_start: 0.7864 (t70) cc_final: 0.7336 (t0) REVERT: T 114 GLU cc_start: 0.8458 (tt0) cc_final: 0.8128 (tm-30) REVERT: T 132 ARG cc_start: 0.8402 (mmm160) cc_final: 0.7951 (mtt90) outliers start: 96 outliers final: 57 residues processed: 285 average time/residue: 1.3470 time to fit residues: 448.2360 Evaluate side-chains 276 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 209 time to evaluate : 2.371 ------------------------------------------------------------------------------- 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 219 ILE Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 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 207 LYS Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 235 SER 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 26 MET Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 60 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain 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 241 ARG Chi-restraints excluded: chain L residue 257 THR Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain P residue 92 PHE Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 121 GLU Chi-restraints excluded: chain P residue 219 ILE Chi-restraints excluded: chain P residue 261 LYS Chi-restraints excluded: chain P residue 274 LYS Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 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: 0.0670 chunk 89 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 248 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 overall best weight: 1.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN C 11 GLN C 255 GLN L 288 ASN L 306 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.175101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108020 restraints weight = 38079.458| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.82 r_work: 0.3139 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2455 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= 0.140 Angle : 0.561 9.276 42241 Z= 0.302 Chirality : 0.036 0.194 4965 Planarity : 0.004 0.051 3477 Dihedral : 27.015 179.318 9394 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.17 % Allowed : 28.73 % 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: 1.10 (0.18), residues: 2108 helix: 1.61 (0.16), residues: 1133 sheet: 1.32 (0.39), residues: 176 loop : -0.67 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP P 78 HIS 0.006 0.001 HIS A 268 PHE 0.017 0.001 PHE K 114 TYR 0.015 0.001 TYR A 260 ARG 0.011 0.000 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 1322) hydrogen bonds : angle 3.57813 ( 3406) covalent geometry : bond 0.00307 (29609) covalent geometry : angle 0.56123 (42241) Misc. bond : bond 0.00128 ( 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: 80 poor density : 215 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.7726 (mm-30) REVERT: A 250 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8263 (mm-40) REVERT: A 257 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.7124 (ttp80) REVERT: A 293 SER cc_start: 0.8649 (m) cc_final: 0.8421 (t) REVERT: A 302 TYR cc_start: 0.6859 (t80) cc_final: 0.6487 (t80) REVERT: B 116 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8962 (tp) REVERT: J 99 GLU cc_start: 0.8812 (pt0) cc_final: 0.8322 (pm20) REVERT: K 206 MET cc_start: 0.7460 (tpp) cc_final: 0.6906 (tmm) REVERT: K 234 ILE cc_start: 0.7764 (mm) cc_final: 0.7429 (mp) REVERT: K 278 ILE cc_start: 0.7927 (OUTLIER) cc_final: 0.7637 (pp) REVERT: L 5 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.6086 (t80) REVERT: L 12 GLN cc_start: 0.7738 (pt0) cc_final: 0.7056 (pm20) REVERT: L 223 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: L 261 GLN cc_start: 0.8225 (tt0) cc_final: 0.7525 (tt0) REVERT: P 54 GLU cc_start: 0.5899 (tp30) cc_final: 0.5069 (tm-30) REVERT: P 261 LYS cc_start: 0.6109 (OUTLIER) cc_final: 0.5513 (mmtm) REVERT: P 268 HIS cc_start: 0.6127 (t-170) cc_final: 0.5765 (t-170) REVERT: P 274 LYS cc_start: 0.5346 (OUTLIER) cc_final: 0.4624 (pmtt) REVERT: T 20 LYS cc_start: 0.8745 (mtpp) cc_final: 0.8222 (ttpp) REVERT: T 69 ASP cc_start: 0.7791 (t70) cc_final: 0.7262 (t0) REVERT: T 132 ARG cc_start: 0.8398 (mmm160) cc_final: 0.8001 (mtt90) outliers start: 80 outliers final: 53 residues processed: 276 average time/residue: 1.4128 time to fit residues: 456.9487 Evaluate side-chains 270 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 2.174 ------------------------------------------------------------------------------- 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 219 ILE Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 207 LYS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 169 VAL Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 216 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 60 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 113 ASN Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 233 CYS Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain 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 L residue 241 ARG 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 36 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 77 optimal weight: 0.3980 chunk 199 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 153 optimal weight: 0.0030 chunk 166 optimal weight: 20.0000 chunk 223 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 GLN C 11 GLN C 255 GLN L 288 ASN L 306 HIS ** P 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 = 0.4225 r_free = 0.4225 target = 0.176528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.111483 restraints weight = 38318.290| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.76 r_work: 0.3183 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2613 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= 0.128 Angle : 0.557 10.005 42241 Z= 0.299 Chirality : 0.036 0.191 4965 Planarity : 0.004 0.051 3477 Dihedral : 26.927 179.076 9394 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.39 % Allowed : 29.67 % 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: 1.23 (0.19), residues: 2108 helix: 1.70 (0.16), residues: 1135 sheet: 1.44 (0.39), residues: 176 loop : -0.61 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 78 HIS 0.008 0.001 HIS A 268 PHE 0.015 0.001 PHE P 92 TYR 0.044 0.001 TYR K 302 ARG 0.017 0.001 ARG K 297 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 1322) hydrogen bonds : angle 3.49604 ( 3406) covalent geometry : bond 0.00276 (29609) covalent geometry : angle 0.55701 (42241) Misc. bond : bond 0.00139 ( 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 286 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 221 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.7711 (mm-30) REVERT: A 62 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7014 (pmm) REVERT: A 151 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8634 (mmtm) REVERT: A 257 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6915 (ttt-90) REVERT: A 264 ARG cc_start: 0.7726 (ptm-80) cc_final: 0.7504 (ptm-80) REVERT: A 293 SER cc_start: 0.8596 (m) cc_final: 0.8385 (t) REVERT: A 302 TYR cc_start: 0.6992 (t80) cc_final: 0.6625 (t80) REVERT: B 116 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8973 (tp) REVERT: J 1 MET cc_start: 0.3258 (mmt) cc_final: 0.3015 (mpm) REVERT: J 99 GLU cc_start: 0.8770 (pt0) cc_final: 0.8288 (pm20) REVERT: K 206 MET cc_start: 0.7383 (tpp) cc_final: 0.6578 (tpp) REVERT: K 234 ILE cc_start: 0.7574 (mm) cc_final: 0.7246 (mp) REVERT: K 278 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7719 (pp) REVERT: L 5 PHE cc_start: 0.6502 (OUTLIER) cc_final: 0.6197 (t80) REVERT: L 12 GLN cc_start: 0.7759 (pt0) cc_final: 0.7062 (pm20) REVERT: L 223 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: L 261 GLN cc_start: 0.8224 (tt0) cc_final: 0.7585 (tt0) REVERT: P 261 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5570 (mmtm) REVERT: P 268 HIS cc_start: 0.6086 (t-170) cc_final: 0.5836 (t-170) REVERT: T 20 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8167 (ttpp) REVERT: T 24 ARG cc_start: 0.8510 (mmt90) cc_final: 0.8062 (mpt90) REVERT: T 69 ASP cc_start: 0.7766 (t70) cc_final: 0.7264 (t0) REVERT: T 132 ARG cc_start: 0.8347 (mmm160) cc_final: 0.8010 (mtt90) REVERT: T 306 HIS cc_start: 0.6021 (t-90) cc_final: 0.5712 (t-170) outliers start: 65 outliers final: 42 residues processed: 272 average time/residue: 1.3795 time to fit residues: 436.9660 Evaluate side-chains 265 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 214 time to evaluate : 2.472 ------------------------------------------------------------------------------- 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 97 GLU Chi-restraints excluded: chain A residue 151 LYS Chi-restraints excluded: chain A residue 257 ARG Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain 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 233 CYS 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 213 LEU Chi-restraints excluded: chain J residue 216 VAL Chi-restraints excluded: chain K residue 34 VAL Chi-restraints excluded: chain K residue 53 VAL 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 233 CYS Chi-restraints excluded: chain K residue 253 VAL Chi-restraints excluded: chain K residue 257 ARG Chi-restraints excluded: chain K residue 278 ILE Chi-restraints excluded: chain 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 L residue 241 ARG 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 281 VAL Chi-restraints excluded: chain T residue 5 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 17 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 0.0870 chunk 251 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 250 GLN C 10 GLN C 11 GLN L 288 ASN L 306 HIS P 269 HIS ** T 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.174559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.107048 restraints weight = 38006.394| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.87 r_work: 0.3129 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2656 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= 0.167 Angle : 0.577 11.395 42241 Z= 0.309 Chirality : 0.037 0.186 4965 Planarity : 0.004 0.053 3477 Dihedral : 26.906 179.477 9394 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.13 % Allowed : 29.77 % 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: 1.02 (0.19), residues: 2108 helix: 1.54 (0.16), residues: 1136 sheet: 0.93 (0.40), residues: 184 loop : -0.63 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 78 HIS 0.005 0.001 HIS B 280 PHE 0.020 0.001 PHE P 92 TYR 0.032 0.001 TYR K 302 ARG 0.011 0.001 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 1322) hydrogen bonds : angle 3.57870 ( 3406) covalent geometry : bond 0.00377 (29609) covalent geometry : angle 0.57690 (42241) Misc. bond : bond 0.00110 ( 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 276 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 216 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.7766 (mm-30) REVERT: A 62 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7107 (pmm) REVERT: A 257 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.6995 (ttp80) REVERT: A 302 TYR cc_start: 0.6932 (t80) cc_final: 0.6558 (t80) REVERT: B 116 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8951 (tp) REVERT: J 99 GLU cc_start: 0.8815 (pt0) cc_final: 0.8317 (pm20) REVERT: K 206 MET cc_start: 0.7390 (tpp) cc_final: 0.6628 (tpp) REVERT: K 234 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7342 (mp) REVERT: K 278 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7721 (pp) REVERT: L 5 PHE cc_start: 0.6357 (OUTLIER) cc_final: 0.6020 (t80) REVERT: L 12 GLN cc_start: 0.7736 (pt0) cc_final: 0.7036 (pm20) REVERT: L 223 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: L 261 GLN cc_start: 0.8168 (tt0) cc_final: 0.7493 (tt0) REVERT: P 261 LYS cc_start: 0.6271 (OUTLIER) cc_final: 0.5488 (mmtp) REVERT: P 268 HIS cc_start: 0.6286 (t-170) cc_final: 0.5923 (t-170) REVERT: P 269 HIS cc_start: 0.5488 (m170) cc_final: 0.5178 (m90) REVERT: P 274 LYS cc_start: 0.5364 (OUTLIER) cc_final: 0.4615 (pmtt) REVERT: T 20 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8184 (ttpp) REVERT: T 69 ASP cc_start: 0.7840 (t70) cc_final: 0.7284 (t0) REVERT: T 132 ARG cc_start: 0.8369 (mmm160) cc_final: 0.7958 (mtt90) REVERT: T 306 HIS cc_start: 0.5985 (t-90) cc_final: 0.5764 (t-170) outliers start: 60 outliers final: 45 residues processed: 261 average time/residue: 1.3737 time to fit residues: 417.2155 Evaluate side-chains 264 residues out of total 1918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 2.289 ------------------------------------------------------------------------------- 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 257 ARG Chi-restraints excluded: chain C residue 5 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain B residue 69 SER Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 150 SER Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 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 60 LYS Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 116 LEU 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 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 L residue 241 ARG 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 5 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 35 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 9 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 236 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 219 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 101 optimal weight: 0.0170 chunk 84 optimal weight: 9.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 ** K 204 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 = 0.4215 r_free = 0.4215 target = 0.175691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108789 restraints weight = 38239.368| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.83 r_work: 0.3151 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29610 Z= 0.131 Angle : 0.566 13.189 42241 Z= 0.302 Chirality : 0.036 0.187 4965 Planarity : 0.004 0.053 3477 Dihedral : 26.892 178.984 9394 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.02 % Allowed : 29.87 % 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: 1.12 (0.19), residues: 2108 helix: 1.66 (0.16), residues: 1127 sheet: 0.98 (0.40), residues: 184 loop : -0.62 (0.22), residues: 797 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 0.022 0.001 PHE K 114 TYR 0.034 0.001 TYR K 302 ARG 0.011 0.001 ARG K 257 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 1322) hydrogen bonds : angle 3.54147 ( 3406) covalent geometry : bond 0.00286 (29609) covalent geometry : angle 0.56610 (42241) Misc. bond : bond 0.00137 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26208.98 seconds wall clock time: 451 minutes 35.47 seconds (27095.47 seconds total)