Starting phenix.real_space_refine on Wed Sep 17 12:34:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zme_60244/09_2025/8zme_60244_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zme_60244/09_2025/8zme_60244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zme_60244/09_2025/8zme_60244_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zme_60244/09_2025/8zme_60244_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zme_60244/09_2025/8zme_60244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zme_60244/09_2025/8zme_60244.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5556 2.51 5 N 1452 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8687 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1692 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'TRP:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2515 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 5, 'ARG:plan': 5, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "E" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1772 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 369 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2339 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 1.97, per 1000 atoms: 0.23 Number of scatterers: 8687 At special positions: 0 Unit cell: (93.5, 116.6, 145.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1624 8.00 N 1452 7.00 C 5556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.06 Simple disulfide: pdb=" SG CYS R 148 " - pdb=" SG CYS R 226 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 438.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 37.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 10 through 31 removed outlier: 4.097A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.808A pdb=" N SER A 91 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.763A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 removed outlier: 4.130A pdb=" N GLN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.606A pdb=" N ASP A 160 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 206 through 227 removed outlier: 3.808A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.748A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.971A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.719A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.707A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.644A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 62 through 70 removed outlier: 3.606A pdb=" N THR R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 103 removed outlier: 4.219A pdb=" N ILE R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL R 81 " --> pdb=" O PHE R 77 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 108 through 126 removed outlier: 3.641A pdb=" N ILE R 112 " --> pdb=" O HIS R 108 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE R 126 " --> pdb=" O LEU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 138 removed outlier: 4.058A pdb=" N LYS R 131 " --> pdb=" O TRP R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 179 removed outlier: 4.351A pdb=" N LEU R 147 " --> pdb=" O TYR R 143 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS R 148 " --> pdb=" O GLY R 144 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR R 156 " --> pdb=" O ILE R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 204 Processing helix chain 'R' and resid 205 through 210 Proline residue: R 208 - end of helix No H-bonds generated for 'chain 'R' and resid 205 through 210' Processing helix chain 'R' and resid 232 through 236 removed outlier: 3.693A pdb=" N VAL R 236 " --> pdb=" O GLU R 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 232 through 236' Processing helix chain 'R' and resid 237 through 250 removed outlier: 3.553A pdb=" N ASN R 241 " --> pdb=" O GLY R 237 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 270 Processing helix chain 'R' and resid 275 through 277 No H-bonds generated for 'chain 'R' and resid 275 through 277' Processing helix chain 'R' and resid 278 through 315 removed outlier: 4.239A pdb=" N ARG R 284 " --> pdb=" O LYS R 280 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR R 291 " --> pdb=" O LYS R 287 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET R 295 " --> pdb=" O THR R 291 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) Proline residue: R 302 - end of helix removed outlier: 4.036A pdb=" N LEU R 306 " --> pdb=" O PRO R 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU R 313 " --> pdb=" O VAL R 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE R 314 " --> pdb=" O HIS R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 335 removed outlier: 3.801A pdb=" N LEU R 335 " --> pdb=" O CYS R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 345 Proline residue: R 341 - end of helix Processing helix chain 'R' and resid 349 through 358 removed outlier: 3.749A pdb=" N ASP R 353 " --> pdb=" O HIS R 349 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.317A pdb=" N VAL A 34 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL A 84 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 36 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 105 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 139 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N HIS A 198 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 141 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N THR A 200 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 143 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.872A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.864A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.849A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.048A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.612A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.997A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.547A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.330A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 143 Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.614A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 244 " --> pdb=" O TYR E 228 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 38 through 40 removed outlier: 5.981A pdb=" N LEU R 38 " --> pdb=" O LEU R 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'R' and resid 215 through 218 393 hydrogen bonds defined for protein. 1116 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: 1.10 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2794 1.34 - 1.47: 2263 1.47 - 1.59: 3733 1.59 - 1.72: 0 1.72 - 1.84: 80 Bond restraints: 8870 Sorted by residual: bond pdb=" C LYS A 145 " pdb=" O LYS A 145 " ideal model delta sigma weight residual 1.235 1.282 -0.046 1.26e-02 6.30e+03 1.36e+01 bond pdb=" N THR A 146 " pdb=" CA THR A 146 " ideal model delta sigma weight residual 1.457 1.505 -0.047 1.29e-02 6.01e+03 1.35e+01 bond pdb=" CA LYS A 145 " pdb=" C LYS A 145 " ideal model delta sigma weight residual 1.523 1.562 -0.039 1.34e-02 5.57e+03 8.38e+00 bond pdb=" C TYR R 210 " pdb=" N VAL R 211 " ideal model delta sigma weight residual 1.338 1.309 0.029 1.01e-02 9.80e+03 8.08e+00 bond pdb=" N LYS A 145 " pdb=" CA LYS A 145 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.47e+00 ... (remaining 8865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 11816 2.49 - 4.99: 224 4.99 - 7.48: 22 7.48 - 9.97: 6 9.97 - 12.46: 1 Bond angle restraints: 12069 Sorted by residual: angle pdb=" N ILE R 126 " pdb=" CA ILE R 126 " pdb=" C ILE R 126 " ideal model delta sigma weight residual 110.53 116.21 -5.68 9.40e-01 1.13e+00 3.65e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.61 117.49 -6.88 1.25e+00 6.40e-01 3.03e+01 angle pdb=" C HIS R 227 " pdb=" CA HIS R 227 " pdb=" CB HIS R 227 " ideal model delta sigma weight residual 111.06 102.73 8.33 1.89e+00 2.80e-01 1.94e+01 angle pdb=" N GLN A 191 " pdb=" CA GLN A 191 " pdb=" C GLN A 191 " ideal model delta sigma weight residual 107.67 116.49 -8.82 2.09e+00 2.29e-01 1.78e+01 angle pdb=" N ASN A 144 " pdb=" CA ASN A 144 " pdb=" C ASN A 144 " ideal model delta sigma weight residual 109.95 116.59 -6.64 1.59e+00 3.96e-01 1.74e+01 ... (remaining 12064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4863 17.53 - 35.06: 289 35.06 - 52.58: 38 52.58 - 70.11: 14 70.11 - 87.64: 7 Dihedral angle restraints: 5211 sinusoidal: 1886 harmonic: 3325 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 142.72 -49.72 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA VAL R 125 " pdb=" C VAL R 125 " pdb=" N ILE R 126 " pdb=" CA ILE R 126 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual 180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1067 0.057 - 0.114: 293 0.114 - 0.170: 49 0.170 - 0.227: 3 0.227 - 0.284: 1 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA ALA B 203 " pdb=" N ALA B 203 " pdb=" C ALA B 203 " pdb=" CB ALA B 203 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA LYS A 145 " pdb=" N LYS A 145 " pdb=" C LYS A 145 " pdb=" CB LYS A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 1410 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 127 " -0.018 2.00e-02 2.50e+03 1.73e-02 7.45e+00 pdb=" CG TRP R 127 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP R 127 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP R 127 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 127 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 127 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 127 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 127 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 127 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 127 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 155 " 0.021 2.00e-02 2.50e+03 2.02e-02 7.13e+00 pdb=" CG PHE R 155 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE R 155 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE R 155 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE R 155 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 155 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE R 155 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 128 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO R 129 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO R 129 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 129 " -0.034 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 46 2.58 - 3.16: 7016 3.16 - 3.74: 11924 3.74 - 4.32: 16170 4.32 - 4.90: 28204 Nonbonded interactions: 63360 Sorted by model distance: nonbonded pdb=" O LYS A 145 " pdb=" OG1 THR A 201 " model vdw 2.000 3.040 nonbonded pdb=" O ASN G 24 " pdb=" OD1 ASN G 24 " model vdw 2.158 3.040 nonbonded pdb=" OG SER E 17 " pdb=" O MET E 83 " model vdw 2.182 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.225 3.040 nonbonded pdb=" O GLY E 8 " pdb=" NH2 ARG E 18 " model vdw 2.290 3.120 ... (remaining 63355 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 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 : 0.008 0.049 8872 Z= 0.342 Angle : 0.870 12.465 12073 Z= 0.511 Chirality : 0.052 0.284 1413 Planarity : 0.005 0.060 1526 Dihedral : 12.335 87.640 3057 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.24), residues: 1125 helix: 0.52 (0.28), residues: 354 sheet: 0.18 (0.30), residues: 281 loop : -1.62 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 219 TYR 0.025 0.003 TYR R 296 PHE 0.047 0.003 PHE R 155 TRP 0.047 0.003 TRP R 127 HIS 0.007 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00751 ( 8870) covalent geometry : angle 0.86942 (12069) SS BOND : bond 0.01849 ( 2) SS BOND : angle 1.79565 ( 4) hydrogen bonds : bond 0.16351 ( 393) hydrogen bonds : angle 6.72936 ( 1116) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 69 ILE cc_start: 0.8371 (mm) cc_final: 0.8136 (mt) REVERT: B 29 THR cc_start: 0.8219 (t) cc_final: 0.7818 (p) REVERT: B 271 CYS cc_start: 0.7314 (m) cc_final: 0.7108 (m) REVERT: E 90 ASP cc_start: 0.8657 (m-30) cc_final: 0.8158 (m-30) REVERT: R 73 LEU cc_start: 0.7448 (mt) cc_final: 0.7194 (mt) REVERT: R 277 ASN cc_start: 0.7777 (m-40) cc_final: 0.7493 (m110) REVERT: R 291 THR cc_start: 0.7824 (t) cc_final: 0.7596 (p) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.1045 time to fit residues: 25.3517 Evaluate side-chains 164 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.0570 chunk 106 optimal weight: 0.0980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.140985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.115779 restraints weight = 12894.251| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.96 r_work: 0.3370 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8872 Z= 0.133 Angle : 0.595 8.664 12073 Z= 0.321 Chirality : 0.044 0.140 1413 Planarity : 0.004 0.062 1526 Dihedral : 4.860 24.698 1221 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.11 % Favored : 96.80 % Rotamer: Outliers : 0.98 % Allowed : 6.43 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.25), residues: 1125 helix: 1.49 (0.28), residues: 370 sheet: 0.42 (0.31), residues: 272 loop : -1.54 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.026 0.002 TYR R 296 PHE 0.017 0.002 PHE R 155 TRP 0.027 0.001 TRP R 127 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8870) covalent geometry : angle 0.59474 (12069) SS BOND : bond 0.01098 ( 2) SS BOND : angle 1.08789 ( 4) hydrogen bonds : bond 0.05979 ( 393) hydrogen bonds : angle 4.64244 ( 1116) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7768 (ttmm) REVERT: A 116 ASN cc_start: 0.8841 (m-40) cc_final: 0.8491 (m-40) REVERT: B 271 CYS cc_start: 0.7586 (m) cc_final: 0.7200 (m) REVERT: E 90 ASP cc_start: 0.8734 (m-30) cc_final: 0.8164 (m-30) REVERT: E 141 MET cc_start: 0.8727 (mmt) cc_final: 0.8411 (mmm) REVERT: E 234 LEU cc_start: 0.8342 (tp) cc_final: 0.8103 (tp) REVERT: R 73 LEU cc_start: 0.7471 (mt) cc_final: 0.7221 (mt) REVERT: R 176 VAL cc_start: 0.7080 (t) cc_final: 0.6755 (t) outliers start: 9 outliers final: 7 residues processed: 171 average time/residue: 0.1061 time to fit residues: 24.1042 Evaluate side-chains 167 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain R residue 216 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 103 optimal weight: 0.0980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN E 184 GLN R 172 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.139972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.114344 restraints weight = 12803.539| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.01 r_work: 0.3354 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8872 Z= 0.140 Angle : 0.585 12.597 12073 Z= 0.313 Chirality : 0.044 0.149 1413 Planarity : 0.004 0.062 1526 Dihedral : 4.726 25.023 1221 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 2.07 % Allowed : 9.15 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1125 helix: 1.83 (0.28), residues: 369 sheet: 0.48 (0.30), residues: 285 loop : -1.52 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 219 TYR 0.025 0.002 TYR R 296 PHE 0.018 0.002 PHE B 199 TRP 0.016 0.001 TRP R 127 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8870) covalent geometry : angle 0.58505 (12069) SS BOND : bond 0.01099 ( 2) SS BOND : angle 0.77980 ( 4) hydrogen bonds : bond 0.05983 ( 393) hydrogen bonds : angle 4.42253 ( 1116) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7776 (ttmm) REVERT: A 116 ASN cc_start: 0.8934 (m-40) cc_final: 0.8665 (m-40) REVERT: B 271 CYS cc_start: 0.7666 (m) cc_final: 0.7422 (m) REVERT: E 90 ASP cc_start: 0.8810 (m-30) cc_final: 0.8245 (m-30) REVERT: E 220 LEU cc_start: 0.7767 (mm) cc_final: 0.7490 (mp) REVERT: E 231 MET cc_start: 0.6986 (ttm) cc_final: 0.6744 (ttm) REVERT: E 234 LEU cc_start: 0.8348 (tp) cc_final: 0.8128 (tp) REVERT: R 73 LEU cc_start: 0.7466 (mt) cc_final: 0.7235 (mt) REVERT: R 176 VAL cc_start: 0.7062 (t) cc_final: 0.6723 (t) outliers start: 19 outliers final: 14 residues processed: 168 average time/residue: 0.1116 time to fit residues: 24.8575 Evaluate side-chains 172 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain R residue 63 GLU Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 274 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 0.0010 chunk 26 optimal weight: 2.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.113102 restraints weight = 12924.950| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.97 r_work: 0.3325 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8872 Z= 0.166 Angle : 0.609 10.235 12073 Z= 0.324 Chirality : 0.044 0.137 1413 Planarity : 0.004 0.064 1526 Dihedral : 4.761 26.188 1221 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 2.40 % Allowed : 10.46 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.25), residues: 1125 helix: 1.87 (0.28), residues: 369 sheet: 0.47 (0.32), residues: 262 loop : -1.47 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.029 0.002 TYR R 296 PHE 0.023 0.002 PHE R 155 TRP 0.012 0.002 TRP B 82 HIS 0.004 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8870) covalent geometry : angle 0.60940 (12069) SS BOND : bond 0.01280 ( 2) SS BOND : angle 0.82566 ( 4) hydrogen bonds : bond 0.06297 ( 393) hydrogen bonds : angle 4.38959 ( 1116) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6994 (tttp) REVERT: A 82 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7777 (ttmm) REVERT: A 116 ASN cc_start: 0.8956 (m-40) cc_final: 0.8716 (m-40) REVERT: B 271 CYS cc_start: 0.7735 (m) cc_final: 0.7473 (m) REVERT: E 90 ASP cc_start: 0.8796 (m-30) cc_final: 0.8284 (m-30) REVERT: E 220 LEU cc_start: 0.7712 (mm) cc_final: 0.7468 (mp) REVERT: E 231 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7333 (ttt) REVERT: E 234 LEU cc_start: 0.8412 (tp) cc_final: 0.8171 (tp) REVERT: R 73 LEU cc_start: 0.7455 (mt) cc_final: 0.7196 (mt) outliers start: 22 outliers final: 16 residues processed: 173 average time/residue: 0.1117 time to fit residues: 25.7970 Evaluate side-chains 178 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 69 optimal weight: 0.0770 chunk 72 optimal weight: 0.0670 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.139595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114181 restraints weight = 12923.974| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.99 r_work: 0.3302 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8872 Z= 0.133 Angle : 0.565 9.243 12073 Z= 0.302 Chirality : 0.043 0.136 1413 Planarity : 0.004 0.063 1526 Dihedral : 4.602 26.345 1221 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 2.07 % Allowed : 12.42 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.25), residues: 1125 helix: 2.07 (0.28), residues: 370 sheet: 0.54 (0.32), residues: 260 loop : -1.46 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.023 0.002 TYR R 296 PHE 0.018 0.002 PHE R 155 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8870) covalent geometry : angle 0.56448 (12069) SS BOND : bond 0.01115 ( 2) SS BOND : angle 0.72024 ( 4) hydrogen bonds : bond 0.05560 ( 393) hydrogen bonds : angle 4.19084 ( 1116) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6943 (tttp) REVERT: A 82 LYS cc_start: 0.8224 (ttmm) cc_final: 0.7781 (ttmm) REVERT: A 116 ASN cc_start: 0.8979 (m-40) cc_final: 0.8753 (m-40) REVERT: B 271 CYS cc_start: 0.7727 (m) cc_final: 0.7441 (m) REVERT: B 298 ASP cc_start: 0.7824 (t0) cc_final: 0.7606 (t0) REVERT: E 90 ASP cc_start: 0.8773 (m-30) cc_final: 0.8175 (m-30) REVERT: E 234 LEU cc_start: 0.8350 (tp) cc_final: 0.8124 (tp) REVERT: R 73 LEU cc_start: 0.7406 (mt) cc_final: 0.7135 (mt) REVERT: R 268 MET cc_start: 0.7598 (tmm) cc_final: 0.7162 (tmm) outliers start: 19 outliers final: 15 residues processed: 171 average time/residue: 0.0963 time to fit residues: 22.8299 Evaluate side-chains 180 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 0.0870 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN R 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.140475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.115636 restraints weight = 12819.320| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.90 r_work: 0.3372 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8872 Z= 0.135 Angle : 0.564 9.698 12073 Z= 0.300 Chirality : 0.043 0.136 1413 Planarity : 0.004 0.064 1526 Dihedral : 4.533 26.016 1221 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 1.96 % Allowed : 13.51 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.25), residues: 1125 helix: 2.20 (0.28), residues: 370 sheet: 0.66 (0.31), residues: 272 loop : -1.42 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.024 0.002 TYR R 296 PHE 0.018 0.002 PHE R 155 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8870) covalent geometry : angle 0.56404 (12069) SS BOND : bond 0.01037 ( 2) SS BOND : angle 0.66248 ( 4) hydrogen bonds : bond 0.05539 ( 393) hydrogen bonds : angle 4.13367 ( 1116) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7438 (ttmm) cc_final: 0.7092 (tttp) REVERT: A 82 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7787 (ttmm) REVERT: A 116 ASN cc_start: 0.9013 (m-40) cc_final: 0.8791 (m-40) REVERT: B 200 VAL cc_start: 0.8125 (m) cc_final: 0.7778 (p) REVERT: B 271 CYS cc_start: 0.7738 (m) cc_final: 0.7474 (m) REVERT: E 90 ASP cc_start: 0.8770 (m-30) cc_final: 0.8204 (m-30) REVERT: E 234 LEU cc_start: 0.8407 (tp) cc_final: 0.8193 (tp) REVERT: R 73 LEU cc_start: 0.7366 (mt) cc_final: 0.7132 (mt) REVERT: R 269 LEU cc_start: 0.7539 (mt) cc_final: 0.7282 (mp) outliers start: 18 outliers final: 14 residues processed: 172 average time/residue: 0.0932 time to fit residues: 21.8833 Evaluate side-chains 179 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 81 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.141108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.116011 restraints weight = 12936.986| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.97 r_work: 0.3369 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8872 Z= 0.124 Angle : 0.546 8.157 12073 Z= 0.293 Chirality : 0.042 0.136 1413 Planarity : 0.004 0.063 1526 Dihedral : 4.450 25.539 1221 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.18 % Allowed : 13.62 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.25), residues: 1125 helix: 2.30 (0.28), residues: 370 sheet: 0.69 (0.31), residues: 272 loop : -1.40 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 137 TYR 0.022 0.001 TYR R 296 PHE 0.016 0.001 PHE B 199 TRP 0.010 0.001 TRP B 169 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 8870) covalent geometry : angle 0.54568 (12069) SS BOND : bond 0.00999 ( 2) SS BOND : angle 0.64421 ( 4) hydrogen bonds : bond 0.05262 ( 393) hydrogen bonds : angle 4.07668 ( 1116) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7322 (ttmm) cc_final: 0.7004 (tttp) REVERT: A 82 LYS cc_start: 0.8232 (ttmm) cc_final: 0.7768 (ttmm) REVERT: A 116 ASN cc_start: 0.9004 (m-40) cc_final: 0.8789 (m-40) REVERT: B 200 VAL cc_start: 0.8127 (m) cc_final: 0.7805 (p) REVERT: B 271 CYS cc_start: 0.7670 (m) cc_final: 0.7380 (m) REVERT: E 90 ASP cc_start: 0.8763 (m-30) cc_final: 0.8175 (m-30) REVERT: E 234 LEU cc_start: 0.8379 (tp) cc_final: 0.8160 (tp) REVERT: R 73 LEU cc_start: 0.7341 (mt) cc_final: 0.7103 (mt) REVERT: R 269 LEU cc_start: 0.7484 (mt) cc_final: 0.7214 (mp) outliers start: 20 outliers final: 18 residues processed: 168 average time/residue: 0.0960 time to fit residues: 22.2506 Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 170 SER Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 0.0000 chunk 87 optimal weight: 0.6980 overall best weight: 0.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN R 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.141289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.116815 restraints weight = 12786.210| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.79 r_work: 0.3397 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8872 Z= 0.120 Angle : 0.545 7.629 12073 Z= 0.291 Chirality : 0.042 0.138 1413 Planarity : 0.004 0.063 1526 Dihedral : 4.410 25.143 1221 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.07 % Allowed : 14.27 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.25), residues: 1125 helix: 2.39 (0.28), residues: 370 sheet: 0.71 (0.31), residues: 277 loop : -1.35 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.021 0.001 TYR R 296 PHE 0.021 0.001 PHE E 68 TRP 0.009 0.001 TRP B 82 HIS 0.003 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8870) covalent geometry : angle 0.54529 (12069) SS BOND : bond 0.00984 ( 2) SS BOND : angle 0.63929 ( 4) hydrogen bonds : bond 0.05105 ( 393) hydrogen bonds : angle 4.04644 ( 1116) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7357 (ttmm) cc_final: 0.7018 (tttp) REVERT: A 82 LYS cc_start: 0.8209 (ttmm) cc_final: 0.7754 (ttmm) REVERT: B 200 VAL cc_start: 0.8110 (m) cc_final: 0.7790 (p) REVERT: B 271 CYS cc_start: 0.7642 (m) cc_final: 0.7368 (m) REVERT: E 90 ASP cc_start: 0.8733 (m-30) cc_final: 0.8159 (m-30) REVERT: E 220 LEU cc_start: 0.7435 (mp) cc_final: 0.7215 (mp) REVERT: E 234 LEU cc_start: 0.8401 (tp) cc_final: 0.8181 (tp) REVERT: R 73 LEU cc_start: 0.7325 (mt) cc_final: 0.7100 (mt) REVERT: R 269 LEU cc_start: 0.7489 (mt) cc_final: 0.7226 (mp) outliers start: 19 outliers final: 18 residues processed: 164 average time/residue: 0.0975 time to fit residues: 22.0575 Evaluate side-chains 175 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 170 SER Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 0.0010 chunk 84 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.116893 restraints weight = 12790.641| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 2.81 r_work: 0.3350 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8872 Z= 0.113 Angle : 0.534 7.363 12073 Z= 0.286 Chirality : 0.042 0.138 1413 Planarity : 0.004 0.063 1526 Dihedral : 4.324 24.800 1221 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.18 % Allowed : 14.16 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.26), residues: 1125 helix: 2.45 (0.28), residues: 370 sheet: 0.73 (0.31), residues: 282 loop : -1.33 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.019 0.001 TYR R 296 PHE 0.015 0.001 PHE B 199 TRP 0.009 0.001 TRP B 169 HIS 0.002 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8870) covalent geometry : angle 0.53422 (12069) SS BOND : bond 0.00934 ( 2) SS BOND : angle 0.62511 ( 4) hydrogen bonds : bond 0.04866 ( 393) hydrogen bonds : angle 3.99711 ( 1116) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7056 (ttmm) cc_final: 0.6742 (tttp) REVERT: A 82 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7697 (ttmm) REVERT: B 200 VAL cc_start: 0.7987 (m) cc_final: 0.7667 (p) REVERT: B 271 CYS cc_start: 0.7676 (m) cc_final: 0.7334 (m) REVERT: E 90 ASP cc_start: 0.8724 (m-30) cc_final: 0.8067 (m-30) REVERT: E 234 LEU cc_start: 0.8284 (tp) cc_final: 0.8075 (tp) REVERT: R 73 LEU cc_start: 0.7263 (mt) cc_final: 0.7031 (mt) REVERT: R 269 LEU cc_start: 0.7193 (mt) cc_final: 0.6919 (mp) REVERT: R 274 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.6821 (mtm) outliers start: 20 outliers final: 18 residues processed: 165 average time/residue: 0.0946 time to fit residues: 21.4608 Evaluate side-chains 178 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 170 SER Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 70 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 108 optimal weight: 0.0170 chunk 105 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN E 180 GLN E 184 GLN E 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.118846 restraints weight = 12915.819| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.96 r_work: 0.3408 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8872 Z= 0.100 Angle : 0.514 7.105 12073 Z= 0.273 Chirality : 0.042 0.144 1413 Planarity : 0.004 0.063 1526 Dihedral : 4.139 23.547 1221 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.74 % Allowed : 14.27 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.26), residues: 1125 helix: 2.59 (0.28), residues: 370 sheet: 0.76 (0.30), residues: 289 loop : -1.22 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.022 0.001 TYR A 29 PHE 0.013 0.001 PHE B 199 TRP 0.010 0.001 TRP R 127 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 8870) covalent geometry : angle 0.51393 (12069) SS BOND : bond 0.00814 ( 2) SS BOND : angle 0.68963 ( 4) hydrogen bonds : bond 0.04274 ( 393) hydrogen bonds : angle 3.87663 ( 1116) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7245 (ttmm) cc_final: 0.6935 (tttp) REVERT: A 82 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7773 (ttmm) REVERT: B 191 SER cc_start: 0.7759 (t) cc_final: 0.7472 (t) REVERT: B 200 VAL cc_start: 0.8102 (m) cc_final: 0.7805 (p) REVERT: B 271 CYS cc_start: 0.7672 (m) cc_final: 0.7392 (m) REVERT: B 314 ARG cc_start: 0.7597 (ttm170) cc_final: 0.7393 (ttm170) REVERT: E 90 ASP cc_start: 0.8685 (m-30) cc_final: 0.8040 (m-30) REVERT: E 141 MET cc_start: 0.8732 (mmt) cc_final: 0.8420 (mmm) REVERT: E 194 SER cc_start: 0.8169 (p) cc_final: 0.7932 (t) REVERT: R 73 LEU cc_start: 0.7270 (mt) cc_final: 0.7008 (mt) REVERT: R 142 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.6847 (tp) REVERT: R 274 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6757 (mtm) outliers start: 16 outliers final: 11 residues processed: 163 average time/residue: 0.1003 time to fit residues: 22.3993 Evaluate side-chains 165 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN ** R 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.143284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118821 restraints weight = 12876.707| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.76 r_work: 0.3430 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.230 8872 Z= 0.206 Angle : 0.867 59.188 12073 Z= 0.524 Chirality : 0.044 0.335 1413 Planarity : 0.004 0.062 1526 Dihedral : 4.145 23.541 1221 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.63 % Allowed : 14.81 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.26), residues: 1125 helix: 2.58 (0.28), residues: 370 sheet: 0.77 (0.30), residues: 289 loop : -1.23 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 52 TYR 0.016 0.001 TYR R 296 PHE 0.038 0.001 PHE A 115 TRP 0.009 0.001 TRP R 127 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 8870) covalent geometry : angle 0.86706 (12069) SS BOND : bond 0.00896 ( 2) SS BOND : angle 0.67690 ( 4) hydrogen bonds : bond 0.04343 ( 393) hydrogen bonds : angle 3.87805 ( 1116) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2178.64 seconds wall clock time: 37 minutes 59.54 seconds (2279.54 seconds total)