Starting phenix.real_space_refine on Sat Sep 12 02:15:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cag_30330/09_2026/7cag_30330.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cag_30330/09_2026/7cag_30330.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cag_30330/09_2026/7cag_30330.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cag_30330/09_2026/7cag_30330.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cag_30330/09_2026/7cag_30330.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cag_30330/09_2026/7cag_30330.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cag_30330/09_2026/7cag_30330.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cag_30330/09_2026/7cag_30330.cif" } resolution = 3.78 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= 0.000 sd= 0.016 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 P 6 5.49 5 Mg 2 5.21 5 S 38 5.16 5 C 8302 2.51 5 N 2188 2.21 5 O 2459 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12995 Number of models: 1 Model: "" Number of chains: 8 Chain: "E" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3298 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 31, 'TRANS': 403} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2155 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 270} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2051 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 256} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 2704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2704 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2700 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain breaks: 2 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 6, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.85, per 1000 atoms: 0.22 Number of scatterers: 12995 At special positions: 0 Unit cell: (81.18, 95.12, 168.1, 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) S 38 16.00 P 6 15.00 Mg 2 11.99 O 2459 8.00 N 2188 7.00 C 8302 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=2, symmetry=0 Links applied ALPHA1-1 " GLC H 1 " - " GLC H 2 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 600.4 milliseconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 13 sheets defined 41.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'E' and resid 41 through 53 Processing helix chain 'E' and resid 71 through 83 removed outlier: 3.621A pdb=" N GLY E 83 " --> pdb=" O ARG E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 Processing helix chain 'E' and resid 165 through 177 removed outlier: 4.052A pdb=" N ASP E 171 " --> pdb=" O ASP E 167 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA E 173 " --> pdb=" O MET E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 205 removed outlier: 3.821A pdb=" N VAL E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR E 201 " --> pdb=" O VAL E 197 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU E 202 " --> pdb=" O TRP E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 240 removed outlier: 4.347A pdb=" N ALA E 229 " --> pdb=" O GLU E 225 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 240 " --> pdb=" O ILE E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.596A pdb=" N ALA E 258 " --> pdb=" O ASP E 254 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU E 263 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 284 Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 314 through 324 Processing helix chain 'E' and resid 360 through 368 removed outlier: 4.035A pdb=" N ARG E 368 " --> pdb=" O PHE E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 382 removed outlier: 4.388A pdb=" N SER E 380 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 409 Processing helix chain 'E' and resid 424 through 432 removed outlier: 4.042A pdb=" N THR E 429 " --> pdb=" O GLN E 425 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG E 430 " --> pdb=" O ALA E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 460 removed outlier: 3.656A pdb=" N THR E 446 " --> pdb=" O ASP E 442 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA E 447 " --> pdb=" O PRO E 443 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU E 449 " --> pdb=" O ARG E 445 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY E 460 " --> pdb=" O LYS E 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 38 removed outlier: 4.178A pdb=" N LEU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP A 26 " --> pdb=" O ARG A 22 " (cutoff:3.500A) Proline residue: A 30 - end of helix removed outlier: 3.715A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 52 removed outlier: 3.678A pdb=" N SER A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 52 " --> pdb=" O TRP A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 74 Processing helix chain 'A' and resid 79 through 110 removed outlier: 3.804A pdb=" N THR A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 96 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.554A pdb=" N TYR A 126 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.947A pdb=" N SER A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 182 removed outlier: 3.559A pdb=" N GLU A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.772A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.794A pdb=" N LEU A 224 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 Processing helix chain 'A' and resid 253 through 261 removed outlier: 3.554A pdb=" N ASN A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 removed outlier: 4.216A pdb=" N ALA A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 16 removed outlier: 3.845A pdb=" N TRP B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TRP B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 36 removed outlier: 4.159A pdb=" N LEU B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 61 removed outlier: 3.589A pdb=" N LYS B 58 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 75 removed outlier: 3.924A pdb=" N ASN B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 97 removed outlier: 4.560A pdb=" N ILE B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA B 92 " --> pdb=" O GLY B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 116 removed outlier: 3.697A pdb=" N LEU B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ALA B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N MET B 115 " --> pdb=" O LEU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.679A pdb=" N ILE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLY B 131 " --> pdb=" O ASN B 127 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLY B 133 " --> pdb=" O TRP B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 156 Proline residue: B 144 - end of helix Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 165 through 175 removed outlier: 3.585A pdb=" N GLU B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 186 removed outlier: 3.641A pdb=" N PHE B 183 " --> pdb=" O PRO B 179 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 195 removed outlier: 3.634A pdb=" N ALA B 192 " --> pdb=" O PRO B 189 " (cutoff:3.500A) Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 200 through 208 removed outlier: 3.714A pdb=" N ASN B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 248 through 253 Processing helix chain 'B' and resid 254 through 259 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.627A pdb=" N ARG C 80 " --> pdb=" O PRO C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 103 Processing helix chain 'C' and resid 104 through 107 removed outlier: 3.623A pdb=" N LEU C 107 " --> pdb=" O PRO C 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 107' Processing helix chain 'C' and resid 111 through 126 removed outlier: 4.140A pdb=" N ALA C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU C 120 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 154 removed outlier: 4.035A pdb=" N ALA C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 188 removed outlier: 3.692A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.758A pdb=" N ILE C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 277 removed outlier: 4.144A pdb=" N ASP C 271 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 272 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 273 " --> pdb=" O MET C 269 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ALA C 277 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 302 removed outlier: 3.786A pdb=" N ALA C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.583A pdb=" N LEU D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.696A pdb=" N ARG D 80 " --> pdb=" O PRO D 77 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP D 81 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 107 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.797A pdb=" N ILE D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA D 117 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 154 removed outlier: 4.083A pdb=" N ARG D 146 " --> pdb=" O GLY D 142 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 181 removed outlier: 3.588A pdb=" N ALA D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 274 removed outlier: 4.203A pdb=" N LEU D 273 " --> pdb=" O MET D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 291 removed outlier: 3.541A pdb=" N HIS D 290 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 90 through 93 removed outlier: 6.402A pdb=" N LEU E 349 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 269 through 272 removed outlier: 3.905A pdb=" N ASN E 272 " --> pdb=" O LEU E 151 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 151 " --> pdb=" O ASN E 272 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 331 " --> pdb=" O LEU E 152 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.602A pdb=" N MET C 212 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL C 211 " --> pdb=" O GLN C 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 163 removed outlier: 7.032A pdb=" N MET C 162 " --> pdb=" O VAL C 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 282 through 283 Processing sheet with id=AA7, first strand: chain 'C' and resid 291 through 292 Processing sheet with id=AA8, first strand: chain 'C' and resid 314 through 316 removed outlier: 4.058A pdb=" N ILE C 314 " --> pdb=" O HIS C 325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 29 through 31 Processing sheet with id=AB1, first strand: chain 'D' and resid 194 through 195 removed outlier: 5.664A pdb=" N ILE D 38 " --> pdb=" O VAL D 210 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N MET D 212 " --> pdb=" O ILE D 38 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL D 40 " --> pdb=" O MET D 212 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 248 through 249 Processing sheet with id=AB3, first strand: chain 'D' and resid 292 through 293 Processing sheet with id=AB4, first strand: chain 'D' and resid 311 through 316 removed outlier: 5.278A pdb=" N ALA D 312 " --> pdb=" O THR D 327 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR D 327 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE D 314 " --> pdb=" O HIS D 325 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1146 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: 1.86 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4243 1.34 - 1.46: 2089 1.46 - 1.57: 6844 1.57 - 1.69: 10 1.69 - 1.81: 73 Bond restraints: 13259 Sorted by residual: bond pdb=" C1 GLC H 1 " pdb=" O5 GLC H 1 " ideal model delta sigma weight residual 1.410 1.499 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C ILE A 124 " pdb=" N PRO A 125 " ideal model delta sigma weight residual 1.334 1.367 -0.033 8.40e-03 1.42e+04 1.57e+01 bond pdb=" C5 GLC H 2 " pdb=" O5 GLC H 2 " ideal model delta sigma weight residual 1.410 1.487 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C5 GLC H 1 " pdb=" O5 GLC H 1 " ideal model delta sigma weight residual 1.410 1.479 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C3 GLC H 2 " pdb=" O3 GLC H 2 " ideal model delta sigma weight residual 1.410 1.478 -0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 13254 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17610 1.97 - 3.93: 398 3.93 - 5.90: 80 5.90 - 7.86: 16 7.86 - 9.83: 2 Bond angle restraints: 18106 Sorted by residual: angle pdb=" N GLN C 87 " pdb=" CA GLN C 87 " pdb=" C GLN C 87 " ideal model delta sigma weight residual 110.97 102.92 8.05 1.09e+00 8.42e-01 5.46e+01 angle pdb=" PB ATP C 502 " pdb=" O3B ATP C 502 " pdb=" PG ATP C 502 " ideal model delta sigma weight residual 139.87 132.53 7.34 1.00e+00 1.00e+00 5.39e+01 angle pdb=" PB ATP D 502 " pdb=" O3B ATP D 502 " pdb=" PG ATP D 502 " ideal model delta sigma weight residual 139.87 132.63 7.24 1.00e+00 1.00e+00 5.24e+01 angle pdb=" N GLN D 87 " pdb=" CA GLN D 87 " pdb=" C GLN D 87 " ideal model delta sigma weight residual 111.07 104.55 6.52 1.07e+00 8.73e-01 3.72e+01 angle pdb=" N THR D 190 " pdb=" CA THR D 190 " pdb=" C THR D 190 " ideal model delta sigma weight residual 108.52 115.20 -6.68 1.52e+00 4.33e-01 1.93e+01 ... (remaining 18101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7122 17.85 - 35.69: 633 35.69 - 53.54: 118 53.54 - 71.38: 13 71.38 - 89.23: 11 Dihedral angle restraints: 7897 sinusoidal: 2953 harmonic: 4944 Sorted by residual: dihedral pdb=" CA THR D 190 " pdb=" C THR D 190 " pdb=" N THR D 191 " pdb=" CA THR D 191 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLY C 240 " pdb=" C GLY C 240 " pdb=" N SER C 241 " pdb=" CA SER C 241 " ideal model delta harmonic sigma weight residual 180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLN C 367 " pdb=" C GLN C 367 " pdb=" N ILE C 368 " pdb=" CA ILE C 368 " ideal model delta harmonic sigma weight residual 180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 7894 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.939: 2145 0.939 - 1.878: 0 1.878 - 2.817: 0 2.817 - 3.756: 0 3.756 - 4.695: 1 Chirality restraints: 2146 Sorted by residual: chirality pdb=" C1 GLC H 2 " pdb=" C2 GLC H 2 " pdb=" O1 GLC H 2 " pdb=" O5 GLC H 2 " both_signs ideal model delta sigma weight residual False 2.33 -2.36 4.70 2.00e-01 2.50e+01 5.51e+02 chirality pdb=" CA GLN C 87 " pdb=" N GLN C 87 " pdb=" C GLN C 87 " pdb=" CB GLN C 87 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA GLN D 87 " pdb=" N GLN D 87 " pdb=" C GLN D 87 " pdb=" CB GLN D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2143 not shown) Planarity restraints: 2322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 258 " 0.056 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO C 259 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO C 259 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 259 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 181 " -0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO E 182 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 182 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 182 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 220 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.06e+00 pdb=" N PRO A 221 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.031 5.00e-02 4.00e+02 ... (remaining 2319 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 84 2.46 - 3.07: 9118 3.07 - 3.68: 19391 3.68 - 4.29: 27180 4.29 - 4.90: 44946 Nonbonded interactions: 100719 Sorted by model distance: nonbonded pdb="MG MG C 501 " pdb=" O3G ATP C 502 " model vdw 1.845 2.170 nonbonded pdb=" OE1 GLN D 87 " pdb="MG MG D 501 " model vdw 2.066 2.170 nonbonded pdb=" OG1 THR C 49 " pdb=" O1A ATP C 502 " model vdw 2.072 3.040 nonbonded pdb=" OG1 THR A 142 " pdb=" O THR A 145 " model vdw 2.158 3.040 nonbonded pdb=" OG SER C 48 " pdb="MG MG C 501 " model vdw 2.170 2.170 ... (remaining 100714 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 'C' and (resid 2 through 53 or (resid 54 through 55 and (name N or name C \ A or name C or name O or name CB )) or resid 56 through 63 or (resid 64 and (nam \ e N or name CA or name C or name O or name CB )) or resid 65 through 90 or (resi \ d 91 and (name N or name CA or name C or name O or name CB )) or resid 92 throug \ h 108 or (resid 109 and (name N or name CA or name C or name O or name CB )) or \ resid 110 through 130 or (resid 131 through 132 and (name N or name CA or name C \ or name O or name CB )) or resid 133 through 187 or (resid 188 and (name N or n \ ame CA or name C or name O or name CB )) or resid 189 or (resid 190 through 191 \ and (name N or name CA or name C or name O or name CB )) or resid 192 through 23 \ 2 or (resid 233 and (name N or name CA or name C or name O or name CB )) or resi \ d 234 through 259 or (resid 260 and (name N or name CA or name C or name O or na \ me CB )) or resid 261 through 303 or (resid 304 through 305 and (name N or name \ CA or name C or name O or name CB )) or resid 306 through 362 or (resid 363 and \ (name N or name CA or name C or name O or name CB )) or resid 364 through 387 or \ (resid 388 and (name N or name CA or name C or name O or name CB )) or resid 38 \ 9 or (resid 390 and (name N or name CA or name C or name O or name CB )) or resi \ d 391 through 502)) selection = (chain 'D' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 44 or (resid 45 and (name N or na \ me CA or name C or name O or name CB )) or resid 46 through 52 or (resid 53 thro \ ugh 55 and (name N or name CA or name C or name O or name CB )) or resid 56 thro \ ugh 65 or (resid 66 and (name N or name CA or name C or name O or name CB )) or \ resid 67 through 69 or (resid 70 and (name N or name CA or name C or name O or n \ ame CB )) or resid 71 through 74 or (resid 75 through 76 and (name N or name CA \ or name C or name O or name CB )) or resid 77 through 114 or (resid 115 through \ 117 and (name N or name CA or name C or name O or name CB )) or resid 118 throug \ h 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or \ resid 167 through 288 or (resid 289 and (name N or name CA or name C or name O o \ r name CB )) or resid 290 through 297 or (resid 298 and (name N or name CA or na \ me C or name O or name CB )) or resid 299 through 309 or (resid 310 through 313 \ and (name N or name CA or name C or name O or name CB )) or resid 314 through 37 \ 5 or (resid 376 and (name N or name CA or name C or name O or name CB )) or resi \ d 377 through 502)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.750 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 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 : 0.011 0.896 13262 Z= 1.039 Angle : 0.758 9.830 18109 Z= 0.429 Chirality : 0.112 4.695 2146 Planarity : 0.005 0.085 2322 Dihedral : 14.205 89.228 4705 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 0.15 % Allowed : 6.73 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.72 (0.16), residues: 1699 helix: -3.20 (0.15), residues: 674 sheet: -4.33 (0.31), residues: 118 loop : -4.36 (0.16), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 80 TYR 0.016 0.001 TYR E 34 PHE 0.016 0.001 PHE C 326 TRP 0.009 0.001 TRP A 141 HIS 0.003 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 (13259) covalent geometry : angle 0.75801 / 0.43 (18106) hydrogen bonds : bond 0.15368 / 9.94 ( 404) hydrogen bonds : angle 6.99067 / 4.85 ( 1146) glycosidic custom : bond 0.05174 / 2.72 ( 1) glycosidic custom : angle 1.60112 / 0.94 ( 3) Misc. bond : bond 0.83151 / 42.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 291 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 73 GLN cc_start: 0.7773 (pt0) cc_final: 0.7261 (tp40) REVERT: E 252 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8294 (tm-30) REVERT: E 297 ASP cc_start: 0.5801 (t0) cc_final: 0.5593 (t0) REVERT: E 405 TYR cc_start: 0.8508 (p90) cc_final: 0.8217 (p90) REVERT: A 52 GLN cc_start: 0.8316 (pp30) cc_final: 0.7008 (pp30) REVERT: A 55 ASN cc_start: 0.7877 (t0) cc_final: 0.7366 (t0) REVERT: A 58 GLU cc_start: 0.8394 (mp0) cc_final: 0.7835 (mp0) REVERT: A 267 ASN cc_start: 0.8204 (t0) cc_final: 0.7989 (m-40) REVERT: B 87 ILE cc_start: 0.9236 (pt) cc_final: 0.9010 (pt) REVERT: B 138 TRP cc_start: 0.8219 (m-10) cc_final: 0.7490 (m-90) REVERT: B 210 LEU cc_start: 0.8577 (pt) cc_final: 0.8261 (pt) REVERT: B 221 ARG cc_start: 0.8184 (ttm170) cc_final: 0.7918 (ttm170) REVERT: C 158 LYS cc_start: 0.8537 (mttt) cc_final: 0.8050 (mtpt) REVERT: C 244 MET cc_start: 0.7423 (tmm) cc_final: 0.6947 (ttp) REVERT: C 379 ILE cc_start: 0.8246 (pt) cc_final: 0.7895 (tt) REVERT: C 390 ARG cc_start: 0.6879 (tpt90) cc_final: 0.5913 (tpt90) REVERT: D 158 LYS cc_start: 0.7919 (mttt) cc_final: 0.7449 (pttt) outliers start: 2 outliers final: 0 residues processed: 293 average time/residue: 0.1189 time to fit residues: 49.8207 Evaluate side-chains 213 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN E 411 GLN E 414 ASN E 455 GLN B 56 ASN B 127 ASN C 138 GLN C 176 GLN D 138 GLN D 145 GLN D 164 GLN D 197 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111884 restraints weight = 25777.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.114823 restraints weight = 13971.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116695 restraints weight = 9104.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.118079 restraints weight = 6807.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.118961 restraints weight = 5502.293| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13262 Z= 0.170 Angle : 0.762 17.295 18109 Z= 0.377 Chirality : 0.048 0.303 2146 Planarity : 0.006 0.080 2322 Dihedral : 6.233 57.629 1853 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer: Outliers : 1.21 % Allowed : 16.04 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.88 (0.17), residues: 1699 helix: -2.42 (0.17), residues: 704 sheet: -4.12 (0.35), residues: 105 loop : -3.94 (0.18), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 8 TYR 0.015 0.002 TYR E 275 PHE 0.015 0.002 PHE B 126 TRP 0.013 0.001 TRP E 153 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (13259) covalent geometry : angle 0.74495 / 0.37 (18106) hydrogen bonds : bond 0.03966 / 2.56 ( 404) hydrogen bonds : angle 5.45960 / 3.75 ( 1146) glycosidic custom : bond 0.02372 / 1.25 ( 1) glycosidic custom : angle 12.46283 / 6.43 ( 3) Misc. bond : bond 0.00397 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 224 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 252 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8239 (tm-30) REVERT: E 270 GLU cc_start: 0.8623 (pp20) cc_final: 0.8007 (pp20) REVERT: E 414 ASN cc_start: 0.7831 (OUTLIER) cc_final: 0.7554 (p0) REVERT: A 52 GLN cc_start: 0.8388 (pp30) cc_final: 0.7060 (pp30) REVERT: A 55 ASN cc_start: 0.7712 (t0) cc_final: 0.7484 (t0) REVERT: A 58 GLU cc_start: 0.8289 (mp0) cc_final: 0.7886 (mp0) REVERT: A 267 ASN cc_start: 0.8149 (t0) cc_final: 0.7887 (m-40) REVERT: B 87 ILE cc_start: 0.9409 (pt) cc_final: 0.9175 (pt) REVERT: B 97 ARG cc_start: 0.8581 (mmm160) cc_final: 0.8239 (mmm160) REVERT: B 138 TRP cc_start: 0.8469 (m-10) cc_final: 0.7629 (m-90) REVERT: C 168 ASN cc_start: 0.8328 (p0) cc_final: 0.7928 (p0) REVERT: C 244 MET cc_start: 0.7420 (tmm) cc_final: 0.6975 (ttp) REVERT: C 390 ARG cc_start: 0.6794 (tpt90) cc_final: 0.5915 (tpt90) REVERT: D 29 MET cc_start: 0.7813 (ppp) cc_final: 0.7502 (ppp) REVERT: D 166 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8833 (pp) outliers start: 16 outliers final: 8 residues processed: 238 average time/residue: 0.1111 time to fit residues: 38.7117 Evaluate side-chains 205 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 375 ASN Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain C residue 138 GLN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 201 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 73 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 99 optimal weight: 0.0070 chunk 111 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 GLN ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN E 411 GLN E 414 ASN C 138 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111016 restraints weight = 26149.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113924 restraints weight = 14237.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115855 restraints weight = 9329.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.116994 restraints weight = 6948.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.118054 restraints weight = 5740.246| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13262 Z= 0.168 Angle : 0.734 14.665 18109 Z= 0.365 Chirality : 0.048 0.379 2146 Planarity : 0.005 0.078 2322 Dihedral : 6.143 50.456 1853 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.42 % Favored : 87.58 % Rotamer: Outliers : 2.50 % Allowed : 18.08 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.45 (0.18), residues: 1699 helix: -2.06 (0.18), residues: 707 sheet: -3.70 (0.35), residues: 122 loop : -3.72 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 418 TYR 0.012 0.001 TYR E 275 PHE 0.014 0.001 PHE C 36 TRP 0.011 0.001 TRP E 153 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (13259) covalent geometry : angle 0.72263 / 0.36 (18106) hydrogen bonds : bond 0.03525 / 2.31 ( 404) hydrogen bonds : angle 5.23571 / 3.57 ( 1146) glycosidic custom : bond 0.01317 / 0.69 ( 1) glycosidic custom : angle 10.06099 / 5.26 ( 3) Misc. bond : bond 0.00211 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 252 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7889 (tm-30) REVERT: E 270 GLU cc_start: 0.8623 (pp20) cc_final: 0.7797 (pp20) REVERT: E 272 ASN cc_start: 0.8155 (m-40) cc_final: 0.7771 (m110) REVERT: A 52 GLN cc_start: 0.8437 (pp30) cc_final: 0.7162 (pp30) REVERT: A 58 GLU cc_start: 0.8247 (mp0) cc_final: 0.7852 (mp0) REVERT: A 267 ASN cc_start: 0.8094 (t0) cc_final: 0.7843 (m-40) REVERT: B 138 TRP cc_start: 0.8417 (m-10) cc_final: 0.7563 (m-90) REVERT: B 250 MET cc_start: 0.8322 (mmm) cc_final: 0.7778 (mmm) REVERT: C 168 ASN cc_start: 0.8296 (p0) cc_final: 0.8015 (p0) REVERT: C 244 MET cc_start: 0.7523 (tmm) cc_final: 0.7045 (ttp) REVERT: C 390 ARG cc_start: 0.6777 (tpt90) cc_final: 0.5923 (tpt90) REVERT: D 166 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8836 (pp) outliers start: 33 outliers final: 22 residues processed: 237 average time/residue: 0.0985 time to fit residues: 35.0538 Evaluate side-chains 215 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 375 ASN Chi-restraints excluded: chain E residue 425 GLN Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 146 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 153 optimal weight: 0.3980 chunk 82 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 156 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.132920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.114503 restraints weight = 25739.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.117441 restraints weight = 14040.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119405 restraints weight = 9177.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.120735 restraints weight = 6817.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.121663 restraints weight = 5546.692| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13262 Z= 0.121 Angle : 0.684 12.143 18109 Z= 0.340 Chirality : 0.046 0.323 2146 Planarity : 0.005 0.073 2322 Dihedral : 5.824 42.765 1853 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 3.48 % Allowed : 18.84 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.03 (0.19), residues: 1699 helix: -1.69 (0.19), residues: 702 sheet: -3.30 (0.38), residues: 129 loop : -3.52 (0.19), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 287 TYR 0.013 0.001 TYR A 45 PHE 0.020 0.001 PHE B 232 TRP 0.024 0.001 TRP E 166 HIS 0.003 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (13259) covalent geometry : angle 0.67675 / 0.34 (18106) hydrogen bonds : bond 0.03016 / 1.97 ( 404) hydrogen bonds : angle 4.92208 / 3.35 ( 1146) glycosidic custom : bond 0.01183 / 0.62 ( 1) glycosidic custom : angle 7.75455 / 4.08 ( 3) Misc. bond : bond 0.00094 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 93 LEU cc_start: 0.8820 (pp) cc_final: 0.8561 (pp) REVERT: E 252 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7748 (tm-30) REVERT: E 272 ASN cc_start: 0.8159 (m-40) cc_final: 0.7951 (m110) REVERT: E 442 ASP cc_start: 0.5559 (OUTLIER) cc_final: 0.5157 (t70) REVERT: A 52 GLN cc_start: 0.8446 (pp30) cc_final: 0.7175 (pp30) REVERT: A 58 GLU cc_start: 0.8094 (mp0) cc_final: 0.7884 (pm20) REVERT: A 218 MET cc_start: 0.8708 (mmt) cc_final: 0.8159 (mmt) REVERT: A 270 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8932 (tt) REVERT: B 130 ARG cc_start: 0.8369 (tpp-160) cc_final: 0.8055 (tpp80) REVERT: B 138 TRP cc_start: 0.8458 (m-10) cc_final: 0.7620 (m-90) REVERT: C 168 ASN cc_start: 0.8215 (p0) cc_final: 0.7766 (p0) REVERT: C 232 ASN cc_start: 0.7934 (t0) cc_final: 0.7676 (t0) REVERT: C 244 MET cc_start: 0.7347 (tmm) cc_final: 0.6880 (ttp) REVERT: C 390 ARG cc_start: 0.6705 (tpt90) cc_final: 0.5844 (tpt90) REVERT: D 29 MET cc_start: 0.7738 (ppp) cc_final: 0.7487 (ppp) REVERT: D 115 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8561 (mt) REVERT: D 158 LYS cc_start: 0.7495 (mttp) cc_final: 0.7271 (pttt) REVERT: D 166 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8876 (pp) REVERT: D 170 ASP cc_start: 0.7078 (p0) cc_final: 0.6585 (p0) outliers start: 46 outliers final: 20 residues processed: 254 average time/residue: 0.0962 time to fit residues: 37.2992 Evaluate side-chains 227 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 102 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 101 optimal weight: 0.0670 chunk 129 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN C 138 GLN C 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.134281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.115673 restraints weight = 26213.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118703 restraints weight = 14140.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.120648 restraints weight = 9107.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122104 restraints weight = 6733.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.122906 restraints weight = 5398.247| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13262 Z= 0.128 Angle : 0.680 10.312 18109 Z= 0.337 Chirality : 0.046 0.275 2146 Planarity : 0.005 0.073 2322 Dihedral : 5.675 44.389 1853 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 3.48 % Allowed : 20.05 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.84 (0.19), residues: 1699 helix: -1.50 (0.19), residues: 706 sheet: -3.06 (0.36), residues: 139 loop : -3.47 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 287 TYR 0.016 0.001 TYR E 378 PHE 0.014 0.001 PHE B 232 TRP 0.011 0.001 TRP E 166 HIS 0.003 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13259) covalent geometry : angle 0.67537 / 0.34 (18106) hydrogen bonds : bond 0.02948 / 1.92 ( 404) hydrogen bonds : angle 4.79975 / 3.25 ( 1146) glycosidic custom : bond 0.00784 / 0.41 ( 1) glycosidic custom : angle 6.48648 / 3.44 ( 3) Misc. bond : bond 0.00101 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: E 93 LEU cc_start: 0.8808 (pp) cc_final: 0.8561 (pp) REVERT: E 252 GLN cc_start: 0.8470 (tm-30) cc_final: 0.7878 (tm-30) REVERT: E 271 VAL cc_start: 0.7895 (OUTLIER) cc_final: 0.7670 (m) REVERT: E 442 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.5062 (t70) REVERT: A 52 GLN cc_start: 0.8477 (pp30) cc_final: 0.7189 (pp30) REVERT: A 58 GLU cc_start: 0.8170 (mp0) cc_final: 0.7874 (pm20) REVERT: A 284 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8352 (tp) REVERT: B 130 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.8020 (tpp80) REVERT: B 221 ARG cc_start: 0.8128 (ttm170) cc_final: 0.6839 (tpt170) REVERT: C 168 ASN cc_start: 0.8198 (p0) cc_final: 0.7766 (p0) REVERT: C 244 MET cc_start: 0.7433 (tmm) cc_final: 0.6954 (ttp) REVERT: C 390 ARG cc_start: 0.6726 (tpt90) cc_final: 0.5994 (tpt90) REVERT: D 29 MET cc_start: 0.7769 (ppp) cc_final: 0.7532 (ppp) REVERT: D 58 GLU cc_start: 0.7547 (tp30) cc_final: 0.7301 (tp30) REVERT: D 115 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8556 (mt) REVERT: D 166 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8849 (pp) REVERT: D 170 ASP cc_start: 0.7094 (p0) cc_final: 0.6623 (p0) outliers start: 46 outliers final: 28 residues processed: 247 average time/residue: 0.0919 time to fit residues: 34.5680 Evaluate side-chains 235 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 62 optimal weight: 0.0030 chunk 10 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 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 = 0.3806 r_free = 0.3806 target = 0.134478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.116090 restraints weight = 25472.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.119028 restraints weight = 13916.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.120994 restraints weight = 9089.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.122292 restraints weight = 6757.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.123270 restraints weight = 5504.187| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13262 Z= 0.117 Angle : 0.672 10.246 18109 Z= 0.331 Chirality : 0.045 0.213 2146 Planarity : 0.005 0.070 2322 Dihedral : 5.485 46.898 1853 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 3.63 % Allowed : 20.57 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.59 (0.19), residues: 1699 helix: -1.29 (0.20), residues: 704 sheet: -2.98 (0.39), residues: 124 loop : -3.34 (0.19), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 287 TYR 0.014 0.001 TYR A 45 PHE 0.022 0.001 PHE B 232 TRP 0.014 0.001 TRP E 166 HIS 0.003 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13259) covalent geometry : angle 0.66942 / 0.33 (18106) hydrogen bonds : bond 0.02788 / 1.81 ( 404) hydrogen bonds : angle 4.75548 / 3.20 ( 1146) glycosidic custom : bond 0.00484 / 0.25 ( 1) glycosidic custom : angle 4.87001 / 2.59 ( 3) Misc. bond : bond 0.00077 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 111 SER cc_start: 0.8474 (m) cc_final: 0.8236 (t) REVERT: E 252 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7836 (tm-30) REVERT: E 442 ASP cc_start: 0.5391 (OUTLIER) cc_final: 0.5013 (t70) REVERT: A 52 GLN cc_start: 0.8447 (pp30) cc_final: 0.7199 (pp30) REVERT: A 58 GLU cc_start: 0.8137 (mp0) cc_final: 0.7864 (pm20) REVERT: A 218 MET cc_start: 0.8689 (mmt) cc_final: 0.8118 (mmt) REVERT: A 284 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8372 (tp) REVERT: B 221 ARG cc_start: 0.8094 (ttm170) cc_final: 0.6828 (tpt170) REVERT: B 238 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.4681 (p90) REVERT: C 168 ASN cc_start: 0.8133 (p0) cc_final: 0.7727 (p0) REVERT: C 232 ASN cc_start: 0.8085 (t0) cc_final: 0.7677 (t0) REVERT: C 244 MET cc_start: 0.7361 (tmm) cc_final: 0.7158 (ttp) REVERT: C 390 ARG cc_start: 0.6783 (tpt90) cc_final: 0.5940 (tpt90) REVERT: D 122 THR cc_start: 0.8973 (t) cc_final: 0.8694 (t) REVERT: D 166 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8810 (pp) REVERT: D 170 ASP cc_start: 0.7057 (p0) cc_final: 0.6625 (p0) outliers start: 48 outliers final: 29 residues processed: 256 average time/residue: 0.0924 time to fit residues: 36.3864 Evaluate side-chains 238 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 264 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 39 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 27 optimal weight: 6.9990 chunk 148 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** A 261 ASN ** 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 = 0.3809 r_free = 0.3809 target = 0.134728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116404 restraints weight = 25463.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.119351 restraints weight = 13892.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.121312 restraints weight = 9082.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.122669 restraints weight = 6761.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.123513 restraints weight = 5478.121| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13262 Z= 0.122 Angle : 0.674 10.923 18109 Z= 0.333 Chirality : 0.046 0.181 2146 Planarity : 0.005 0.070 2322 Dihedral : 5.412 48.208 1853 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 3.63 % Allowed : 21.86 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.19), residues: 1699 helix: -1.16 (0.20), residues: 701 sheet: -2.79 (0.37), residues: 144 loop : -3.28 (0.19), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 97 TYR 0.017 0.001 TYR E 378 PHE 0.020 0.001 PHE B 232 TRP 0.019 0.001 TRP E 166 HIS 0.003 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (13259) covalent geometry : angle 0.67229 / 0.33 (18106) hydrogen bonds : bond 0.02798 / 1.79 ( 404) hydrogen bonds : angle 4.72386 / 3.18 ( 1146) glycosidic custom : bond 0.00301 / 0.16 ( 1) glycosidic custom : angle 4.28704 / 2.29 ( 3) Misc. bond : bond 0.00081 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 216 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: E 111 SER cc_start: 0.8529 (m) cc_final: 0.8300 (t) REVERT: E 252 GLN cc_start: 0.8446 (tm-30) cc_final: 0.7839 (tm-30) REVERT: E 297 ASP cc_start: 0.6194 (t0) cc_final: 0.5918 (t0) REVERT: E 442 ASP cc_start: 0.5363 (OUTLIER) cc_final: 0.5011 (t70) REVERT: A 52 GLN cc_start: 0.8464 (pp30) cc_final: 0.7189 (pp30) REVERT: A 58 GLU cc_start: 0.8152 (mp0) cc_final: 0.7874 (pm20) REVERT: A 218 MET cc_start: 0.8719 (mmt) cc_final: 0.8105 (mmt) REVERT: A 284 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8367 (tp) REVERT: B 221 ARG cc_start: 0.8060 (ttm170) cc_final: 0.6858 (tpt170) REVERT: B 238 PHE cc_start: 0.6642 (OUTLIER) cc_final: 0.4762 (p90) REVERT: C 168 ASN cc_start: 0.8091 (p0) cc_final: 0.7704 (p0) REVERT: C 232 ASN cc_start: 0.8076 (t0) cc_final: 0.7686 (t0) REVERT: C 244 MET cc_start: 0.7370 (tmm) cc_final: 0.6967 (ttp) REVERT: C 390 ARG cc_start: 0.6788 (tpt90) cc_final: 0.5874 (tpt90) REVERT: D 29 MET cc_start: 0.7742 (ppp) cc_final: 0.7436 (ppp) REVERT: D 58 GLU cc_start: 0.7449 (tp30) cc_final: 0.7198 (tp30) REVERT: D 115 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8632 (mt) REVERT: D 166 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8617 (pp) REVERT: D 170 ASP cc_start: 0.7082 (p0) cc_final: 0.6666 (p0) outliers start: 48 outliers final: 32 residues processed: 253 average time/residue: 0.0936 time to fit residues: 36.3845 Evaluate side-chains 243 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 368 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 108 optimal weight: 0.9980 chunk 84 optimal weight: 0.0060 chunk 146 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.5774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.119105 restraints weight = 25184.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.122062 restraints weight = 13843.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.124090 restraints weight = 9097.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.125466 restraints weight = 6736.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.126432 restraints weight = 5420.132| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13262 Z= 0.117 Angle : 0.669 11.561 18109 Z= 0.331 Chirality : 0.045 0.170 2146 Planarity : 0.005 0.069 2322 Dihedral : 5.308 50.744 1853 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 3.25 % Allowed : 23.07 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.20), residues: 1699 helix: -0.98 (0.20), residues: 692 sheet: -2.68 (0.38), residues: 144 loop : -3.08 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 97 TYR 0.015 0.001 TYR E 378 PHE 0.022 0.001 PHE B 126 TRP 0.019 0.001 TRP E 166 HIS 0.003 0.001 HIS C 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13259) covalent geometry : angle 0.66758 / 0.33 (18106) hydrogen bonds : bond 0.02855 / 1.85 ( 404) hydrogen bonds : angle 4.70155 / 3.18 ( 1146) glycosidic custom : bond 0.00459 / 0.24 ( 1) glycosidic custom : angle 3.52841 / 1.88 ( 3) Misc. bond : bond 0.00061 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 217 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: E 41 GLU cc_start: 0.8666 (pp20) cc_final: 0.8448 (pp20) REVERT: E 111 SER cc_start: 0.8518 (m) cc_final: 0.8277 (t) REVERT: E 252 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7833 (tm-30) REVERT: E 442 ASP cc_start: 0.5151 (OUTLIER) cc_final: 0.4830 (t70) REVERT: A 26 TRP cc_start: 0.7634 (m100) cc_final: 0.7174 (m-90) REVERT: A 52 GLN cc_start: 0.8405 (pp30) cc_final: 0.7991 (pt0) REVERT: A 218 MET cc_start: 0.8649 (mmt) cc_final: 0.8055 (mmt) REVERT: A 284 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8389 (tp) REVERT: B 93 TYR cc_start: 0.8463 (t80) cc_final: 0.8081 (t80) REVERT: B 221 ARG cc_start: 0.8057 (ttm170) cc_final: 0.6845 (tpt170) REVERT: B 233 THR cc_start: 0.7544 (OUTLIER) cc_final: 0.7267 (p) REVERT: B 238 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.4776 (p90) REVERT: C 168 ASN cc_start: 0.8024 (p0) cc_final: 0.7665 (p0) REVERT: C 232 ASN cc_start: 0.8072 (t0) cc_final: 0.7688 (t0) REVERT: C 244 MET cc_start: 0.7331 (tmm) cc_final: 0.6934 (ttp) REVERT: C 390 ARG cc_start: 0.6721 (tpt90) cc_final: 0.5816 (tpt90) REVERT: D 115 ILE cc_start: 0.9070 (OUTLIER) cc_final: 0.8764 (mt) REVERT: D 166 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8650 (pp) REVERT: D 170 ASP cc_start: 0.6984 (p0) cc_final: 0.6615 (p0) outliers start: 43 outliers final: 32 residues processed: 248 average time/residue: 0.0933 time to fit residues: 36.1496 Evaluate side-chains 240 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 30 optimal weight: 0.0670 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 ASN ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN A 201 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.136987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118864 restraints weight = 25416.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.121839 restraints weight = 13773.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.123844 restraints weight = 8998.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.125283 restraints weight = 6665.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.126136 restraints weight = 5346.431| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13262 Z= 0.120 Angle : 0.670 12.168 18109 Z= 0.331 Chirality : 0.045 0.181 2146 Planarity : 0.005 0.069 2322 Dihedral : 5.246 51.513 1853 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 3.33 % Allowed : 24.43 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.20), residues: 1699 helix: -0.82 (0.20), residues: 694 sheet: -2.65 (0.38), residues: 142 loop : -3.04 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.014 0.001 TYR E 378 PHE 0.017 0.001 PHE A 279 TRP 0.021 0.001 TRP E 166 HIS 0.009 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (13259) covalent geometry : angle 0.66908 / 0.33 (18106) hydrogen bonds : bond 0.02817 / 1.84 ( 404) hydrogen bonds : angle 4.68304 / 3.17 ( 1146) glycosidic custom : bond 0.00466 / 0.25 ( 1) glycosidic custom : angle 3.11166 / 1.66 ( 3) Misc. bond : bond 0.00066 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: E 41 GLU cc_start: 0.8651 (pp20) cc_final: 0.8427 (pp20) REVERT: E 252 GLN cc_start: 0.8436 (tm-30) cc_final: 0.7773 (tm-30) REVERT: E 442 ASP cc_start: 0.4958 (OUTLIER) cc_final: 0.4634 (t0) REVERT: A 26 TRP cc_start: 0.7608 (m100) cc_final: 0.7148 (m-90) REVERT: A 52 GLN cc_start: 0.8488 (pp30) cc_final: 0.8017 (pt0) REVERT: A 218 MET cc_start: 0.8657 (mmt) cc_final: 0.8057 (mmt) REVERT: A 284 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8390 (tp) REVERT: B 93 TYR cc_start: 0.8493 (t80) cc_final: 0.8124 (t80) REVERT: B 221 ARG cc_start: 0.8032 (ttm170) cc_final: 0.6814 (tpt170) REVERT: B 233 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7270 (p) REVERT: B 238 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.4854 (p90) REVERT: C 168 ASN cc_start: 0.8040 (p0) cc_final: 0.7738 (p0) REVERT: C 232 ASN cc_start: 0.8103 (t0) cc_final: 0.7739 (t0) REVERT: C 244 MET cc_start: 0.7379 (tmm) cc_final: 0.6956 (ttp) REVERT: C 390 ARG cc_start: 0.6702 (tpt90) cc_final: 0.5798 (tpt90) REVERT: D 115 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8742 (mt) REVERT: D 166 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8572 (pp) REVERT: D 170 ASP cc_start: 0.7052 (p0) cc_final: 0.6662 (p0) outliers start: 44 outliers final: 35 residues processed: 240 average time/residue: 0.0969 time to fit residues: 35.8413 Evaluate side-chains 237 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 411 GLN Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 160 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 368 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 GLN A 201 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.116561 restraints weight = 25675.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.119526 restraints weight = 13806.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.121598 restraints weight = 8961.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.122803 restraints weight = 6562.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.123837 restraints weight = 5353.041| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13262 Z= 0.150 Angle : 0.698 12.488 18109 Z= 0.346 Chirality : 0.046 0.259 2146 Planarity : 0.005 0.071 2322 Dihedral : 5.342 50.131 1853 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 3.25 % Allowed : 24.58 % Favored : 72.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.20), residues: 1699 helix: -0.84 (0.20), residues: 697 sheet: -2.69 (0.38), residues: 142 loop : -3.01 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 21 TYR 0.014 0.001 TYR E 378 PHE 0.022 0.001 PHE B 126 TRP 0.019 0.001 TRP E 166 HIS 0.011 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (13259) covalent geometry : angle 0.69729 / 0.35 (18106) hydrogen bonds : bond 0.02970 / 1.96 ( 404) hydrogen bonds : angle 4.72944 / 3.20 ( 1146) glycosidic custom : bond 0.00337 / 0.18 ( 1) glycosidic custom : angle 2.86716 / 1.53 ( 3) Misc. bond : bond 0.00099 / 0.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: E 41 GLU cc_start: 0.8680 (pp20) cc_final: 0.8441 (pp20) REVERT: E 252 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7850 (tm-30) REVERT: E 442 ASP cc_start: 0.5067 (OUTLIER) cc_final: 0.4745 (t70) REVERT: A 26 TRP cc_start: 0.7626 (m100) cc_final: 0.7171 (m-90) REVERT: A 52 GLN cc_start: 0.8526 (pp30) cc_final: 0.8081 (pt0) REVERT: A 284 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8379 (tp) REVERT: B 138 TRP cc_start: 0.8494 (m-10) cc_final: 0.7441 (m-90) REVERT: B 233 THR cc_start: 0.7468 (OUTLIER) cc_final: 0.7254 (p) REVERT: B 238 PHE cc_start: 0.6762 (OUTLIER) cc_final: 0.4925 (p90) REVERT: C 168 ASN cc_start: 0.8093 (p0) cc_final: 0.7784 (p0) REVERT: C 232 ASN cc_start: 0.8151 (t0) cc_final: 0.7795 (t0) REVERT: C 244 MET cc_start: 0.7462 (tmm) cc_final: 0.7028 (ttp) REVERT: C 390 ARG cc_start: 0.6720 (tpt90) cc_final: 0.5818 (tpt90) REVERT: D 115 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8722 (mt) REVERT: D 166 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8584 (pp) REVERT: D 170 ASP cc_start: 0.7111 (p0) cc_final: 0.6704 (p0) REVERT: D 351 GLN cc_start: 0.7862 (mp10) cc_final: 0.7574 (mp10) outliers start: 43 outliers final: 33 residues processed: 232 average time/residue: 0.0967 time to fit residues: 34.6571 Evaluate side-chains 237 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 160 PHE Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain D residue 45 CYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 368 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 94 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 139 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 148 optimal weight: 0.0010 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 387 ASN ** 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 = 0.3822 r_free = 0.3822 target = 0.136054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.117886 restraints weight = 25205.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120919 restraints weight = 13849.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.122937 restraints weight = 9043.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.124201 restraints weight = 6695.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.125206 restraints weight = 5443.235| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13262 Z= 0.125 Angle : 0.682 12.903 18109 Z= 0.338 Chirality : 0.045 0.221 2146 Planarity : 0.005 0.068 2322 Dihedral : 5.274 51.804 1853 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 3.10 % Allowed : 24.89 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.94 (0.20), residues: 1699 helix: -0.74 (0.21), residues: 693 sheet: -2.65 (0.39), residues: 142 loop : -2.95 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.013 0.001 TYR E 378 PHE 0.017 0.001 PHE A 279 TRP 0.020 0.001 TRP E 166 HIS 0.008 0.001 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (13259) covalent geometry : angle 0.68122 / 0.34 (18106) hydrogen bonds : bond 0.02856 / 1.87 ( 404) hydrogen bonds : angle 4.67469 / 3.16 ( 1146) glycosidic custom : bond 0.00408 / 0.21 ( 1) glycosidic custom : angle 2.76639 / 1.48 ( 3) Misc. bond : bond 0.00069 / 0.03 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2052.10 seconds wall clock time: 36 minutes 16.27 seconds (2176.27 seconds total)