Starting phenix.real_space_refine on Wed Feb 12 08:20:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c9c_30311/02_2025/7c9c_30311.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c9c_30311/02_2025/7c9c_30311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7c9c_30311/02_2025/7c9c_30311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c9c_30311/02_2025/7c9c_30311.map" model { file = "/net/cci-nas-00/data/ceres_data/7c9c_30311/02_2025/7c9c_30311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c9c_30311/02_2025/7c9c_30311.cif" } resolution = 3.33 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= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 P 18 5.49 5 S 33 5.16 5 C 4656 2.51 5 N 1293 2.21 5 O 1449 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7452 Number of models: 1 Model: "" Number of chains: 7 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 180 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2392 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.52, per 1000 atoms: 0.74 Number of scatterers: 7452 At special positions: 0 Unit cell: (72.24, 113.4, 112.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 33 16.00 P 18 15.00 O 1449 8.00 N 1293 7.00 C 4656 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1686 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 12 sheets defined 46.5% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 removed outlier: 4.096A pdb=" N LEU A 26 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 27 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 28 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS A 29 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY A 31 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.730A pdb=" N LYS A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.861A pdb=" N ILE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 47 through 52' Processing helix chain 'A' and resid 56 through 64 removed outlier: 4.242A pdb=" N VAL A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.713A pdb=" N GLU A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 97 removed outlier: 4.059A pdb=" N MET A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 94 through 97' Processing helix chain 'A' and resid 105 through 113 removed outlier: 3.574A pdb=" N ASP A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 111 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 143 removed outlier: 3.609A pdb=" N CYS A 140 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.829A pdb=" N GLY A 150 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 175 removed outlier: 4.020A pdb=" N ASP A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 186 removed outlier: 3.722A pdb=" N VAL A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 213 removed outlier: 4.152A pdb=" N LEU A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP A 204 " --> pdb=" O MET A 200 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 207 " --> pdb=" O LEU A 203 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 3.680A pdb=" N PHE A 233 " --> pdb=" O PHE A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 260 removed outlier: 3.571A pdb=" N ALA A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 258 " --> pdb=" O GLN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.504A pdb=" N ALA A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 31 removed outlier: 4.094A pdb=" N LEU B 26 " --> pdb=" O ASP B 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 27 " --> pdb=" O ILE B 24 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 28 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS B 29 " --> pdb=" O LEU B 26 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY B 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.730A pdb=" N LYS B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 removed outlier: 3.860A pdb=" N ILE B 51 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 47 through 52' Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.711A pdb=" N GLU B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 97 removed outlier: 4.059A pdb=" N MET B 97 " --> pdb=" O LYS B 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 94 through 97' Processing helix chain 'B' and resid 105 through 113 removed outlier: 3.574A pdb=" N ASP B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 143 removed outlier: 3.609A pdb=" N CYS B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.828A pdb=" N GLY B 150 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 175 removed outlier: 4.020A pdb=" N ASP B 172 " --> pdb=" O ASP B 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 186 removed outlier: 3.722A pdb=" N VAL B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 213 removed outlier: 4.153A pdb=" N LEU B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP B 204 " --> pdb=" O MET B 200 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR B 205 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 207 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU B 213 " --> pdb=" O LYS B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 removed outlier: 3.679A pdb=" N PHE B 233 " --> pdb=" O PHE B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 260 removed outlier: 3.570A pdb=" N ALA B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET B 249 " --> pdb=" O LYS B 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 removed outlier: 3.504A pdb=" N ALA B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 31 removed outlier: 4.094A pdb=" N LEU C 26 " --> pdb=" O ASP C 23 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 27 " --> pdb=" O ILE C 24 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 28 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS C 29 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 31 " --> pdb=" O GLN C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.730A pdb=" N LYS C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 removed outlier: 3.860A pdb=" N ILE C 51 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN C 52 " --> pdb=" O ILE C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 47 through 52' Processing helix chain 'C' and resid 56 through 64 removed outlier: 4.242A pdb=" N VAL C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 77 Processing helix chain 'C' and resid 88 through 93 removed outlier: 3.714A pdb=" N GLU C 93 " --> pdb=" O PHE C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 97 removed outlier: 4.059A pdb=" N MET C 97 " --> pdb=" O LYS C 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 94 through 97' Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.575A pdb=" N ASP C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 112 " --> pdb=" O PHE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 143 removed outlier: 3.608A pdb=" N CYS C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.828A pdb=" N GLY C 150 " --> pdb=" O GLY C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 175 removed outlier: 4.020A pdb=" N ASP C 172 " --> pdb=" O ASP C 168 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 186 removed outlier: 3.721A pdb=" N VAL C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 removed outlier: 4.152A pdb=" N LEU C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP C 204 " --> pdb=" O MET C 200 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 207 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.681A pdb=" N PHE C 233 " --> pdb=" O PHE C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 260 removed outlier: 3.570A pdb=" N ALA C 247 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET C 249 " --> pdb=" O LYS C 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 297 removed outlier: 3.504A pdb=" N ALA C 294 " --> pdb=" O GLY C 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 101 Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.521A pdb=" N ALA A 313 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN A 268 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 126 " --> pdb=" O ASN A 268 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR A 267 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS A 155 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE A 221 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 157 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE A 156 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ALA A 191 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE A 158 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 272 Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 331 removed outlier: 3.546A pdb=" N GLY A 334 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'B' and resid 325 through 327 removed outlier: 3.520A pdb=" N ALA B 313 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN B 268 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 126 " --> pdb=" O ASN B 268 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 267 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS B 155 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE B 221 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 157 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA B 191 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE B 158 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 270 through 272 Processing sheet with id=AA8, first strand: chain 'B' and resid 330 through 331 removed outlier: 3.545A pdb=" N GLY B 334 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AB1, first strand: chain 'C' and resid 188 through 192 removed outlier: 6.629A pdb=" N ILE C 156 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA C 191 " --> pdb=" O ILE C 156 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE C 158 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LYS C 155 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE C 221 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 157 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 267 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN C 268 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 126 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 313 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 270 through 272 Processing sheet with id=AB3, first strand: chain 'C' and resid 330 through 331 removed outlier: 3.547A pdb=" N GLY C 334 " --> pdb=" O THR C 331 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 2.16 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: 1654 1.33 - 1.45: 1544 1.45 - 1.57: 4302 1.57 - 1.69: 26 1.69 - 1.81: 57 Bond restraints: 7583 Sorted by residual: bond pdb=" O3A ANP A 402 " pdb=" PB ANP A 402 " ideal model delta sigma weight residual 1.700 1.544 0.156 2.00e-02 2.50e+03 6.11e+01 bond pdb=" O3A ANP B 402 " pdb=" PB ANP B 402 " ideal model delta sigma weight residual 1.700 1.544 0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" O3A ANP C 402 " pdb=" PB ANP C 402 " ideal model delta sigma weight residual 1.700 1.545 0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 1.795 1.682 0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 1.795 1.682 0.113 2.00e-02 2.50e+03 3.20e+01 ... (remaining 7578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 10152 3.84 - 7.68: 83 7.68 - 11.52: 12 11.52 - 15.36: 0 15.36 - 19.20: 3 Bond angle restraints: 10250 Sorted by residual: angle pdb=" PB ANP C 402 " pdb=" N3B ANP C 402 " pdb=" PG ANP C 402 " ideal model delta sigma weight residual 126.95 107.75 19.20 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PB ANP A 402 " pdb=" N3B ANP A 402 " pdb=" PG ANP A 402 " ideal model delta sigma weight residual 126.95 107.76 19.19 3.00e+00 1.11e-01 4.09e+01 angle pdb=" PB ANP B 402 " pdb=" N3B ANP B 402 " pdb=" PG ANP B 402 " ideal model delta sigma weight residual 126.95 107.77 19.18 3.00e+00 1.11e-01 4.09e+01 angle pdb=" C LYS A 79 " pdb=" N LEU A 80 " pdb=" CA LEU A 80 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 angle pdb=" C LYS B 79 " pdb=" N LEU B 80 " pdb=" CA LEU B 80 " ideal model delta sigma weight residual 121.54 128.57 -7.03 1.91e+00 2.74e-01 1.35e+01 ... (remaining 10245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.10: 4251 26.10 - 52.20: 270 52.20 - 78.30: 72 78.30 - 104.40: 21 104.40 - 130.50: 3 Dihedral angle restraints: 4617 sinusoidal: 1992 harmonic: 2625 Sorted by residual: dihedral pdb=" CA GLU A 82 " pdb=" C GLU A 82 " pdb=" N PRO A 83 " pdb=" CA PRO A 83 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA GLU C 82 " pdb=" C GLU C 82 " pdb=" N PRO C 83 " pdb=" CA PRO C 83 " ideal model delta harmonic sigma weight residual 180.00 153.83 26.17 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA GLU B 82 " pdb=" C GLU B 82 " pdb=" N PRO B 83 " pdb=" CA PRO B 83 " ideal model delta harmonic sigma weight residual 180.00 153.84 26.16 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 4614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 914 0.062 - 0.124: 209 0.124 - 0.186: 25 0.186 - 0.248: 4 0.248 - 0.310: 3 Chirality restraints: 1155 Sorted by residual: chirality pdb=" C3' ANP A 402 " pdb=" C2' ANP A 402 " pdb=" C4' ANP A 402 " pdb=" O3' ANP A 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.67 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C3' ANP C 402 " pdb=" C2' ANP C 402 " pdb=" C4' ANP C 402 " pdb=" O3' ANP C 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C3' ANP B 402 " pdb=" C2' ANP B 402 " pdb=" C4' ANP B 402 " pdb=" O3' ANP B 402 " both_signs ideal model delta sigma weight residual False -2.36 -2.66 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 1152 not shown) Planarity restraints: 1278 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 128 " -0.009 2.00e-02 2.50e+03 1.51e-02 4.00e+00 pdb=" CG PHE B 128 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 128 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 128 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 128 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 128 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 128 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 128 " -0.009 2.00e-02 2.50e+03 1.51e-02 4.00e+00 pdb=" CG PHE C 128 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE C 128 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE C 128 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 128 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 128 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 128 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 128 " 0.008 2.00e-02 2.50e+03 1.49e-02 3.88e+00 pdb=" CG PHE A 128 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 128 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE A 128 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 128 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 128 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 128 " -0.001 2.00e-02 2.50e+03 ... (remaining 1275 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 4 1.97 - 2.70: 235 2.70 - 3.43: 9286 3.43 - 4.17: 16840 4.17 - 4.90: 31357 Nonbonded interactions: 57722 Sorted by model distance: nonbonded pdb=" NH1 ARG C 56 " pdb=" OD1 ASP C 71 " model vdw 1.232 3.120 nonbonded pdb="CA CA B 401 " pdb=" O1G ANP B 402 " model vdw 1.678 2.510 nonbonded pdb="CA CA C 401 " pdb=" O1G ANP C 402 " model vdw 1.763 2.510 nonbonded pdb=" CZ ARG C 56 " pdb=" OD1 ASP C 71 " model vdw 1.789 3.270 nonbonded pdb="CA CA A 401 " pdb=" O1G ANP A 402 " model vdw 1.989 2.510 ... (remaining 57717 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 'C' } 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.440 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 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 : 0.009 0.156 7583 Z= 0.533 Angle : 1.035 19.200 10250 Z= 0.529 Chirality : 0.056 0.310 1155 Planarity : 0.005 0.041 1278 Dihedral : 19.223 130.497 2931 Min Nonbonded Distance : 1.232 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.79 % Allowed : 6.98 % Favored : 92.23 % 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: -5.45 (0.20), residues: 912 helix: -5.12 (0.06), residues: 351 sheet: -1.95 (0.38), residues: 156 loop : -2.68 (0.24), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 181 PHE 0.033 0.003 PHE C 128 TYR 0.014 0.002 TYR A 316 ARG 0.005 0.001 ARG B 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 ASP cc_start: 0.7771 (p0) cc_final: 0.7493 (m-30) REVERT: A 252 ARG cc_start: 0.8046 (tpt-90) cc_final: 0.7747 (ttt90) REVERT: B 41 LYS cc_start: 0.6961 (mttt) cc_final: 0.6394 (mttm) REVERT: B 171 ARG cc_start: 0.7424 (tpt170) cc_final: 0.7139 (mtt90) REVERT: C 36 ASP cc_start: 0.6220 (m-30) cc_final: 0.6009 (m-30) REVERT: C 41 LYS cc_start: 0.6410 (mttt) cc_final: 0.5726 (tptt) REVERT: C 285 LYS cc_start: 0.8990 (mttt) cc_final: 0.8372 (mmmt) outliers start: 6 outliers final: 3 residues processed: 177 average time/residue: 0.2965 time to fit residues: 64.2597 Evaluate side-chains 116 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain C residue 22 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 36 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 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 61 ASN A 78 ASN A 199 GLN A 248 GLN B 61 ASN B 78 ASN B 199 GLN B 295 HIS C 61 ASN C 78 ASN C 187 ASN C 199 GLN C 248 GLN C 295 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.131635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.097705 restraints weight = 8961.782| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.81 r_work: 0.2780 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7583 Z= 0.232 Angle : 0.573 7.488 10250 Z= 0.298 Chirality : 0.043 0.138 1155 Planarity : 0.005 0.074 1278 Dihedral : 15.666 155.367 1184 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.19 % Allowed : 12.78 % Favored : 86.03 % 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: -4.50 (0.23), residues: 912 helix: -3.88 (0.15), residues: 390 sheet: -1.94 (0.36), residues: 189 loop : -2.07 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 181 PHE 0.021 0.002 PHE A 128 TYR 0.010 0.001 TYR C 316 ARG 0.011 0.001 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 168 ASP cc_start: 0.8364 (p0) cc_final: 0.7978 (m-30) REVERT: B 41 LYS cc_start: 0.6596 (mttt) cc_final: 0.5849 (mttm) REVERT: B 325 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8617 (mt-10) REVERT: C 41 LYS cc_start: 0.6088 (mttt) cc_final: 0.5428 (tptt) REVERT: C 285 LYS cc_start: 0.9035 (mttt) cc_final: 0.7964 (mmmt) outliers start: 9 outliers final: 3 residues processed: 118 average time/residue: 0.2197 time to fit residues: 34.3233 Evaluate side-chains 101 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 0.0030 chunk 84 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 ASN C 291 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.133190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.097077 restraints weight = 9149.372| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.00 r_work: 0.2809 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7583 Z= 0.140 Angle : 0.470 6.277 10250 Z= 0.249 Chirality : 0.041 0.155 1155 Planarity : 0.005 0.111 1278 Dihedral : 14.512 157.553 1173 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.45 % Allowed : 12.78 % Favored : 85.77 % 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: -3.71 (0.24), residues: 912 helix: -2.94 (0.20), residues: 405 sheet: -1.60 (0.37), residues: 189 loop : -1.95 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 181 PHE 0.015 0.001 PHE A 128 TYR 0.010 0.001 TYR B 316 ARG 0.014 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.814 Fit side-chains REVERT: A 168 ASP cc_start: 0.8280 (p0) cc_final: 0.8052 (m-30) REVERT: B 41 LYS cc_start: 0.6567 (mttt) cc_final: 0.5819 (mttm) REVERT: B 186 ASP cc_start: 0.8371 (m-30) cc_final: 0.7756 (m-30) REVERT: B 325 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8503 (mt-10) REVERT: C 41 LYS cc_start: 0.6049 (mttt) cc_final: 0.5373 (tptt) REVERT: C 96 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8893 (mttp) REVERT: C 285 LYS cc_start: 0.9045 (mttt) cc_final: 0.7934 (mmmt) outliers start: 11 outliers final: 4 residues processed: 110 average time/residue: 0.2548 time to fit residues: 36.0312 Evaluate side-chains 99 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 65 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 0.0470 chunk 64 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.127541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.091205 restraints weight = 9200.132| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.05 r_work: 0.2711 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7583 Z= 0.278 Angle : 0.551 7.654 10250 Z= 0.286 Chirality : 0.044 0.132 1155 Planarity : 0.007 0.152 1278 Dihedral : 14.937 164.579 1173 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.77 % Allowed : 13.18 % Favored : 84.06 % 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: -3.09 (0.26), residues: 912 helix: -2.25 (0.23), residues: 396 sheet: -1.50 (0.37), residues: 189 loop : -1.78 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 295 PHE 0.017 0.002 PHE A 128 TYR 0.016 0.001 TYR B 316 ARG 0.021 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8766 (tt0) cc_final: 0.8527 (tt0) REVERT: B 41 LYS cc_start: 0.6667 (mttt) cc_final: 0.5883 (mttm) REVERT: B 197 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8240 (mp0) REVERT: B 273 ASP cc_start: 0.8648 (t0) cc_final: 0.8420 (t0) REVERT: B 325 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8613 (mt-10) REVERT: C 36 ASP cc_start: 0.7151 (m-30) cc_final: 0.6823 (m-30) REVERT: C 41 LYS cc_start: 0.6073 (mttt) cc_final: 0.5426 (tptt) outliers start: 21 outliers final: 11 residues processed: 120 average time/residue: 0.2218 time to fit residues: 34.8259 Evaluate side-chains 108 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.130370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.094065 restraints weight = 9130.788| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 2.05 r_work: 0.2745 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7583 Z= 0.166 Angle : 0.470 6.189 10250 Z= 0.247 Chirality : 0.042 0.139 1155 Planarity : 0.007 0.177 1278 Dihedral : 14.778 170.163 1173 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.50 % Allowed : 13.97 % Favored : 83.53 % 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: -2.64 (0.27), residues: 912 helix: -1.77 (0.24), residues: 396 sheet: -1.37 (0.38), residues: 189 loop : -1.62 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 295 PHE 0.015 0.001 PHE A 128 TYR 0.008 0.001 TYR B 316 ARG 0.020 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8692 (tt0) cc_final: 0.8444 (tt0) REVERT: B 41 LYS cc_start: 0.6595 (mttt) cc_final: 0.5812 (mttm) REVERT: B 80 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6977 (mm) REVERT: B 197 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8276 (mp0) REVERT: B 325 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8628 (mt-10) REVERT: C 36 ASP cc_start: 0.7062 (m-30) cc_final: 0.6804 (m-30) REVERT: C 41 LYS cc_start: 0.5987 (mttt) cc_final: 0.5375 (tptt) outliers start: 19 outliers final: 11 residues processed: 114 average time/residue: 0.2189 time to fit residues: 32.9451 Evaluate side-chains 107 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 223 ASP Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 71 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 144 GLN C 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.137125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.103202 restraints weight = 9018.812| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.04 r_work: 0.2784 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 7583 Z= 0.149 Angle : 0.453 5.875 10250 Z= 0.238 Chirality : 0.041 0.132 1155 Planarity : 0.005 0.130 1278 Dihedral : 14.737 179.463 1173 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.98 % Allowed : 14.36 % Favored : 83.66 % 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: -2.28 (0.27), residues: 912 helix: -1.42 (0.25), residues: 399 sheet: -1.21 (0.38), residues: 189 loop : -1.52 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 295 PHE 0.013 0.001 PHE A 128 TYR 0.007 0.001 TYR B 316 ARG 0.013 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8636 (tt0) cc_final: 0.8384 (tt0) REVERT: B 41 LYS cc_start: 0.6576 (mttt) cc_final: 0.5813 (mttm) REVERT: B 325 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8589 (mt-10) REVERT: C 36 ASP cc_start: 0.7054 (m-30) cc_final: 0.6848 (m-30) REVERT: C 41 LYS cc_start: 0.5999 (mttt) cc_final: 0.5398 (tptt) REVERT: C 201 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7305 (tt0) outliers start: 15 outliers final: 7 residues processed: 109 average time/residue: 0.2327 time to fit residues: 32.9943 Evaluate side-chains 100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 0.0050 chunk 84 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 chunk 37 optimal weight: 0.0470 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 0.0980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 overall best weight: 0.2092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 GLN C 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.135413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.099058 restraints weight = 9153.238| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.08 r_work: 0.2821 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.016 7583 Z= 0.090 Angle : 0.420 6.054 10250 Z= 0.219 Chirality : 0.040 0.141 1155 Planarity : 0.004 0.095 1278 Dihedral : 14.081 170.448 1173 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.32 % Allowed : 14.89 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.27), residues: 912 helix: -1.14 (0.25), residues: 405 sheet: -0.75 (0.39), residues: 168 loop : -1.45 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 181 PHE 0.012 0.001 PHE A 128 TYR 0.003 0.000 TYR B 260 ARG 0.011 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8633 (tt0) cc_final: 0.8396 (tt0) REVERT: B 41 LYS cc_start: 0.6573 (mttt) cc_final: 0.5825 (mttm) REVERT: B 168 ASP cc_start: 0.8451 (p0) cc_final: 0.8092 (p0) REVERT: B 325 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8575 (mt-10) REVERT: C 41 LYS cc_start: 0.5900 (mttt) cc_final: 0.5368 (tptt) REVERT: C 201 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7264 (tt0) outliers start: 10 outliers final: 8 residues processed: 117 average time/residue: 0.2136 time to fit residues: 33.3605 Evaluate side-chains 107 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 8 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 51 optimal weight: 0.0970 chunk 14 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN C 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.132033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.099408 restraints weight = 9100.087| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.68 r_work: 0.2840 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7583 Z= 0.143 Angle : 0.444 5.514 10250 Z= 0.232 Chirality : 0.041 0.133 1155 Planarity : 0.004 0.096 1278 Dihedral : 13.943 169.897 1173 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.45 % Allowed : 15.28 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.68 (0.28), residues: 912 helix: -0.91 (0.26), residues: 408 sheet: -0.65 (0.39), residues: 168 loop : -1.38 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 295 PHE 0.011 0.001 PHE A 128 TYR 0.005 0.001 TYR C 316 ARG 0.014 0.001 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 241 GLU cc_start: 0.8741 (tt0) cc_final: 0.8514 (tt0) REVERT: B 41 LYS cc_start: 0.6698 (mttt) cc_final: 0.5915 (mttm) REVERT: B 325 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8562 (mt-10) REVERT: C 41 LYS cc_start: 0.5997 (mttt) cc_final: 0.5469 (tptt) REVERT: C 86 LEU cc_start: 0.8542 (mt) cc_final: 0.8298 (mt) REVERT: C 201 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7297 (tt0) outliers start: 11 outliers final: 9 residues processed: 108 average time/residue: 0.2376 time to fit residues: 33.4233 Evaluate side-chains 106 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 chunk 84 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.125952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.092751 restraints weight = 9254.503| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.70 r_work: 0.2730 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7583 Z= 0.371 Angle : 0.604 7.650 10250 Z= 0.310 Chirality : 0.047 0.137 1155 Planarity : 0.009 0.219 1278 Dihedral : 14.701 165.917 1173 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.58 % Allowed : 15.68 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.98 (0.27), residues: 912 helix: -1.03 (0.26), residues: 411 sheet: -0.78 (0.39), residues: 183 loop : -1.78 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 295 PHE 0.019 0.002 PHE B 125 TYR 0.016 0.001 TYR C 316 ARG 0.033 0.001 ARG C 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.814 Fit side-chains REVERT: A 241 GLU cc_start: 0.8840 (tt0) cc_final: 0.8626 (tt0) REVERT: B 41 LYS cc_start: 0.6776 (mttt) cc_final: 0.5990 (mttm) REVERT: B 56 ARG cc_start: 0.7205 (mtt180) cc_final: 0.6640 (mtp-110) REVERT: B 186 ASP cc_start: 0.8542 (m-30) cc_final: 0.8101 (m-30) REVERT: B 325 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8543 (mt-10) REVERT: C 41 LYS cc_start: 0.6148 (mttt) cc_final: 0.5607 (tptt) REVERT: C 96 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8762 (mttp) REVERT: C 201 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7252 (tt0) outliers start: 12 outliers final: 8 residues processed: 111 average time/residue: 0.2519 time to fit residues: 36.0126 Evaluate side-chains 103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 48 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.133022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.102349 restraints weight = 9131.946| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.75 r_work: 0.2803 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7583 Z= 0.165 Angle : 0.487 7.387 10250 Z= 0.252 Chirality : 0.043 0.151 1155 Planarity : 0.009 0.228 1278 Dihedral : 14.353 170.765 1173 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.45 % Allowed : 16.21 % Favored : 82.35 % 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: -1.70 (0.28), residues: 912 helix: -0.90 (0.26), residues: 414 sheet: -0.85 (0.39), residues: 189 loop : -1.33 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS B 295 PHE 0.015 0.001 PHE A 128 TYR 0.007 0.001 TYR C 316 ARG 0.028 0.001 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.889 Fit side-chains REVERT: A 241 GLU cc_start: 0.8799 (tt0) cc_final: 0.8591 (tt0) REVERT: B 41 LYS cc_start: 0.6806 (mttt) cc_final: 0.5992 (mttm) REVERT: B 186 ASP cc_start: 0.8479 (m-30) cc_final: 0.8088 (m-30) REVERT: B 325 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8540 (mt-10) REVERT: C 41 LYS cc_start: 0.6261 (mttt) cc_final: 0.5735 (tptt) REVERT: C 96 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8751 (mttp) REVERT: C 307 ARG cc_start: 0.8240 (mmt-90) cc_final: 0.7858 (mmm160) outliers start: 11 outliers final: 6 residues processed: 105 average time/residue: 0.2278 time to fit residues: 31.5610 Evaluate side-chains 103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 96 LYS Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 257 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 6 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 67 optimal weight: 0.0040 chunk 82 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.131936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.095651 restraints weight = 9108.132| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.16 r_work: 0.2750 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7583 Z= 0.142 Angle : 0.461 6.447 10250 Z= 0.239 Chirality : 0.042 0.128 1155 Planarity : 0.008 0.210 1278 Dihedral : 14.202 179.399 1173 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.19 % Allowed : 16.07 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.66 (0.28), residues: 912 helix: -0.78 (0.26), residues: 417 sheet: -0.97 (0.38), residues: 195 loop : -1.34 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 295 PHE 0.012 0.001 PHE A 128 TYR 0.006 0.001 TYR C 316 ARG 0.022 0.001 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4022.09 seconds wall clock time: 72 minutes 0.28 seconds (4320.28 seconds total)