Starting phenix.real_space_refine on Wed Sep 17 15:06:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gnq_51477/09_2025/9gnq_51477.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gnq_51477/09_2025/9gnq_51477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gnq_51477/09_2025/9gnq_51477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gnq_51477/09_2025/9gnq_51477.map" model { file = "/net/cci-nas-00/data/ceres_data/9gnq_51477/09_2025/9gnq_51477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gnq_51477/09_2025/9gnq_51477.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 60 5.16 5 C 5843 2.51 5 N 1583 2.21 5 O 1815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9309 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3358 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "K" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2450 Classifications: {'peptide': 312} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.91, per 1000 atoms: 0.21 Number of scatterers: 9309 At special positions: 0 Unit cell: (70.395, 109.383, 114.798, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 60 16.00 P 7 15.00 Mg 1 11.99 O 1815 8.00 N 1583 7.00 C 5843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 374.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 47.7% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 48 removed outlier: 4.311A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG B 48 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 71 through 80 removed outlier: 4.553A pdb=" N MET B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 102 through 109 Processing helix chain 'B' and resid 114 through 127 removed outlier: 3.556A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.606A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 216 removed outlier: 3.537A pdb=" N LEU B 209 " --> pdb=" O ASP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 239 removed outlier: 3.687A pdb=" N LEU B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 243 removed outlier: 3.613A pdb=" N ARG B 243 " --> pdb=" O THR B 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 251 through 260 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 301 removed outlier: 3.997A pdb=" N MET B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 339 removed outlier: 3.887A pdb=" N GLN B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 removed outlier: 3.678A pdb=" N PHE B 343 " --> pdb=" O SER B 340 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 340 through 343' Processing helix chain 'B' and resid 384 through 401 removed outlier: 3.834A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ARG B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 414 through 435 removed outlier: 3.773A pdb=" N PHE B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.414A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.652A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N HIS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.689A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.834A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.956A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.504A pdb=" N CYS A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.585A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 4.200A pdb=" N TRP A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.938A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 437 removed outlier: 4.345A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 57 through 66 Processing helix chain 'K' and resid 66 through 74 Processing helix chain 'K' and resid 90 through 95 Processing helix chain 'K' and resid 107 through 120 removed outlier: 3.567A pdb=" N ILE K 119 " --> pdb=" O ILE K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 188 Processing helix chain 'K' and resid 237 through 241 Processing helix chain 'K' and resid 245 through 270 Processing helix chain 'K' and resid 276 through 279 removed outlier: 3.753A pdb=" N ASP K 279 " --> pdb=" O PRO K 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 276 through 279' Processing helix chain 'K' and resid 280 through 286 Processing helix chain 'K' and resid 286 through 291 removed outlier: 3.885A pdb=" N GLY K 291 " --> pdb=" O GLN K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 305 through 307 No H-bonds generated for 'chain 'K' and resid 305 through 307' Processing helix chain 'K' and resid 308 through 323 removed outlier: 3.781A pdb=" N ALA K 322 " --> pdb=" O PHE K 318 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS K 323 " --> pdb=" O GLY K 319 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 92 through 94 removed outlier: 8.284A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU B 3 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLN B 136 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B 5 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N THR B 138 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 7 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N SER B 140 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ALA B 9 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS B 139 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N MET B 166 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N TYR B 202 " --> pdb=" O MET B 166 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR B 168 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ILE B 204 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N SER B 170 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 379 " --> pdb=" O MET B 269 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N SER B 374 " --> pdb=" O PHE B 319 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE B 319 " --> pdb=" O SER B 374 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR B 376 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA B 317 " --> pdb=" O THR B 376 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 378 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ASN B 380 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.848A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.128A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLU A 3 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N LEU A 136 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 269 through 273 removed outlier: 4.069A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 50 through 51 removed outlier: 3.656A pdb=" N ARG K 50 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR K 80 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL K 299 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE K 82 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N CYS K 301 " --> pdb=" O PHE K 82 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR K 84 " --> pdb=" O CYS K 301 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY K 79 " --> pdb=" O TYR K 228 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N VAL K 230 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE K 81 " --> pdb=" O VAL K 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 50 through 51 removed outlier: 3.656A pdb=" N ARG K 50 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR K 80 " --> pdb=" O THR K 297 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL K 299 " --> pdb=" O THR K 80 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE K 82 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N CYS K 301 " --> pdb=" O PHE K 82 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR K 84 " --> pdb=" O CYS K 301 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY K 79 " --> pdb=" O TYR K 228 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N VAL K 230 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE K 81 " --> pdb=" O VAL K 230 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE K 130 " --> pdb=" O VAL K 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.536A pdb=" N THR K 38 " --> pdb=" O GLN K 34 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 154 through 156 removed outlier: 4.402A pdb=" N SER K 154 " --> pdb=" O LYS K 166 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 192 through 193 removed outlier: 3.857A pdb=" N SER K 201 " --> pdb=" O ALA K 193 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1296 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1644 1.32 - 1.44: 2481 1.44 - 1.56: 5276 1.56 - 1.69: 15 1.69 - 1.81: 94 Bond restraints: 9510 Sorted by residual: bond pdb=" C PRO A 268 " pdb=" N LEU A 269 " ideal model delta sigma weight residual 1.330 1.537 -0.208 1.32e-02 5.74e+03 2.47e+02 bond pdb=" C LEU A 269 " pdb=" N ALA A 270 " ideal model delta sigma weight residual 1.328 1.479 -0.151 1.42e-02 4.96e+03 1.13e+02 bond pdb=" C GLU A 155 " pdb=" N ARG A 156 " ideal model delta sigma weight residual 1.334 1.225 0.109 1.33e-02 5.65e+03 6.76e+01 bond pdb=" C ARG A 221 " pdb=" N PRO A 222 " ideal model delta sigma weight residual 1.328 1.429 -0.101 1.26e-02 6.30e+03 6.41e+01 bond pdb=" C GLU A 220 " pdb=" N ARG A 221 " ideal model delta sigma weight residual 1.331 1.424 -0.093 1.35e-02 5.49e+03 4.73e+01 ... (remaining 9505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 12641 2.03 - 4.06: 209 4.06 - 6.09: 38 6.09 - 8.12: 13 8.12 - 10.15: 5 Bond angle restraints: 12906 Sorted by residual: angle pdb=" O PRO A 268 " pdb=" C PRO A 268 " pdb=" N LEU A 269 " ideal model delta sigma weight residual 123.14 133.04 -9.90 1.22e+00 6.72e-01 6.58e+01 angle pdb=" CA PRO A 268 " pdb=" C PRO A 268 " pdb=" N LEU A 269 " ideal model delta sigma weight residual 114.65 104.79 9.86 1.27e+00 6.20e-01 6.03e+01 angle pdb=" N VAL B 62 " pdb=" CA VAL B 62 " pdb=" CB VAL B 62 " ideal model delta sigma weight residual 112.37 106.97 5.40 1.06e+00 8.90e-01 2.59e+01 angle pdb=" C GLU A 220 " pdb=" N ARG A 221 " pdb=" CA ARG A 221 " ideal model delta sigma weight residual 123.15 117.36 5.79 1.21e+00 6.83e-01 2.29e+01 angle pdb=" N TYR K 307 " pdb=" CA TYR K 307 " pdb=" CB TYR K 307 " ideal model delta sigma weight residual 110.40 102.80 7.60 1.63e+00 3.76e-01 2.17e+01 ... (remaining 12901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.46: 5590 33.46 - 66.92: 139 66.92 - 100.38: 9 100.38 - 133.85: 16 133.85 - 167.31: 5 Dihedral angle restraints: 5759 sinusoidal: 2384 harmonic: 3375 Sorted by residual: dihedral pdb=" CD ARG A 221 " pdb=" NE ARG A 221 " pdb=" CZ ARG A 221 " pdb=" NH1 ARG A 221 " ideal model delta sinusoidal sigma weight residual 0.00 61.78 -61.78 1 1.00e+01 1.00e-02 5.06e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -123.42 -167.31 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -51.79 156.38 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 5756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1168 0.061 - 0.122: 222 0.122 - 0.184: 21 0.184 - 0.245: 5 0.245 - 0.306: 3 Chirality restraints: 1419 Sorted by residual: chirality pdb=" CA ILE K 30 " pdb=" N ILE K 30 " pdb=" C ILE K 30 " pdb=" CB ILE K 30 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA VAL B 62 " pdb=" N VAL B 62 " pdb=" C VAL B 62 " pdb=" CB VAL B 62 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CG LEU A 269 " pdb=" CB LEU A 269 " pdb=" CD1 LEU A 269 " pdb=" CD2 LEU A 269 " both_signs ideal model delta sigma weight residual False -2.59 -2.85 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1416 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 221 " -0.978 9.50e-02 1.11e+02 4.38e-01 1.16e+02 pdb=" NE ARG A 221 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG A 221 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 221 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 221 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " 0.348 9.50e-02 1.11e+02 1.56e-01 1.49e+01 pdb=" NE ARG A 156 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS K 93 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.04e+00 pdb=" C HIS K 93 " -0.052 2.00e-02 2.50e+03 pdb=" O HIS K 93 " 0.019 2.00e-02 2.50e+03 pdb=" N THR K 94 " 0.017 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 89 2.65 - 3.21: 8197 3.21 - 3.77: 13791 3.77 - 4.34: 19221 4.34 - 4.90: 32861 Nonbonded interactions: 74159 Sorted by model distance: nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 2.084 2.170 nonbonded pdb=" O ASN B 50 " pdb=" NH2 ARG B 64 " model vdw 2.221 3.120 nonbonded pdb=" OE1 GLU A 27 " pdb=" NH1 ARG A 243 " model vdw 2.285 3.120 nonbonded pdb=" OG SER B 324 " pdb=" O PRO A 222 " model vdw 2.287 3.040 nonbonded pdb=" O MET K 105 " pdb=" NH1 ARG K 110 " model vdw 2.288 3.120 ... (remaining 74154 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.070 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.813 9511 Z= 0.910 Angle : 0.695 10.146 12906 Z= 0.395 Chirality : 0.050 0.306 1419 Planarity : 0.012 0.438 1668 Dihedral : 17.137 167.308 3593 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.15 % Rotamer: Outliers : 0.99 % Allowed : 10.54 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.25), residues: 1156 helix: 1.31 (0.24), residues: 477 sheet: 0.74 (0.35), residues: 221 loop : -1.00 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 402 TYR 0.014 0.002 TYR K 29 PHE 0.016 0.002 PHE B 92 TRP 0.010 0.002 TRP A 21 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00649 ( 9510) covalent geometry : angle 0.69466 (12906) hydrogen bonds : bond 0.17736 ( 416) hydrogen bonds : angle 5.86438 ( 1296) Misc. bond : bond 0.81286 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6065 (mttt) cc_final: 0.5820 (mttt) outliers start: 10 outliers final: 3 residues processed: 217 average time/residue: 0.7041 time to fit residues: 160.5773 Evaluate side-chains 118 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 337 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.0030 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN K 34 GLN K 125 ASN ** K 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.081779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.065125 restraints weight = 17581.024| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.90 r_work: 0.2677 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9511 Z= 0.150 Angle : 0.626 11.303 12906 Z= 0.310 Chirality : 0.046 0.316 1419 Planarity : 0.004 0.067 1668 Dihedral : 13.828 170.102 1413 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.78 % Allowed : 16.00 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.25), residues: 1156 helix: 1.86 (0.24), residues: 480 sheet: 0.96 (0.34), residues: 218 loop : -0.73 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 339 TYR 0.015 0.001 TYR K 307 PHE 0.007 0.001 PHE K 116 TRP 0.014 0.001 TRP A 21 HIS 0.007 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9510) covalent geometry : angle 0.62575 (12906) hydrogen bonds : bond 0.04898 ( 416) hydrogen bonds : angle 4.19730 ( 1296) Misc. bond : bond 0.00076 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 113 GLU cc_start: 0.8532 (mp0) cc_final: 0.8297 (mp0) REVERT: B 205 ASP cc_start: 0.9019 (p0) cc_final: 0.8669 (p0) REVERT: B 290 GLU cc_start: 0.8114 (mp0) cc_final: 0.7818 (mp0) REVERT: B 299 LYS cc_start: 0.9327 (ptpp) cc_final: 0.9062 (ptmt) REVERT: B 323 MET cc_start: 0.8901 (ptp) cc_final: 0.8529 (ptp) REVERT: B 416 MET cc_start: 0.8485 (mmm) cc_final: 0.8095 (mmm) REVERT: A 50 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8234 (t0) REVERT: A 91 GLN cc_start: 0.8718 (mt0) cc_final: 0.8500 (mt0) REVERT: A 279 GLU cc_start: 0.8911 (mp0) cc_final: 0.8690 (mp0) REVERT: A 326 LYS cc_start: 0.5635 (mttt) cc_final: 0.5279 (mttt) REVERT: A 425 MET cc_start: 0.9101 (tpt) cc_final: 0.8771 (tpt) REVERT: K 72 ASP cc_start: 0.8792 (m-30) cc_final: 0.8389 (t0) REVERT: K 122 MET cc_start: 0.8374 (tpp) cc_final: 0.8157 (tpp) REVERT: K 184 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8614 (p0) REVERT: K 231 ASP cc_start: 0.8441 (t0) cc_final: 0.8199 (t0) outliers start: 28 outliers final: 9 residues processed: 138 average time/residue: 0.6486 time to fit residues: 94.5763 Evaluate side-chains 114 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain K residue 184 ASP Chi-restraints excluded: chain K residue 314 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 7 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS B 139 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.077023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.060652 restraints weight = 17810.825| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.88 r_work: 0.2592 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 9511 Z= 0.257 Angle : 0.630 6.196 12906 Z= 0.321 Chirality : 0.048 0.389 1419 Planarity : 0.004 0.066 1668 Dihedral : 10.936 171.356 1409 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.49 % Allowed : 17.20 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.25), residues: 1156 helix: 1.75 (0.24), residues: 486 sheet: 0.94 (0.34), residues: 221 loop : -0.72 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 339 TYR 0.008 0.001 TYR B 161 PHE 0.011 0.001 PHE B 395 TRP 0.014 0.002 TRP A 21 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 9510) covalent geometry : angle 0.63045 (12906) hydrogen bonds : bond 0.05809 ( 416) hydrogen bonds : angle 4.20515 ( 1296) Misc. bond : bond 0.00381 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: B 26 ASP cc_start: 0.9281 (t0) cc_final: 0.9020 (t0) REVERT: B 59 ASN cc_start: 0.8933 (m-40) cc_final: 0.8612 (m-40) REVERT: B 113 GLU cc_start: 0.8614 (mp0) cc_final: 0.8347 (mp0) REVERT: B 205 ASP cc_start: 0.8979 (p0) cc_final: 0.8709 (p0) REVERT: B 299 LYS cc_start: 0.9306 (ptpp) cc_final: 0.9081 (ptmt) REVERT: B 416 MET cc_start: 0.8698 (mmm) cc_final: 0.8342 (mmm) REVERT: A 90 GLU cc_start: 0.8667 (tp30) cc_final: 0.8382 (tm-30) REVERT: A 326 LYS cc_start: 0.5472 (mttt) cc_final: 0.4750 (mttt) REVERT: A 398 MET cc_start: 0.9073 (mtp) cc_final: 0.8873 (mtm) REVERT: A 414 GLU cc_start: 0.8771 (tt0) cc_final: 0.8427 (tp30) REVERT: K 72 ASP cc_start: 0.8786 (m-30) cc_final: 0.8421 (t0) REVERT: K 122 MET cc_start: 0.8486 (tpp) cc_final: 0.7965 (tpp) REVERT: K 231 ASP cc_start: 0.8550 (t0) cc_final: 0.8244 (t0) outliers start: 25 outliers final: 14 residues processed: 125 average time/residue: 0.6673 time to fit residues: 88.1911 Evaluate side-chains 113 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 423 GLU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 314 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN K 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.078447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.061944 restraints weight = 17814.724| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.99 r_work: 0.2615 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9511 Z= 0.150 Angle : 0.567 7.651 12906 Z= 0.285 Chirality : 0.045 0.307 1419 Planarity : 0.004 0.065 1668 Dihedral : 10.652 169.502 1409 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.68 % Allowed : 17.00 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.25), residues: 1156 helix: 1.83 (0.25), residues: 485 sheet: 0.95 (0.34), residues: 221 loop : -0.61 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 339 TYR 0.009 0.001 TYR A 108 PHE 0.007 0.001 PHE B 377 TRP 0.015 0.001 TRP A 21 HIS 0.002 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9510) covalent geometry : angle 0.56739 (12906) hydrogen bonds : bond 0.04660 ( 416) hydrogen bonds : angle 4.01128 ( 1296) Misc. bond : bond 0.00254 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.9014 (tpp) cc_final: 0.8796 (tpp) REVERT: B 26 ASP cc_start: 0.9132 (t0) cc_final: 0.8830 (t0) REVERT: B 59 ASN cc_start: 0.8934 (m-40) cc_final: 0.8614 (m-40) REVERT: B 113 GLU cc_start: 0.8693 (mp0) cc_final: 0.8414 (mp0) REVERT: B 205 ASP cc_start: 0.9009 (p0) cc_final: 0.8719 (p0) REVERT: B 416 MET cc_start: 0.8589 (mmm) cc_final: 0.8231 (mmm) REVERT: A 1 MET cc_start: 0.6804 (tmm) cc_final: 0.6197 (tmm) REVERT: A 50 ASN cc_start: 0.8571 (t0) cc_final: 0.7792 (t0) REVERT: A 90 GLU cc_start: 0.8670 (tp30) cc_final: 0.8380 (tm-30) REVERT: A 279 GLU cc_start: 0.8839 (mp0) cc_final: 0.8637 (mp0) REVERT: A 302 MET cc_start: 0.9190 (mmm) cc_final: 0.8986 (mtm) REVERT: A 326 LYS cc_start: 0.5314 (mttt) cc_final: 0.4997 (mttt) REVERT: A 339 ARG cc_start: 0.8702 (mmm160) cc_final: 0.8438 (mmp80) REVERT: A 377 MET cc_start: 0.9155 (ttp) cc_final: 0.8948 (ttm) REVERT: A 414 GLU cc_start: 0.8790 (tt0) cc_final: 0.8440 (tp30) REVERT: K 72 ASP cc_start: 0.8798 (m-30) cc_final: 0.8403 (t0) REVERT: K 122 MET cc_start: 0.8512 (tpp) cc_final: 0.8011 (tpp) REVERT: K 231 ASP cc_start: 0.8523 (t0) cc_final: 0.8180 (t0) outliers start: 27 outliers final: 16 residues processed: 125 average time/residue: 0.6061 time to fit residues: 80.5420 Evaluate side-chains 118 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 141 LYS Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 314 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 78 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 71 optimal weight: 0.0980 chunk 95 optimal weight: 0.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.080995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.064616 restraints weight = 17641.445| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.97 r_work: 0.2678 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9511 Z= 0.101 Angle : 0.532 6.687 12906 Z= 0.264 Chirality : 0.043 0.239 1419 Planarity : 0.004 0.064 1668 Dihedral : 10.154 165.727 1409 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.49 % Allowed : 19.18 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.26), residues: 1156 helix: 1.89 (0.25), residues: 491 sheet: 1.13 (0.34), residues: 215 loop : -0.56 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 161 TYR 0.010 0.001 TYR A 108 PHE 0.007 0.001 PHE B 377 TRP 0.014 0.001 TRP A 21 HIS 0.002 0.000 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 9510) covalent geometry : angle 0.53186 (12906) hydrogen bonds : bond 0.03517 ( 416) hydrogen bonds : angle 3.80660 ( 1296) Misc. bond : bond 0.00133 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.259 Fit side-chains REVERT: B 59 ASN cc_start: 0.8902 (m-40) cc_final: 0.8572 (m-40) REVERT: B 113 GLU cc_start: 0.8704 (mp0) cc_final: 0.8404 (mp0) REVERT: B 205 ASP cc_start: 0.8891 (p0) cc_final: 0.8615 (p0) REVERT: B 416 MET cc_start: 0.8475 (mmm) cc_final: 0.8129 (mmm) REVERT: A 1 MET cc_start: 0.7070 (tmm) cc_final: 0.6644 (tmm) REVERT: A 50 ASN cc_start: 0.8433 (t0) cc_final: 0.7504 (t0) REVERT: A 90 GLU cc_start: 0.8661 (tp30) cc_final: 0.8429 (tm-30) REVERT: A 279 GLU cc_start: 0.8794 (mp0) cc_final: 0.8549 (mp0) REVERT: A 302 MET cc_start: 0.9025 (mmm) cc_final: 0.8823 (mtm) REVERT: A 313 MET cc_start: 0.9156 (mtp) cc_final: 0.8954 (mtp) REVERT: A 326 LYS cc_start: 0.5321 (mttt) cc_final: 0.5048 (mttt) REVERT: A 339 ARG cc_start: 0.8709 (mmm160) cc_final: 0.8410 (mmp80) REVERT: A 414 GLU cc_start: 0.8825 (tt0) cc_final: 0.8494 (tp30) REVERT: K 72 ASP cc_start: 0.8814 (m-30) cc_final: 0.8402 (t0) REVERT: K 122 MET cc_start: 0.8510 (tpp) cc_final: 0.8066 (tpp) REVERT: K 231 ASP cc_start: 0.8467 (t0) cc_final: 0.8132 (t0) outliers start: 15 outliers final: 5 residues processed: 126 average time/residue: 0.6003 time to fit residues: 80.3629 Evaluate side-chains 107 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 114 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 0.0050 chunk 42 optimal weight: 10.0000 chunk 82 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.081331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.064957 restraints weight = 17678.246| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.99 r_work: 0.2683 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9511 Z= 0.106 Angle : 0.545 7.100 12906 Z= 0.273 Chirality : 0.043 0.226 1419 Planarity : 0.004 0.063 1668 Dihedral : 9.892 162.709 1409 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.09 % Allowed : 18.99 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.25), residues: 1156 helix: 1.86 (0.24), residues: 497 sheet: 1.21 (0.35), residues: 215 loop : -0.62 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG K 161 TYR 0.009 0.001 TYR A 108 PHE 0.006 0.001 PHE K 116 TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9510) covalent geometry : angle 0.54512 (12906) hydrogen bonds : bond 0.03545 ( 416) hydrogen bonds : angle 3.74375 ( 1296) Misc. bond : bond 0.00140 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.260 Fit side-chains REVERT: B 59 ASN cc_start: 0.8941 (m-40) cc_final: 0.8612 (m-40) REVERT: B 113 GLU cc_start: 0.8770 (mp0) cc_final: 0.8451 (mp0) REVERT: B 205 ASP cc_start: 0.8871 (p0) cc_final: 0.8594 (p0) REVERT: B 295 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8503 (mtp) REVERT: B 416 MET cc_start: 0.8467 (mmm) cc_final: 0.8118 (mmm) REVERT: A 1 MET cc_start: 0.7115 (tmm) cc_final: 0.6648 (tmm) REVERT: A 50 ASN cc_start: 0.8475 (t0) cc_final: 0.7563 (t0) REVERT: A 90 GLU cc_start: 0.8657 (tp30) cc_final: 0.8432 (tm-30) REVERT: A 279 GLU cc_start: 0.8793 (mp0) cc_final: 0.8521 (mp0) REVERT: A 302 MET cc_start: 0.9063 (mmm) cc_final: 0.8803 (mtm) REVERT: A 326 LYS cc_start: 0.5314 (mttt) cc_final: 0.4910 (mttt) REVERT: A 339 ARG cc_start: 0.8699 (mmm160) cc_final: 0.8462 (mmp80) REVERT: A 414 GLU cc_start: 0.8802 (tt0) cc_final: 0.8480 (tp30) REVERT: K 122 MET cc_start: 0.8552 (tpp) cc_final: 0.8174 (tpp) REVERT: K 231 ASP cc_start: 0.8439 (t0) cc_final: 0.8073 (t0) outliers start: 21 outliers final: 10 residues processed: 118 average time/residue: 0.6231 time to fit residues: 78.2569 Evaluate side-chains 115 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 314 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 125 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.060539 restraints weight = 18057.504| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.95 r_work: 0.2587 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 9511 Z= 0.231 Angle : 0.622 7.409 12906 Z= 0.316 Chirality : 0.047 0.227 1419 Planarity : 0.004 0.064 1668 Dihedral : 10.036 165.570 1409 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.58 % Allowed : 19.18 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.25), residues: 1156 helix: 1.80 (0.24), residues: 493 sheet: 1.09 (0.34), residues: 215 loop : -0.59 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 161 TYR 0.007 0.001 TYR B 61 PHE 0.010 0.001 PHE B 395 TRP 0.008 0.002 TRP A 21 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 9510) covalent geometry : angle 0.62235 (12906) hydrogen bonds : bond 0.05366 ( 416) hydrogen bonds : angle 4.03781 ( 1296) Misc. bond : bond 0.00368 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.368 Fit side-chains REVERT: B 59 ASN cc_start: 0.9010 (m-40) cc_final: 0.8672 (m-40) REVERT: B 113 GLU cc_start: 0.8779 (mp0) cc_final: 0.8461 (mp0) REVERT: B 205 ASP cc_start: 0.8925 (p0) cc_final: 0.8662 (p0) REVERT: B 295 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8472 (mtp) REVERT: B 416 MET cc_start: 0.8717 (mmm) cc_final: 0.8368 (mmm) REVERT: A 50 ASN cc_start: 0.8760 (t0) cc_final: 0.8376 (t0) REVERT: A 326 LYS cc_start: 0.5472 (mttt) cc_final: 0.4905 (mttt) REVERT: A 414 GLU cc_start: 0.8832 (tt0) cc_final: 0.8501 (tp30) REVERT: K 122 MET cc_start: 0.8632 (tpp) cc_final: 0.8202 (tpp) REVERT: K 231 ASP cc_start: 0.8504 (t0) cc_final: 0.8176 (t0) outliers start: 26 outliers final: 12 residues processed: 118 average time/residue: 0.6299 time to fit residues: 78.7975 Evaluate side-chains 111 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 314 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 89 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.079862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.063574 restraints weight = 17655.711| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.96 r_work: 0.2637 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9511 Z= 0.121 Angle : 0.586 8.207 12906 Z= 0.295 Chirality : 0.044 0.208 1419 Planarity : 0.004 0.073 1668 Dihedral : 9.758 162.582 1409 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.69 % Allowed : 21.07 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.25), residues: 1156 helix: 1.87 (0.25), residues: 493 sheet: 1.09 (0.34), residues: 221 loop : -0.55 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 339 TYR 0.009 0.001 TYR A 108 PHE 0.007 0.001 PHE K 116 TRP 0.015 0.001 TRP A 21 HIS 0.002 0.001 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9510) covalent geometry : angle 0.58641 (12906) hydrogen bonds : bond 0.03996 ( 416) hydrogen bonds : angle 3.84303 ( 1296) Misc. bond : bond 0.00190 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.360 Fit side-chains REVERT: B 59 ASN cc_start: 0.8986 (m-40) cc_final: 0.8680 (m-40) REVERT: B 113 GLU cc_start: 0.8811 (mp0) cc_final: 0.8481 (mp0) REVERT: B 205 ASP cc_start: 0.8839 (p0) cc_final: 0.8560 (p0) REVERT: B 295 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8445 (mtp) REVERT: B 416 MET cc_start: 0.8527 (mmm) cc_final: 0.8143 (mmm) REVERT: A 1 MET cc_start: 0.7092 (tmm) cc_final: 0.6752 (tmm) REVERT: A 50 ASN cc_start: 0.8684 (t0) cc_final: 0.7692 (t0) REVERT: A 154 MET cc_start: 0.9175 (mmm) cc_final: 0.8686 (mmm) REVERT: A 168 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8662 (mm-30) REVERT: A 279 GLU cc_start: 0.8816 (mp0) cc_final: 0.8566 (mp0) REVERT: A 326 LYS cc_start: 0.5195 (mttt) cc_final: 0.4887 (mttt) REVERT: A 414 GLU cc_start: 0.8863 (tt0) cc_final: 0.8519 (tp30) REVERT: K 122 MET cc_start: 0.8601 (tpp) cc_final: 0.8230 (tpp) REVERT: K 231 ASP cc_start: 0.8457 (t0) cc_final: 0.8107 (t0) outliers start: 17 outliers final: 11 residues processed: 116 average time/residue: 0.6689 time to fit residues: 82.0890 Evaluate side-chains 117 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 314 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.077563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.061035 restraints weight = 17918.695| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.01 r_work: 0.2598 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 9511 Z= 0.215 Angle : 0.641 7.466 12906 Z= 0.325 Chirality : 0.046 0.220 1419 Planarity : 0.004 0.067 1668 Dihedral : 9.860 164.273 1409 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.69 % Allowed : 21.67 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.25), residues: 1156 helix: 1.84 (0.25), residues: 493 sheet: 1.05 (0.34), residues: 216 loop : -0.55 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 161 TYR 0.007 0.001 TYR B 61 PHE 0.009 0.001 PHE B 395 TRP 0.009 0.001 TRP A 21 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 9510) covalent geometry : angle 0.64118 (12906) hydrogen bonds : bond 0.04992 ( 416) hydrogen bonds : angle 3.98820 ( 1296) Misc. bond : bond 0.00341 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.414 Fit side-chains REVERT: B 26 ASP cc_start: 0.9227 (t0) cc_final: 0.9003 (t0) REVERT: B 59 ASN cc_start: 0.9037 (m-40) cc_final: 0.8745 (m-40) REVERT: B 113 GLU cc_start: 0.8801 (mp0) cc_final: 0.8447 (mp0) REVERT: B 205 ASP cc_start: 0.8878 (p0) cc_final: 0.8601 (p0) REVERT: B 295 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8456 (mtp) REVERT: B 416 MET cc_start: 0.8706 (mmm) cc_final: 0.8357 (mmm) REVERT: A 1 MET cc_start: 0.7030 (tmm) cc_final: 0.6733 (tmm) REVERT: A 50 ASN cc_start: 0.8775 (t0) cc_final: 0.7773 (t0) REVERT: A 279 GLU cc_start: 0.8811 (mp0) cc_final: 0.8562 (mp0) REVERT: A 326 LYS cc_start: 0.5413 (mttt) cc_final: 0.4920 (mttt) REVERT: A 414 GLU cc_start: 0.8878 (tt0) cc_final: 0.8528 (tp30) REVERT: A 433 GLU cc_start: 0.8638 (pp20) cc_final: 0.8372 (pp20) REVERT: K 122 MET cc_start: 0.8657 (tpp) cc_final: 0.8283 (tpp) REVERT: K 231 ASP cc_start: 0.8488 (t0) cc_final: 0.8152 (t0) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.6790 time to fit residues: 81.1441 Evaluate side-chains 113 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 314 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 31 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 0.0030 chunk 112 optimal weight: 0.0070 chunk 90 optimal weight: 0.9980 overall best weight: 0.8010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.081726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.065025 restraints weight = 17563.402| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.97 r_work: 0.2674 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9511 Z= 0.118 Angle : 0.608 8.120 12906 Z= 0.306 Chirality : 0.044 0.203 1419 Planarity : 0.004 0.062 1668 Dihedral : 9.494 159.952 1409 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.59 % Allowed : 21.37 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.25), residues: 1156 helix: 1.83 (0.24), residues: 498 sheet: 1.12 (0.35), residues: 215 loop : -0.55 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 161 TYR 0.010 0.001 TYR A 108 PHE 0.007 0.001 PHE B 377 TRP 0.016 0.002 TRP A 21 HIS 0.002 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9510) covalent geometry : angle 0.60828 (12906) hydrogen bonds : bond 0.03601 ( 416) hydrogen bonds : angle 3.80173 ( 1296) Misc. bond : bond 0.00148 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2312 Ramachandran restraints generated. 1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.296 Fit side-chains REVERT: B 59 ASN cc_start: 0.9021 (m-40) cc_final: 0.8739 (m-40) REVERT: B 113 GLU cc_start: 0.8812 (mp0) cc_final: 0.8477 (mp0) REVERT: B 205 ASP cc_start: 0.8817 (p0) cc_final: 0.8561 (p0) REVERT: B 295 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8530 (mtp) REVERT: B 299 LYS cc_start: 0.9283 (mtmm) cc_final: 0.8920 (mtpp) REVERT: B 416 MET cc_start: 0.8524 (mmm) cc_final: 0.8152 (mmm) REVERT: B 417 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8189 (mt-10) REVERT: A 1 MET cc_start: 0.7160 (tmm) cc_final: 0.6778 (tmm) REVERT: A 50 ASN cc_start: 0.8646 (t0) cc_final: 0.7649 (t0) REVERT: A 279 GLU cc_start: 0.8759 (mp0) cc_final: 0.8528 (mp0) REVERT: A 326 LYS cc_start: 0.5359 (mttt) cc_final: 0.5065 (mttt) REVERT: A 414 GLU cc_start: 0.8863 (tt0) cc_final: 0.8547 (tp30) REVERT: K 99 LEU cc_start: 0.9459 (mm) cc_final: 0.9104 (tm) REVERT: K 122 MET cc_start: 0.8576 (tpp) cc_final: 0.8295 (tpp) REVERT: K 231 ASP cc_start: 0.8423 (t0) cc_final: 0.8076 (t0) outliers start: 16 outliers final: 12 residues processed: 118 average time/residue: 0.6544 time to fit residues: 81.7619 Evaluate side-chains 120 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 314 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 1 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 24 optimal weight: 0.1980 chunk 71 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.065960 restraints weight = 17753.637| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.90 r_work: 0.2675 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9511 Z= 0.128 Angle : 0.617 9.062 12906 Z= 0.308 Chirality : 0.044 0.209 1419 Planarity : 0.004 0.066 1668 Dihedral : 9.295 156.119 1409 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.49 % Allowed : 21.77 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1156 helix: 1.84 (0.24), residues: 498 sheet: 1.18 (0.35), residues: 214 loop : -0.55 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG K 161 TYR 0.009 0.001 TYR A 108 PHE 0.007 0.001 PHE B 377 TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9510) covalent geometry : angle 0.61724 (12906) hydrogen bonds : bond 0.03802 ( 416) hydrogen bonds : angle 3.77773 ( 1296) Misc. bond : bond 0.00188 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2695.27 seconds wall clock time: 46 minutes 41.21 seconds (2801.21 seconds total)