Starting phenix.real_space_refine on Sun Jun 15 12:44:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6gj3_0010/06_2025/6gj3_0010.cif Found real_map, /net/cci-nas-00/data/ceres_data/6gj3_0010/06_2025/6gj3_0010.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6gj3_0010/06_2025/6gj3_0010.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6gj3_0010/06_2025/6gj3_0010.map" model { file = "/net/cci-nas-00/data/ceres_data/6gj3_0010/06_2025/6gj3_0010.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6gj3_0010/06_2025/6gj3_0010.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 11009 2.51 5 N 3160 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17405 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 479 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 7, 'TRANS': 54} Chain breaks: 1 Chain: "D" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2473 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 289} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2479 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 289} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2482 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 21, 'TRANS': 289} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3509 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 29, 'TRANS': 414} Chain: "H" Number of atoms: 3498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3498 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 29, 'TRANS': 414} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2485 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 21, 'TRANS': 289} Time building chain proxies: 10.61, per 1000 atoms: 0.61 Number of scatterers: 17405 At special positions: 0 Unit cell: (106.7, 159.5, 140.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 3156 8.00 N 3160 7.00 C 11009 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=0, symmetry=0 Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 2.1 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 24 sheets defined 31.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'D' and resid 15 through 35 removed outlier: 3.972A pdb=" N PHE D 19 " --> pdb=" O MET D 15 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN D 21 " --> pdb=" O GLN D 17 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TRP D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N HIS D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER D 32 " --> pdb=" O HIS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 193 Processing helix chain 'D' and resid 194 through 218 removed outlier: 3.784A pdb=" N MET D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 210 " --> pdb=" O HIS D 206 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG D 211 " --> pdb=" O HIS D 207 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 245 removed outlier: 3.637A pdb=" N ALA D 242 " --> pdb=" O TRP D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 removed outlier: 3.908A pdb=" N LEU D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N MET D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 275 removed outlier: 4.372A pdb=" N LEU D 264 " --> pdb=" O HIS D 260 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 297 Processing helix chain 'D' and resid 298 through 310 Processing helix chain 'E' and resid 15 through 33 removed outlier: 3.987A pdb=" N PHE E 19 " --> pdb=" O MET E 15 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN E 21 " --> pdb=" O GLN E 17 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN E 22 " --> pdb=" O GLN E 18 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA E 30 " --> pdb=" O ASP E 26 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP E 31 " --> pdb=" O VAL E 27 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 32 " --> pdb=" O HIS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 193 Processing helix chain 'E' and resid 194 through 218 removed outlier: 4.424A pdb=" N MET E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR E 199 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 200 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN E 209 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.611A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 251 removed outlier: 3.547A pdb=" N LEU E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 277 removed outlier: 3.660A pdb=" N ARG E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU E 271 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR E 277 " --> pdb=" O GLY E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 297 removed outlier: 3.713A pdb=" N ASN E 297 " --> pdb=" O THR E 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 294 through 297' Processing helix chain 'E' and resid 298 through 310 removed outlier: 3.573A pdb=" N ASN E 307 " --> pdb=" O LEU E 303 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG E 308 " --> pdb=" O SER E 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 35 removed outlier: 3.843A pdb=" N GLN F 20 " --> pdb=" O PRO F 16 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN F 21 " --> pdb=" O GLN F 17 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL F 27 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 194 through 222 removed outlier: 4.437A pdb=" N MET F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR F 199 " --> pdb=" O PRO F 195 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU F 215 " --> pdb=" O ARG F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 244 Processing helix chain 'F' and resid 246 through 251 removed outlier: 3.705A pdb=" N LEU F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 275 removed outlier: 3.545A pdb=" N GLU F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 297 Processing helix chain 'F' and resid 298 through 310 removed outlier: 3.582A pdb=" N ASN F 307 " --> pdb=" O LEU F 303 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 308 " --> pdb=" O SER F 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 36 removed outlier: 4.351A pdb=" N GLN G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA G 30 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N MET G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 218 removed outlier: 4.264A pdb=" N THR G 199 " --> pdb=" O PRO G 195 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 218 through 223 Processing helix chain 'G' and resid 230 through 245 removed outlier: 3.732A pdb=" N VAL G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU G 236 " --> pdb=" O ALA G 232 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER G 245 " --> pdb=" O ASN G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 253 removed outlier: 3.630A pdb=" N LEU G 250 " --> pdb=" O ALA G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 276 removed outlier: 4.410A pdb=" N LEU G 264 " --> pdb=" O HIS G 260 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG G 266 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU G 267 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU G 271 " --> pdb=" O GLU G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 297 removed outlier: 3.503A pdb=" N ASN G 297 " --> pdb=" O THR G 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 294 through 297' Processing helix chain 'G' and resid 298 through 310 Processing helix chain 'G' and resid 354 through 366 removed outlier: 4.407A pdb=" N THR G 360 " --> pdb=" O HIS G 356 " (cutoff:3.500A) Proline residue: G 363 - end of helix Processing helix chain 'G' and resid 411 through 420 removed outlier: 3.735A pdb=" N ASP G 420 " --> pdb=" O ARG G 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 35 removed outlier: 4.331A pdb=" N PHE H 19 " --> pdb=" O MET H 15 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 223 removed outlier: 4.105A pdb=" N MET H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG H 211 " --> pdb=" O HIS H 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG H 212 " --> pdb=" O LEU H 208 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN H 213 " --> pdb=" O GLN H 209 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN H 222 " --> pdb=" O MET H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 254 removed outlier: 4.037A pdb=" N SER H 245 " --> pdb=" O ASN H 241 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU H 247 " --> pdb=" O LEU H 243 " (cutoff:3.500A) Proline residue: H 248 - end of helix removed outlier: 5.335A pdb=" N GLU H 252 " --> pdb=" O PRO H 248 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU H 253 " --> pdb=" O VAL H 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU H 254 " --> pdb=" O LEU H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 260 through 275 removed outlier: 4.121A pdb=" N LEU H 264 " --> pdb=" O HIS H 260 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU H 267 " --> pdb=" O LEU H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 287 Processing helix chain 'H' and resid 298 through 310 removed outlier: 3.785A pdb=" N LEU H 302 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG H 308 " --> pdb=" O SER H 304 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 341 removed outlier: 3.940A pdb=" N ARG H 340 " --> pdb=" O ALA H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 422 removed outlier: 3.958A pdb=" N ARG H 416 " --> pdb=" O THR H 412 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 24 removed outlier: 4.277A pdb=" N PHE I 19 " --> pdb=" O MET I 15 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN I 20 " --> pdb=" O PRO I 16 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN I 21 " --> pdb=" O GLN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 35 Processing helix chain 'I' and resid 51 through 56 removed outlier: 3.572A pdb=" N LEU I 54 " --> pdb=" O ASP I 51 " (cutoff:3.500A) Proline residue: I 55 - end of helix No H-bonds generated for 'chain 'I' and resid 51 through 56' Processing helix chain 'I' and resid 89 through 92 Processing helix chain 'I' and resid 194 through 220 removed outlier: 4.138A pdb=" N LEU I 202 " --> pdb=" O MET I 198 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU I 203 " --> pdb=" O THR I 199 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA I 210 " --> pdb=" O HIS I 206 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG I 211 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG I 219 " --> pdb=" O LEU I 215 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 228 removed outlier: 3.740A pdb=" N ASP I 228 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 245 removed outlier: 3.900A pdb=" N SER I 235 " --> pdb=" O VAL I 231 " (cutoff:3.500A) Processing helix chain 'I' and resid 246 through 254 removed outlier: 4.074A pdb=" N LEU I 250 " --> pdb=" O ALA I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 260 through 276 removed outlier: 4.093A pdb=" N LEU I 264 " --> pdb=" O HIS I 260 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG I 270 " --> pdb=" O ARG I 266 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU I 271 " --> pdb=" O GLU I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 298 through 310 removed outlier: 3.559A pdb=" N LEU I 303 " --> pdb=" O PHE I 299 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG I 308 " --> pdb=" O SER I 304 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU I 309 " --> pdb=" O LEU I 305 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU I 310 " --> pdb=" O LEU I 306 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 44 through 49 removed outlier: 4.327A pdb=" N ALA D 47 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ARG D 63 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE D 49 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA D 61 " --> pdb=" O PHE D 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 151 through 153 removed outlier: 5.588A pdb=" N LEU D 101 " --> pdb=" O PRO D 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 124 through 131 removed outlier: 6.211A pdb=" N VAL D 143 " --> pdb=" O ARG D 129 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 44 through 49 removed outlier: 5.195A pdb=" N VAL E 44 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG E 67 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 46 " --> pdb=" O ILE E 65 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 63 " --> pdb=" O GLU E 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.033A pdb=" N THR E 151 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 151 through 154 removed outlier: 4.033A pdb=" N THR E 151 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL E 97 " --> pdb=" O ARG E 169 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG E 169 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 99 " --> pdb=" O VAL E 167 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 171 " --> pdb=" O CYS E 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 126 through 133 removed outlier: 3.777A pdb=" N GLU E 128 " --> pdb=" O VAL E 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 44 through 49 removed outlier: 6.372A pdb=" N ILE F 65 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA F 47 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG F 63 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE F 49 " --> pdb=" O ALA F 61 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA F 61 " --> pdb=" O PHE F 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 128 through 132 removed outlier: 3.796A pdb=" N SER F 141 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 170 through 173 Processing sheet with id=AB2, first strand: chain 'G' and resid 44 through 50 removed outlier: 6.568A pdb=" N ILE G 65 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA G 47 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG G 63 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE G 49 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA G 61 " --> pdb=" O PHE G 49 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 44 through 50 removed outlier: 6.568A pdb=" N ILE G 65 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA G 47 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ARG G 63 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE G 49 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA G 61 " --> pdb=" O PHE G 49 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU G 59 " --> pdb=" O CYS G 86 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 151 through 154 removed outlier: 3.712A pdb=" N THR G 151 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE G 99 " --> pdb=" O VAL G 167 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS G 165 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 125 through 131 removed outlier: 5.136A pdb=" N LYS G 126 " --> pdb=" O ARG G 147 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG G 147 " --> pdb=" O LYS G 126 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU G 128 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 318 through 321 removed outlier: 3.537A pdb=" N ILE G 321 " --> pdb=" O LEU G 439 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU G 439 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 325 through 326 removed outlier: 3.892A pdb=" N THR G 425 " --> pdb=" O GLY G 369 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 44 through 49 removed outlier: 6.771A pdb=" N ILE H 65 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA H 47 " --> pdb=" O ARG H 63 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG H 63 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N PHE H 49 " --> pdb=" O ALA H 61 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA H 61 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 151 through 154 removed outlier: 3.613A pdb=" N THR H 151 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU H 101 " --> pdb=" O PRO H 166 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 125 through 132 removed outlier: 3.508A pdb=" N VAL H 130 " --> pdb=" O VAL H 143 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL H 132 " --> pdb=" O SER H 141 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER H 141 " --> pdb=" O VAL H 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 387 through 390 Processing sheet with id=AC3, first strand: chain 'I' and resid 44 through 49 removed outlier: 5.361A pdb=" N VAL I 44 " --> pdb=" O ARG I 67 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG I 67 " --> pdb=" O VAL I 44 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG I 63 " --> pdb=" O GLU I 48 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 58 through 59 Processing sheet with id=AC5, first strand: chain 'I' and resid 151 through 153 removed outlier: 3.581A pdb=" N THR I 151 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA I 102 " --> pdb=" O THR I 151 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL I 97 " --> pdb=" O ARG I 169 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG I 169 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE I 99 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL I 171 " --> pdb=" O CYS I 179 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 126 through 127 490 hydrogen bonds defined for protein. 1389 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: 4.67 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5874 1.34 - 1.46: 3141 1.46 - 1.58: 8655 1.58 - 1.69: 0 1.69 - 1.81: 137 Bond restraints: 17807 Sorted by residual: bond pdb=" C SER H 370 " pdb=" N PRO H 371 " ideal model delta sigma weight residual 1.326 1.387 -0.060 1.44e-02 4.82e+03 1.76e+01 bond pdb=" C LEU G 14 " pdb=" N MET G 15 " ideal model delta sigma weight residual 1.333 1.278 0.055 1.59e-02 3.96e+03 1.19e+01 bond pdb=" C ASN D 81 " pdb=" N LEU D 82 " ideal model delta sigma weight residual 1.331 1.279 0.052 2.07e-02 2.33e+03 6.29e+00 bond pdb=" C HIS C 232 " pdb=" N PRO C 233 " ideal model delta sigma weight residual 1.334 1.392 -0.058 2.34e-02 1.83e+03 6.06e+00 bond pdb=" C ARG D 121 " pdb=" N PRO D 122 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.07e+00 ... (remaining 17802 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 23756 3.43 - 6.87: 462 6.87 - 10.30: 47 10.30 - 13.74: 5 13.74 - 17.17: 3 Bond angle restraints: 24273 Sorted by residual: angle pdb=" C ARG G 67 " pdb=" N PHE G 68 " pdb=" CA PHE G 68 " ideal model delta sigma weight residual 120.68 131.95 -11.27 1.52e+00 4.33e-01 5.50e+01 angle pdb=" N ILE C 220 " pdb=" CA ILE C 220 " pdb=" C ILE C 220 " ideal model delta sigma weight residual 108.88 123.67 -14.79 2.16e+00 2.14e-01 4.69e+01 angle pdb=" N VAL C 324 " pdb=" CA VAL C 324 " pdb=" C VAL C 324 " ideal model delta sigma weight residual 112.17 105.71 6.46 9.50e-01 1.11e+00 4.63e+01 angle pdb=" C ARG C 219 " pdb=" N ILE C 220 " pdb=" CA ILE C 220 " ideal model delta sigma weight residual 122.13 134.38 -12.25 1.85e+00 2.92e-01 4.38e+01 angle pdb=" N MET G 256 " pdb=" CA MET G 256 " pdb=" C MET G 256 " ideal model delta sigma weight residual 109.81 120.98 -11.17 2.21e+00 2.05e-01 2.55e+01 ... (remaining 24268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 10130 15.02 - 30.03: 612 30.03 - 45.05: 113 45.05 - 60.07: 18 60.07 - 75.08: 4 Dihedral angle restraints: 10877 sinusoidal: 4433 harmonic: 6444 Sorted by residual: dihedral pdb=" CA ILE C 220 " pdb=" C ILE C 220 " pdb=" N PRO C 221 " pdb=" CA PRO C 221 " ideal model delta harmonic sigma weight residual -180.00 -114.89 -65.11 0 5.00e+00 4.00e-02 1.70e+02 dihedral pdb=" CA TRP F 162 " pdb=" C TRP F 162 " pdb=" N LEU F 163 " pdb=" CA LEU F 163 " ideal model delta harmonic sigma weight residual 180.00 -124.15 -55.85 0 5.00e+00 4.00e-02 1.25e+02 dihedral pdb=" CA CYS C 310 " pdb=" C CYS C 310 " pdb=" N ARG C 311 " pdb=" CA ARG C 311 " ideal model delta harmonic sigma weight residual 180.00 127.03 52.97 0 5.00e+00 4.00e-02 1.12e+02 ... (remaining 10874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2430 0.096 - 0.192: 314 0.192 - 0.289: 12 0.289 - 0.385: 3 0.385 - 0.481: 1 Chirality restraints: 2760 Sorted by residual: chirality pdb=" CA HIS G 40 " pdb=" N HIS G 40 " pdb=" C HIS G 40 " pdb=" CB HIS G 40 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" CG LEU I 38 " pdb=" CB LEU I 38 " pdb=" CD1 LEU I 38 " pdb=" CD2 LEU I 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB VAL G 234 " pdb=" CA VAL G 234 " pdb=" CG1 VAL G 234 " pdb=" CG2 VAL G 234 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 2757 not shown) Planarity restraints: 3184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 220 " -0.080 5.00e-02 4.00e+02 1.22e-01 2.37e+01 pdb=" N PRO C 221 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO C 221 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 221 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 40 " -0.057 5.00e-02 4.00e+02 8.70e-02 1.21e+01 pdb=" N PRO G 41 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO G 41 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO G 41 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 299 " -0.050 5.00e-02 4.00e+02 7.46e-02 8.90e+00 pdb=" N PRO I 300 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO I 300 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO I 300 " -0.042 5.00e-02 4.00e+02 ... (remaining 3181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3437 2.78 - 3.31: 15085 3.31 - 3.84: 26299 3.84 - 4.37: 29769 4.37 - 4.90: 50884 Nonbonded interactions: 125474 Sorted by model distance: nonbonded pdb=" OG SER F 119 " pdb=" O ARG F 121 " model vdw 2.248 3.040 nonbonded pdb=" ND1 HIS H 40 " pdb=" O PRO H 41 " model vdw 2.310 3.120 nonbonded pdb=" N ASP G 80 " pdb=" OD1 ASP G 80 " model vdw 2.331 3.120 nonbonded pdb=" NH1 ARG D 212 " pdb=" OE1 GLU D 247 " model vdw 2.336 3.120 nonbonded pdb=" O MET G 256 " pdb=" N TYR G 258 " model vdw 2.350 3.120 ... (remaining 125469 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 'D' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 311)) selection = (chain 'E' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 221 or (resid 222 th \ rough 225 and (name N or name CA or name C or name O or name CB )) or resid 226 \ through 311)) selection = (chain 'F' and (resid 1 through 221 or (resid 222 through 225 and (name N or nam \ e CA or name C or name O or name CB )) or resid 226 through 311)) selection = (chain 'I' and (resid 1 through 158 or (resid 159 through 161 and (name N or nam \ e CA or name C or name O or name CB )) or resid 162 through 221 or (resid 222 th \ rough 225 and (name N or name CA or name C or name O or name CB )) or resid 226 \ through 311)) } ncs_group { reference = (chain 'G' and (resid 1 through 333 or (resid 334 through 335 and (name N or nam \ e CA or name C or name O or name CB )) or resid 336 through 346 or (resid 347 an \ d (name N or name CA or name C or name O or name CB )) or resid 348 through 444) \ ) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 37.390 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 17807 Z= 0.361 Angle : 1.187 17.170 24273 Z= 0.652 Chirality : 0.064 0.481 2760 Planarity : 0.010 0.122 3184 Dihedral : 10.340 75.082 6647 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 13.45 % Favored : 86.23 % Rotamer: Outliers : 0.37 % Allowed : 2.17 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.36 % Twisted General : 0.88 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.14), residues: 2178 helix: -3.07 (0.13), residues: 681 sheet: -2.70 (0.25), residues: 330 loop : -3.43 (0.14), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP G 125 HIS 0.018 0.003 HIS H 206 PHE 0.029 0.003 PHE H 19 TYR 0.027 0.004 TYR G 427 ARG 0.013 0.001 ARG G 153 Details of bonding type rmsd hydrogen bonds : bond 0.21860 ( 486) hydrogen bonds : angle 8.03884 ( 1389) covalent geometry : bond 0.00823 (17807) covalent geometry : angle 1.18730 (24273) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 356 time to evaluate : 1.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 ARG cc_start: 0.7877 (ttt180) cc_final: 0.7649 (ttm170) REVERT: C 224 THR cc_start: 0.8284 (p) cc_final: 0.8073 (p) REVERT: C 319 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6350 (mm) REVERT: C 325 MET cc_start: 0.5595 (mmt) cc_final: 0.5303 (mmt) REVERT: D 237 PHE cc_start: 0.7946 (p90) cc_final: 0.7627 (t80) REVERT: D 238 TRP cc_start: 0.6927 (m100) cc_final: 0.6404 (m100) REVERT: D 251 LYS cc_start: 0.9063 (tttt) cc_final: 0.8659 (ttpt) REVERT: E 292 HIS cc_start: 0.4961 (t-90) cc_final: 0.4660 (t70) REVERT: F 198 MET cc_start: 0.8192 (mmm) cc_final: 0.7835 (mmt) REVERT: G 120 GLU cc_start: 0.7703 (pm20) cc_final: 0.7324 (pp20) REVERT: G 154 MET cc_start: 0.7808 (ttp) cc_final: 0.7468 (ttp) REVERT: G 367 LYS cc_start: 0.6536 (mttt) cc_final: 0.6135 (mtpt) REVERT: G 397 ILE cc_start: 0.5455 (mt) cc_final: 0.4936 (mt) REVERT: H 2 LYS cc_start: 0.8423 (mmtt) cc_final: 0.7801 (mmmm) REVERT: H 4 TYR cc_start: 0.8529 (m-10) cc_final: 0.7852 (m-10) REVERT: H 67 ARG cc_start: 0.8073 (mmm-85) cc_final: 0.7473 (mmm-85) REVERT: H 188 LEU cc_start: 0.9336 (mt) cc_final: 0.9088 (mt) REVERT: H 419 LEU cc_start: 0.8829 (mt) cc_final: 0.8325 (pp) REVERT: I 138 HIS cc_start: 0.8189 (p-80) cc_final: 0.7835 (p-80) REVERT: I 258 TYR cc_start: 0.7017 (p90) cc_final: 0.6369 (p90) REVERT: I 277 THR cc_start: 0.9123 (p) cc_final: 0.8864 (t) outliers start: 7 outliers final: 3 residues processed: 362 average time/residue: 0.3520 time to fit residues: 181.4848 Evaluate side-chains 197 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 193 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 HIS D 292 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN F 40 HIS F 291 HIS F 292 HIS G 156 HIS G 157 GLN H 206 HIS ** H 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 HIS I 241 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.101232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.081669 restraints weight = 48793.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.083818 restraints weight = 29975.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.085321 restraints weight = 21137.663| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17807 Z= 0.137 Angle : 0.742 14.155 24273 Z= 0.380 Chirality : 0.046 0.290 2760 Planarity : 0.007 0.117 3184 Dihedral : 7.468 59.063 2401 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.60 % Favored : 90.31 % Rotamer: Outliers : 0.05 % Allowed : 3.01 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.16), residues: 2178 helix: -1.46 (0.18), residues: 688 sheet: -2.12 (0.26), residues: 346 loop : -3.10 (0.15), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP I 162 HIS 0.010 0.001 HIS E 206 PHE 0.020 0.001 PHE H 426 TYR 0.016 0.002 TYR H 427 ARG 0.007 0.001 ARG I 259 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 486) hydrogen bonds : angle 5.68924 ( 1389) covalent geometry : bond 0.00296 (17807) covalent geometry : angle 0.74218 (24273) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 MET cc_start: 0.5710 (mmt) cc_final: 0.5176 (mmt) REVERT: D 237 PHE cc_start: 0.7827 (p90) cc_final: 0.7510 (t80) REVERT: D 238 TRP cc_start: 0.7071 (m100) cc_final: 0.6010 (m100) REVERT: D 251 LYS cc_start: 0.8833 (tttt) cc_final: 0.8542 (ttpt) REVERT: E 292 HIS cc_start: 0.5225 (t-90) cc_final: 0.3004 (t-90) REVERT: F 184 PHE cc_start: 0.8463 (t80) cc_final: 0.8247 (t80) REVERT: F 238 TRP cc_start: 0.5196 (m100) cc_final: 0.4270 (m-90) REVERT: G 120 GLU cc_start: 0.7746 (pm20) cc_final: 0.7344 (pp20) REVERT: G 154 MET cc_start: 0.7662 (ttp) cc_final: 0.7332 (ttp) REVERT: G 367 LYS cc_start: 0.6479 (mttt) cc_final: 0.6235 (mtpp) REVERT: G 397 ILE cc_start: 0.5934 (mt) cc_final: 0.5582 (mt) REVERT: G 410 LEU cc_start: 0.5675 (mp) cc_final: 0.5266 (tt) REVERT: H 2 LYS cc_start: 0.8451 (mmtt) cc_final: 0.8112 (mmmm) REVERT: H 4 TYR cc_start: 0.8229 (m-10) cc_final: 0.7994 (m-80) REVERT: H 293 GLU cc_start: 0.8514 (pm20) cc_final: 0.8227 (mp0) REVERT: H 419 LEU cc_start: 0.8821 (mt) cc_final: 0.8346 (pp) REVERT: I 138 HIS cc_start: 0.8078 (p-80) cc_final: 0.7650 (p-80) REVERT: I 154 MET cc_start: 0.7402 (ppp) cc_final: 0.6738 (ppp) REVERT: I 258 TYR cc_start: 0.6965 (p90) cc_final: 0.6367 (p90) REVERT: I 263 LEU cc_start: 0.9132 (tt) cc_final: 0.8636 (mp) outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.3946 time to fit residues: 164.0782 Evaluate side-chains 194 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 143 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 150 optimal weight: 0.9980 chunk 135 optimal weight: 0.2980 chunk 139 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 190 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 HIS F 244 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 ASN I 138 HIS I 159 ASN I 207 HIS I 282 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.078071 restraints weight = 49735.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.080073 restraints weight = 30905.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.081454 restraints weight = 22015.145| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17807 Z= 0.219 Angle : 0.799 13.458 24273 Z= 0.403 Chirality : 0.048 0.327 2760 Planarity : 0.007 0.109 3184 Dihedral : 7.408 60.753 2401 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.08 % Favored : 87.83 % Rotamer: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.68 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.16), residues: 2178 helix: -0.74 (0.19), residues: 681 sheet: -2.03 (0.26), residues: 353 loop : -2.97 (0.16), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP G 125 HIS 0.010 0.002 HIS D 40 PHE 0.018 0.002 PHE H 426 TYR 0.013 0.002 TYR G 427 ARG 0.020 0.001 ARG F 67 Details of bonding type rmsd hydrogen bonds : bond 0.04910 ( 486) hydrogen bonds : angle 5.60288 ( 1389) covalent geometry : bond 0.00511 (17807) covalent geometry : angle 0.79914 (24273) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 MET cc_start: 0.5423 (mmt) cc_final: 0.5142 (mmt) REVERT: D 238 TRP cc_start: 0.7000 (m100) cc_final: 0.6050 (m100) REVERT: D 251 LYS cc_start: 0.8898 (tttt) cc_final: 0.8578 (ttpt) REVERT: E 292 HIS cc_start: 0.5225 (t-90) cc_final: 0.4594 (t-90) REVERT: E 296 GLU cc_start: 0.8831 (mp0) cc_final: 0.8168 (tt0) REVERT: F 36 MET cc_start: 0.8995 (mmm) cc_final: 0.8612 (mtp) REVERT: G 120 GLU cc_start: 0.7466 (pm20) cc_final: 0.7131 (pp20) REVERT: G 154 MET cc_start: 0.7916 (ttp) cc_final: 0.7626 (ttp) REVERT: G 329 MET cc_start: 0.3992 (pmm) cc_final: 0.3773 (pmm) REVERT: G 367 LYS cc_start: 0.6385 (mttt) cc_final: 0.6135 (mtpt) REVERT: G 397 ILE cc_start: 0.5979 (mt) cc_final: 0.5596 (mt) REVERT: G 443 LEU cc_start: 0.8159 (mt) cc_final: 0.7957 (mm) REVERT: H 154 MET cc_start: 0.7939 (mpp) cc_final: 0.7701 (mpp) REVERT: H 204 LEU cc_start: 0.8943 (tp) cc_final: 0.8604 (tt) REVERT: H 293 GLU cc_start: 0.8531 (pm20) cc_final: 0.8327 (pm20) REVERT: I 42 TRP cc_start: 0.6965 (m-10) cc_final: 0.6762 (m-10) REVERT: I 138 HIS cc_start: 0.8016 (p90) cc_final: 0.7640 (p-80) REVERT: I 258 TYR cc_start: 0.7277 (p90) cc_final: 0.6772 (p90) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.3196 time to fit residues: 108.5390 Evaluate side-chains 171 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 212 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 205 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 71 optimal weight: 0.2980 chunk 138 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.081535 restraints weight = 49108.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.083661 restraints weight = 30320.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085121 restraints weight = 21454.718| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17807 Z= 0.119 Angle : 0.668 11.965 24273 Z= 0.340 Chirality : 0.044 0.271 2760 Planarity : 0.006 0.081 3184 Dihedral : 6.727 56.067 2401 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.17), residues: 2178 helix: -0.13 (0.20), residues: 683 sheet: -1.90 (0.27), residues: 333 loop : -2.78 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP G 42 HIS 0.006 0.001 HIS G 40 PHE 0.019 0.001 PHE G 237 TYR 0.010 0.001 TYR H 405 ARG 0.008 0.000 ARG I 169 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 486) hydrogen bonds : angle 5.01922 ( 1389) covalent geometry : bond 0.00266 (17807) covalent geometry : angle 0.66820 (24273) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 325 MET cc_start: 0.5779 (mmt) cc_final: 0.5495 (mmt) REVERT: D 238 TRP cc_start: 0.6904 (m100) cc_final: 0.6013 (m100) REVERT: D 251 LYS cc_start: 0.8951 (tttt) cc_final: 0.8632 (tttt) REVERT: E 292 HIS cc_start: 0.5043 (t-90) cc_final: 0.4509 (t-90) REVERT: F 36 MET cc_start: 0.8884 (mmm) cc_final: 0.8628 (mtp) REVERT: F 184 PHE cc_start: 0.8548 (t80) cc_final: 0.8118 (t80) REVERT: G 26 ASP cc_start: 0.6879 (m-30) cc_final: 0.6069 (m-30) REVERT: G 48 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7449 (mt-10) REVERT: G 120 GLU cc_start: 0.7645 (pm20) cc_final: 0.7374 (pp20) REVERT: G 154 MET cc_start: 0.7617 (ttp) cc_final: 0.7339 (ttp) REVERT: G 324 LYS cc_start: 0.7106 (mmmm) cc_final: 0.6884 (mmtp) REVERT: G 367 LYS cc_start: 0.6556 (mttt) cc_final: 0.6311 (mtpt) REVERT: G 397 ILE cc_start: 0.6179 (mt) cc_final: 0.5782 (mt) REVERT: G 434 ASP cc_start: 0.6682 (t70) cc_final: 0.6430 (t0) REVERT: G 436 LYS cc_start: 0.6872 (mptt) cc_final: 0.6055 (mtpt) REVERT: H 26 ASP cc_start: 0.7902 (t0) cc_final: 0.7404 (t0) REVERT: H 67 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7867 (mmm-85) REVERT: H 189 LEU cc_start: 0.9192 (mt) cc_final: 0.8935 (mp) REVERT: H 204 LEU cc_start: 0.8863 (tp) cc_final: 0.8595 (tt) REVERT: H 356 HIS cc_start: 0.5542 (t-90) cc_final: 0.5146 (t-90) REVERT: H 436 LYS cc_start: 0.7087 (mmpt) cc_final: 0.6874 (mmmt) REVERT: I 138 HIS cc_start: 0.7685 (p90) cc_final: 0.7326 (p-80) REVERT: I 258 TYR cc_start: 0.7159 (p90) cc_final: 0.6526 (p90) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.3771 time to fit residues: 142.8952 Evaluate side-chains 191 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 189 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 65 optimal weight: 0.0670 chunk 161 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 184 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 318 GLN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** F 244 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 = 0.3528 r_free = 0.3528 target = 0.100650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.081247 restraints weight = 48824.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083325 restraints weight = 30328.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.084727 restraints weight = 21546.564| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17807 Z= 0.128 Angle : 0.675 15.782 24273 Z= 0.339 Chirality : 0.045 0.279 2760 Planarity : 0.006 0.073 3184 Dihedral : 6.515 54.984 2401 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.28 % Favored : 89.62 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.17), residues: 2178 helix: 0.17 (0.21), residues: 674 sheet: -1.78 (0.27), residues: 349 loop : -2.68 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP G 42 HIS 0.005 0.001 HIS H 292 PHE 0.030 0.001 PHE H 362 TYR 0.008 0.001 TYR H 405 ARG 0.008 0.000 ARG E 172 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 486) hydrogen bonds : angle 4.86614 ( 1389) covalent geometry : bond 0.00299 (17807) covalent geometry : angle 0.67489 (24273) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 36 MET cc_start: 0.7819 (mtm) cc_final: 0.7467 (mtt) REVERT: D 154 MET cc_start: 0.7457 (ttm) cc_final: 0.7132 (ttm) REVERT: D 238 TRP cc_start: 0.6915 (m100) cc_final: 0.5994 (m100) REVERT: D 251 LYS cc_start: 0.8993 (tttt) cc_final: 0.8684 (tttt) REVERT: E 15 MET cc_start: 0.7359 (mmt) cc_final: 0.7115 (mmm) REVERT: E 172 ARG cc_start: 0.6099 (ttp80) cc_final: 0.5764 (ttp80) REVERT: E 198 MET cc_start: 0.8198 (mmm) cc_final: 0.7550 (mtm) REVERT: E 292 HIS cc_start: 0.5229 (t-90) cc_final: 0.4148 (t-90) REVERT: F 36 MET cc_start: 0.8913 (mmm) cc_final: 0.8707 (mtp) REVERT: F 184 PHE cc_start: 0.8549 (t80) cc_final: 0.8094 (t80) REVERT: G 26 ASP cc_start: 0.6883 (m-30) cc_final: 0.6195 (m-30) REVERT: G 99 ILE cc_start: 0.9144 (mm) cc_final: 0.8752 (mm) REVERT: G 120 GLU cc_start: 0.7657 (pm20) cc_final: 0.7387 (pp20) REVERT: G 154 MET cc_start: 0.7669 (ttp) cc_final: 0.7428 (ttp) REVERT: G 329 MET cc_start: 0.3787 (pmm) cc_final: 0.3545 (pmm) REVERT: G 367 LYS cc_start: 0.6492 (mttt) cc_final: 0.6291 (mtpt) REVERT: G 397 ILE cc_start: 0.6433 (mt) cc_final: 0.6018 (mt) REVERT: G 436 LYS cc_start: 0.6798 (mptt) cc_final: 0.5979 (mtpt) REVERT: H 26 ASP cc_start: 0.7966 (t0) cc_final: 0.7410 (t0) REVERT: H 189 LEU cc_start: 0.9152 (mt) cc_final: 0.8930 (mp) REVERT: H 204 LEU cc_start: 0.8884 (tp) cc_final: 0.8651 (tt) REVERT: H 356 HIS cc_start: 0.5543 (t-90) cc_final: 0.5037 (t-90) REVERT: H 436 LYS cc_start: 0.7123 (mmpt) cc_final: 0.6901 (mmmt) REVERT: I 42 TRP cc_start: 0.6941 (m-10) cc_final: 0.6530 (m-10) REVERT: I 138 HIS cc_start: 0.7709 (p90) cc_final: 0.7424 (p-80) REVERT: I 154 MET cc_start: 0.7212 (ptm) cc_final: 0.6647 (ppp) REVERT: I 229 PHE cc_start: 0.5726 (t80) cc_final: 0.5435 (p90) REVERT: I 258 TYR cc_start: 0.7307 (p90) cc_final: 0.6630 (p90) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.3139 time to fit residues: 112.4032 Evaluate side-chains 191 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 48 optimal weight: 8.9990 chunk 199 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 128 optimal weight: 0.0970 chunk 188 optimal weight: 0.1980 chunk 43 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS ** E 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** F 244 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 = 0.3547 r_free = 0.3547 target = 0.101966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.082510 restraints weight = 48554.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.084626 restraints weight = 30282.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.086083 restraints weight = 21552.619| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17807 Z= 0.113 Angle : 0.648 12.398 24273 Z= 0.326 Chirality : 0.044 0.286 2760 Planarity : 0.005 0.066 3184 Dihedral : 6.234 54.397 2401 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.29 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.18), residues: 2178 helix: 0.47 (0.21), residues: 662 sheet: -1.53 (0.28), residues: 340 loop : -2.63 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP I 238 HIS 0.006 0.001 HIS H 292 PHE 0.019 0.001 PHE G 237 TYR 0.010 0.001 TYR G 265 ARG 0.014 0.000 ARG I 123 Details of bonding type rmsd hydrogen bonds : bond 0.03414 ( 486) hydrogen bonds : angle 4.68011 ( 1389) covalent geometry : bond 0.00253 (17807) covalent geometry : angle 0.64830 (24273) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 238 TRP cc_start: 0.6943 (m100) cc_final: 0.6122 (m100) REVERT: D 251 LYS cc_start: 0.8989 (tttt) cc_final: 0.8719 (tttt) REVERT: E 198 MET cc_start: 0.8164 (mmm) cc_final: 0.7514 (mtm) REVERT: E 292 HIS cc_start: 0.5234 (t-90) cc_final: 0.4186 (t-90) REVERT: F 4 TYR cc_start: 0.8684 (m-80) cc_final: 0.8443 (m-80) REVERT: F 184 PHE cc_start: 0.8530 (t80) cc_final: 0.8059 (t80) REVERT: F 196 SER cc_start: 0.8122 (m) cc_final: 0.7787 (t) REVERT: G 26 ASP cc_start: 0.6733 (m-30) cc_final: 0.6503 (m-30) REVERT: G 120 GLU cc_start: 0.7653 (pm20) cc_final: 0.7388 (pp20) REVERT: G 397 ILE cc_start: 0.6404 (mt) cc_final: 0.5842 (mt) REVERT: G 434 ASP cc_start: 0.6168 (t0) cc_final: 0.5906 (t0) REVERT: G 436 LYS cc_start: 0.6914 (mptt) cc_final: 0.6337 (mtpt) REVERT: H 204 LEU cc_start: 0.8863 (tp) cc_final: 0.8652 (tt) REVERT: H 356 HIS cc_start: 0.5826 (t-90) cc_final: 0.5244 (t-90) REVERT: H 436 LYS cc_start: 0.7091 (mmpt) cc_final: 0.6888 (mmmt) REVERT: I 42 TRP cc_start: 0.6875 (m-10) cc_final: 0.6344 (m-10) REVERT: I 138 HIS cc_start: 0.7745 (p90) cc_final: 0.7524 (p-80) REVERT: I 154 MET cc_start: 0.7181 (ptm) cc_final: 0.6676 (ppp) REVERT: I 258 TYR cc_start: 0.7259 (p90) cc_final: 0.6641 (p90) REVERT: I 263 LEU cc_start: 0.9098 (tt) cc_final: 0.8875 (mp) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.3400 time to fit residues: 128.2416 Evaluate side-chains 196 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 2.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 4 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 86 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS E 20 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 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 = 0.3522 r_free = 0.3522 target = 0.100339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.080931 restraints weight = 48804.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.083016 restraints weight = 30520.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.084424 restraints weight = 21741.736| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17807 Z= 0.141 Angle : 0.676 11.388 24273 Z= 0.337 Chirality : 0.045 0.288 2760 Planarity : 0.006 0.064 3184 Dihedral : 6.244 53.540 2401 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.79 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.18), residues: 2178 helix: 0.60 (0.21), residues: 655 sheet: -1.52 (0.28), residues: 335 loop : -2.58 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP I 238 HIS 0.009 0.001 HIS H 292 PHE 0.022 0.001 PHE H 362 TYR 0.011 0.001 TYR G 265 ARG 0.005 0.000 ARG I 123 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 486) hydrogen bonds : angle 4.72386 ( 1389) covalent geometry : bond 0.00332 (17807) covalent geometry : angle 0.67598 (24273) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 129 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7480 (mtm180) REVERT: D 238 TRP cc_start: 0.7018 (m100) cc_final: 0.6091 (m100) REVERT: D 251 LYS cc_start: 0.9036 (tttt) cc_final: 0.8733 (tttt) REVERT: E 292 HIS cc_start: 0.5894 (t-90) cc_final: 0.4265 (t-90) REVERT: F 162 TRP cc_start: 0.7361 (t-100) cc_final: 0.7062 (t-100) REVERT: F 184 PHE cc_start: 0.8532 (t80) cc_final: 0.8104 (t80) REVERT: F 196 SER cc_start: 0.8105 (m) cc_final: 0.7789 (t) REVERT: G 26 ASP cc_start: 0.6768 (m-30) cc_final: 0.6211 (m-30) REVERT: G 120 GLU cc_start: 0.7634 (pm20) cc_final: 0.7352 (pp20) REVERT: G 397 ILE cc_start: 0.6113 (mt) cc_final: 0.5466 (mt) REVERT: G 436 LYS cc_start: 0.6877 (mptt) cc_final: 0.6261 (mtpt) REVERT: H 26 ASP cc_start: 0.7971 (t0) cc_final: 0.7305 (t0) REVERT: H 154 MET cc_start: 0.8033 (mpp) cc_final: 0.7742 (mpp) REVERT: H 329 MET cc_start: 0.7105 (mmp) cc_final: 0.6900 (mmp) REVERT: H 356 HIS cc_start: 0.6032 (t-90) cc_final: 0.5300 (t-90) REVERT: H 436 LYS cc_start: 0.7077 (mmpt) cc_final: 0.6812 (mmmt) REVERT: I 42 TRP cc_start: 0.7037 (m-10) cc_final: 0.6478 (m-10) REVERT: I 138 HIS cc_start: 0.7660 (p90) cc_final: 0.7455 (p-80) REVERT: I 258 TYR cc_start: 0.7283 (p90) cc_final: 0.6580 (p90) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3197 time to fit residues: 111.2232 Evaluate side-chains 192 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 147 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 188 optimal weight: 0.0270 chunk 183 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 138 optimal weight: 0.2980 chunk 141 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 overall best weight: 0.8642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS E 20 GLN ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 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 = 0.3548 r_free = 0.3548 target = 0.101978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.082492 restraints weight = 48166.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084598 restraints weight = 29944.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086038 restraints weight = 21357.892| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17807 Z= 0.110 Angle : 0.650 16.749 24273 Z= 0.322 Chirality : 0.044 0.282 2760 Planarity : 0.005 0.098 3184 Dihedral : 6.011 52.931 2401 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.18), residues: 2178 helix: 0.76 (0.21), residues: 664 sheet: -1.42 (0.29), residues: 325 loop : -2.51 (0.16), residues: 1189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP I 238 HIS 0.007 0.001 HIS H 292 PHE 0.030 0.001 PHE I 229 TYR 0.013 0.001 TYR G 265 ARG 0.004 0.000 ARG E 172 Details of bonding type rmsd hydrogen bonds : bond 0.03335 ( 486) hydrogen bonds : angle 4.54558 ( 1389) covalent geometry : bond 0.00256 (17807) covalent geometry : angle 0.64952 (24273) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 129 ARG cc_start: 0.7899 (mtt90) cc_final: 0.7430 (mtm180) REVERT: D 238 TRP cc_start: 0.7035 (m100) cc_final: 0.6100 (m100) REVERT: D 251 LYS cc_start: 0.9020 (tttt) cc_final: 0.8750 (ttpt) REVERT: E 198 MET cc_start: 0.8369 (mmm) cc_final: 0.7454 (mtm) REVERT: E 292 HIS cc_start: 0.5242 (t-90) cc_final: 0.4272 (t-90) REVERT: F 82 LEU cc_start: 0.6785 (tp) cc_final: 0.6539 (tp) REVERT: F 184 PHE cc_start: 0.8526 (t80) cc_final: 0.8046 (t80) REVERT: F 196 SER cc_start: 0.8199 (m) cc_final: 0.7770 (t) REVERT: G 26 ASP cc_start: 0.6712 (m-30) cc_final: 0.6160 (m-30) REVERT: G 120 GLU cc_start: 0.7681 (pm20) cc_final: 0.7445 (pp20) REVERT: G 154 MET cc_start: 0.7849 (ttm) cc_final: 0.7526 (tmm) REVERT: G 397 ILE cc_start: 0.6145 (mt) cc_final: 0.5475 (mt) REVERT: G 434 ASP cc_start: 0.5751 (t0) cc_final: 0.5446 (t0) REVERT: G 436 LYS cc_start: 0.6907 (mptt) cc_final: 0.6348 (mtpt) REVERT: H 26 ASP cc_start: 0.8000 (t0) cc_final: 0.7600 (t0) REVERT: H 329 MET cc_start: 0.6999 (mmp) cc_final: 0.6194 (mmt) REVERT: H 356 HIS cc_start: 0.5967 (t-90) cc_final: 0.5256 (t-90) REVERT: H 426 PHE cc_start: 0.5852 (t80) cc_final: 0.5525 (t80) REVERT: H 436 LYS cc_start: 0.7090 (mmpt) cc_final: 0.6867 (mmmt) REVERT: I 42 TRP cc_start: 0.6869 (m-90) cc_final: 0.6307 (m-10) REVERT: I 258 TYR cc_start: 0.7213 (p90) cc_final: 0.6520 (p90) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.3232 time to fit residues: 116.4557 Evaluate side-chains 193 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 43 optimal weight: 0.8980 chunk 110 optimal weight: 0.0470 chunk 134 optimal weight: 0.3980 chunk 89 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 167 optimal weight: 0.0980 chunk 20 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 HIS E 20 GLN ** I 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 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 = 0.3557 r_free = 0.3557 target = 0.102329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.082564 restraints weight = 48655.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.084720 restraints weight = 29968.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.086195 restraints weight = 21278.633| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17807 Z= 0.110 Angle : 0.640 11.285 24273 Z= 0.320 Chirality : 0.043 0.278 2760 Planarity : 0.005 0.094 3184 Dihedral : 5.876 51.108 2401 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.18), residues: 2178 helix: 0.96 (0.21), residues: 662 sheet: -1.36 (0.29), residues: 325 loop : -2.46 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP I 238 HIS 0.011 0.001 HIS D 156 PHE 0.021 0.001 PHE I 229 TYR 0.011 0.001 TYR G 265 ARG 0.003 0.000 ARG E 172 Details of bonding type rmsd hydrogen bonds : bond 0.03255 ( 486) hydrogen bonds : angle 4.41837 ( 1389) covalent geometry : bond 0.00252 (17807) covalent geometry : angle 0.64029 (24273) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 129 ARG cc_start: 0.7800 (mtt90) cc_final: 0.7399 (mtm180) REVERT: D 238 TRP cc_start: 0.7038 (m100) cc_final: 0.6073 (m100) REVERT: D 251 LYS cc_start: 0.8993 (tttt) cc_final: 0.8698 (tttt) REVERT: E 198 MET cc_start: 0.8381 (mmm) cc_final: 0.7468 (mtm) REVERT: E 292 HIS cc_start: 0.5718 (t-90) cc_final: 0.4348 (t-90) REVERT: F 184 PHE cc_start: 0.8543 (t80) cc_final: 0.8021 (t80) REVERT: G 26 ASP cc_start: 0.6723 (m-30) cc_final: 0.6167 (m-30) REVERT: G 120 GLU cc_start: 0.7668 (pm20) cc_final: 0.7431 (pp20) REVERT: G 154 MET cc_start: 0.7807 (ttm) cc_final: 0.7518 (tmm) REVERT: G 190 THR cc_start: 0.8321 (p) cc_final: 0.7736 (t) REVERT: G 397 ILE cc_start: 0.6111 (mt) cc_final: 0.5418 (mt) REVERT: G 434 ASP cc_start: 0.5787 (t0) cc_final: 0.5558 (t0) REVERT: G 436 LYS cc_start: 0.6848 (mptt) cc_final: 0.6302 (mtpt) REVERT: H 26 ASP cc_start: 0.8009 (t0) cc_final: 0.7585 (t0) REVERT: H 329 MET cc_start: 0.7067 (mmp) cc_final: 0.6238 (mmt) REVERT: H 353 MET cc_start: 0.4273 (ptp) cc_final: 0.3885 (ptp) REVERT: H 356 HIS cc_start: 0.6077 (t-90) cc_final: 0.5334 (t-90) REVERT: H 426 PHE cc_start: 0.5647 (t80) cc_final: 0.5378 (t80) REVERT: H 436 LYS cc_start: 0.7150 (mmpt) cc_final: 0.6947 (mmmt) REVERT: H 443 LEU cc_start: 0.6961 (pp) cc_final: 0.6488 (mt) REVERT: I 42 TRP cc_start: 0.6803 (m-90) cc_final: 0.6318 (m-10) REVERT: I 258 TYR cc_start: 0.7153 (p90) cc_final: 0.6398 (p90) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2875 time to fit residues: 98.5242 Evaluate side-chains 187 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 52 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 196 optimal weight: 4.9990 chunk 175 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 128 optimal weight: 0.0060 chunk 73 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 171 optimal weight: 0.2980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 318 GLN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** I 241 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 = 0.3573 r_free = 0.3573 target = 0.103292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.083694 restraints weight = 47967.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085823 restraints weight = 29617.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087298 restraints weight = 21087.342| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17807 Z= 0.104 Angle : 0.633 11.314 24273 Z= 0.315 Chirality : 0.043 0.273 2760 Planarity : 0.005 0.091 3184 Dihedral : 5.722 53.053 2401 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.18), residues: 2178 helix: 1.09 (0.22), residues: 662 sheet: -1.35 (0.29), residues: 316 loop : -2.35 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 162 HIS 0.015 0.001 HIS D 156 PHE 0.023 0.001 PHE I 229 TYR 0.010 0.001 TYR G 265 ARG 0.003 0.000 ARG E 172 Details of bonding type rmsd hydrogen bonds : bond 0.03037 ( 486) hydrogen bonds : angle 4.29704 ( 1389) covalent geometry : bond 0.00240 (17807) covalent geometry : angle 0.63332 (24273) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 129 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7426 (mtm180) REVERT: D 238 TRP cc_start: 0.7071 (m100) cc_final: 0.6105 (m100) REVERT: D 251 LYS cc_start: 0.9017 (tttt) cc_final: 0.8718 (tttt) REVERT: E 292 HIS cc_start: 0.5173 (t-90) cc_final: 0.4182 (t-90) REVERT: F 184 PHE cc_start: 0.8560 (t80) cc_final: 0.7969 (t80) REVERT: G 26 ASP cc_start: 0.6638 (m-30) cc_final: 0.6128 (m-30) REVERT: G 120 GLU cc_start: 0.7653 (pm20) cc_final: 0.7418 (pp20) REVERT: G 154 MET cc_start: 0.7620 (ttm) cc_final: 0.7336 (tmm) REVERT: G 190 THR cc_start: 0.8291 (p) cc_final: 0.7754 (t) REVERT: G 434 ASP cc_start: 0.6005 (t0) cc_final: 0.5666 (t0) REVERT: G 436 LYS cc_start: 0.7091 (mptt) cc_final: 0.6548 (mtpt) REVERT: H 26 ASP cc_start: 0.7993 (t0) cc_final: 0.7555 (t0) REVERT: H 329 MET cc_start: 0.7098 (mmp) cc_final: 0.6281 (mmt) REVERT: H 353 MET cc_start: 0.4135 (ptp) cc_final: 0.3655 (ptp) REVERT: H 436 LYS cc_start: 0.7210 (mmpt) cc_final: 0.6981 (mmmt) REVERT: I 42 TRP cc_start: 0.6756 (m-90) cc_final: 0.6253 (m-10) REVERT: I 258 TYR cc_start: 0.7196 (p90) cc_final: 0.6428 (p90) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3009 time to fit residues: 106.5652 Evaluate side-chains 190 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 41 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 209 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 356 HIS ** I 241 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 = 0.3556 r_free = 0.3556 target = 0.102295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082997 restraints weight = 48267.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.085017 restraints weight = 30283.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086409 restraints weight = 21742.317| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17807 Z= 0.114 Angle : 0.642 10.549 24273 Z= 0.317 Chirality : 0.044 0.282 2760 Planarity : 0.005 0.090 3184 Dihedral : 5.702 54.165 2401 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.01 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.18), residues: 2178 helix: 1.16 (0.21), residues: 663 sheet: -1.26 (0.29), residues: 319 loop : -2.32 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP G 238 HIS 0.012 0.001 HIS D 156 PHE 0.023 0.001 PHE I 229 TYR 0.011 0.001 TYR G 265 ARG 0.003 0.000 ARG I 123 Details of bonding type rmsd hydrogen bonds : bond 0.03138 ( 486) hydrogen bonds : angle 4.31492 ( 1389) covalent geometry : bond 0.00266 (17807) covalent geometry : angle 0.64170 (24273) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5283.25 seconds wall clock time: 94 minutes 2.41 seconds (5642.41 seconds total)