Starting phenix.real_space_refine on Thu Jan 16 09:03:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gnq_51477/01_2025/9gnq_51477.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gnq_51477/01_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_51477/01_2025/9gnq_51477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gnq_51477/01_2025/9gnq_51477.map" model { file = "/net/cci-nas-00/data/ceres_data/9gnq_51477/01_2025/9gnq_51477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gnq_51477/01_2025/9gnq_51477.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 5.77, per 1000 atoms: 0.62 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: 2.61 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.16 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: 3.04 Time building geometry restraints manager: 2.93 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: 0.810 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.840 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 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:14.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.050 ------------------------------------------------------------------------------- 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 : 0.006 0.208 9510 Z= 0.416 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 : 5.18 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 (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: 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 TRP 0.010 0.002 TRP A 21 HIS 0.005 0.001 HIS B 192 PHE 0.016 0.002 PHE B 92 TYR 0.014 0.002 TYR K 29 ARG 0.003 0.000 ARG A 402 *********************** 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 : 1.051 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: 1.5869 time to fit residues: 362.7069 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 : 1.119 ------------------------------------------------------------------------------- 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 97 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 overall best weight: 1.4982 ------------------------------------------------------------------------------- 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 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.082069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.065627 restraints weight = 17426.615| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.88 r_work: 0.2693 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9510 Z= 0.189 Angle : 0.624 11.604 12906 Z= 0.307 Chirality : 0.045 0.291 1419 Planarity : 0.004 0.066 1668 Dihedral : 14.054 169.362 1413 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.49 % Allowed : 16.20 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.25), residues: 1156 helix: 1.90 (0.25), residues: 480 sheet: 0.97 (0.34), residues: 218 loop : -0.72 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.005 0.001 HIS K 200 PHE 0.008 0.001 PHE K 116 TYR 0.016 0.001 TYR K 307 ARG 0.007 0.001 ARG K 161 *********************** 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: 25 poor density : 123 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: B 113 GLU cc_start: 0.8503 (mp0) cc_final: 0.8276 (mp0) REVERT: B 205 ASP cc_start: 0.8992 (p0) cc_final: 0.8660 (p0) REVERT: B 290 GLU cc_start: 0.8106 (mp0) cc_final: 0.7820 (mp0) REVERT: B 299 LYS cc_start: 0.9324 (ptpp) cc_final: 0.9056 (ptmt) REVERT: B 323 MET cc_start: 0.8868 (ptp) cc_final: 0.8547 (ptp) REVERT: B 332 MET cc_start: 0.9460 (mmt) cc_final: 0.9259 (mmm) REVERT: B 416 MET cc_start: 0.8409 (mmm) cc_final: 0.8037 (mmm) REVERT: B 417 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8163 (mt-10) REVERT: A 50 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8192 (t0) REVERT: A 90 GLU cc_start: 0.8537 (tp30) cc_final: 0.8232 (tm-30) REVERT: A 279 GLU cc_start: 0.8915 (mp0) cc_final: 0.8693 (mp0) REVERT: A 326 LYS cc_start: 0.5668 (mttt) cc_final: 0.5324 (mttt) REVERT: A 425 MET cc_start: 0.9091 (tpt) cc_final: 0.8720 (tpt) REVERT: A 433 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8695 (pp20) REVERT: K 72 ASP cc_start: 0.8783 (m-30) cc_final: 0.8383 (t0) REVERT: K 122 MET cc_start: 0.8345 (tpp) cc_final: 0.8108 (tpp) REVERT: K 178 GLU cc_start: 0.8755 (mp0) cc_final: 0.8417 (mp0) REVERT: K 184 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8589 (p0) REVERT: K 231 ASP cc_start: 0.8426 (t0) cc_final: 0.8191 (t0) outliers start: 25 outliers final: 8 residues processed: 138 average time/residue: 1.4462 time to fit residues: 212.2320 Evaluate side-chains 117 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 36 optimal weight: 6.9990 chunk 43 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 B 436 GLN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.075731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.059274 restraints weight = 18120.532| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.90 r_work: 0.2560 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 9510 Z= 0.493 Angle : 0.674 6.383 12906 Z= 0.344 Chirality : 0.049 0.384 1419 Planarity : 0.005 0.067 1668 Dihedral : 11.068 172.841 1409 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.68 % Allowed : 16.80 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1156 helix: 1.68 (0.24), residues: 483 sheet: 0.89 (0.33), residues: 221 loop : -0.72 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 21 HIS 0.005 0.001 HIS A 266 PHE 0.014 0.001 PHE B 395 TYR 0.009 0.001 TYR A 83 ARG 0.012 0.001 ARG A 339 *********************** 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 132 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: B 26 ASP cc_start: 0.9285 (t0) cc_final: 0.9071 (t0) REVERT: B 59 ASN cc_start: 0.8954 (m-40) cc_final: 0.8639 (m-40) REVERT: B 113 GLU cc_start: 0.8626 (mp0) cc_final: 0.8372 (mp0) REVERT: B 205 ASP cc_start: 0.9021 (p0) cc_final: 0.8772 (p0) REVERT: B 416 MET cc_start: 0.8755 (mmm) cc_final: 0.8398 (mmm) REVERT: A 1 MET cc_start: 0.6885 (tmm) cc_final: 0.6378 (tmm) REVERT: A 50 ASN cc_start: 0.8894 (t0) cc_final: 0.8551 (t0) REVERT: A 90 GLU cc_start: 0.8782 (tp30) cc_final: 0.8488 (tm-30) REVERT: A 192 HIS cc_start: 0.7833 (OUTLIER) cc_final: 0.7538 (t-170) REVERT: A 326 LYS cc_start: 0.5424 (mttt) cc_final: 0.4976 (mttt) REVERT: A 414 GLU cc_start: 0.8802 (tt0) cc_final: 0.8448 (tp30) REVERT: A 433 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8739 (pp20) REVERT: K 122 MET cc_start: 0.8595 (tpp) cc_final: 0.7994 (tpp) REVERT: K 178 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8346 (mp0) REVERT: K 221 GLN cc_start: 0.8448 (pp30) cc_final: 0.8167 (pp30) REVERT: K 231 ASP cc_start: 0.8585 (t0) cc_final: 0.8298 (t0) outliers start: 27 outliers final: 15 residues processed: 126 average time/residue: 1.4954 time to fit residues: 199.9326 Evaluate side-chains 115 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 190 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 387 LEU 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 192 HIS Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 178 GLU 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 33 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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** K 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.078610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.062125 restraints weight = 17571.468| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.95 r_work: 0.2610 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9510 Z= 0.188 Angle : 0.558 7.078 12906 Z= 0.280 Chirality : 0.044 0.294 1419 Planarity : 0.004 0.065 1668 Dihedral : 10.629 169.904 1409 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.88 % Allowed : 16.70 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1156 helix: 1.90 (0.25), residues: 485 sheet: 0.98 (0.33), residues: 221 loop : -0.61 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 21 HIS 0.002 0.001 HIS B 229 PHE 0.007 0.001 PHE B 377 TYR 0.009 0.001 TYR A 108 ARG 0.012 0.001 ARG A 339 *********************** 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 138 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.9039 (tpp) cc_final: 0.8805 (tpp) REVERT: B 26 ASP cc_start: 0.9131 (t0) cc_final: 0.8825 (t0) REVERT: B 59 ASN cc_start: 0.8960 (m-40) cc_final: 0.8642 (m-40) REVERT: B 113 GLU cc_start: 0.8681 (mp0) cc_final: 0.8384 (mp0) REVERT: B 205 ASP cc_start: 0.9022 (p0) cc_final: 0.8724 (p0) REVERT: B 299 LYS cc_start: 0.9300 (ptpp) cc_final: 0.9041 (ptmt) REVERT: B 416 MET cc_start: 0.8531 (mmm) cc_final: 0.8180 (mmm) REVERT: A 90 GLU cc_start: 0.8765 (tp30) cc_final: 0.8441 (tm-30) REVERT: A 279 GLU cc_start: 0.8854 (mp0) cc_final: 0.8654 (mp0) REVERT: A 326 LYS cc_start: 0.5266 (mttt) cc_final: 0.4830 (mttt) REVERT: A 339 ARG cc_start: 0.8706 (mmm160) cc_final: 0.8424 (mmp80) REVERT: A 377 MET cc_start: 0.9129 (ttp) cc_final: 0.8917 (ttm) REVERT: A 414 GLU cc_start: 0.8801 (tt0) cc_final: 0.8435 (tp30) REVERT: A 420 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8263 (mt-10) REVERT: A 433 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8641 (pp20) REVERT: K 72 ASP cc_start: 0.8785 (m-30) cc_final: 0.8391 (t0) REVERT: K 122 MET cc_start: 0.8554 (tpp) cc_final: 0.8041 (tpp) REVERT: K 178 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8396 (mp0) REVERT: K 231 ASP cc_start: 0.8501 (t0) cc_final: 0.8172 (t0) outliers start: 29 outliers final: 13 residues processed: 128 average time/residue: 1.3476 time to fit residues: 183.9253 Evaluate side-chains 117 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 190 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 425 MET 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 K residue 132 VAL Chi-restraints excluded: chain K residue 178 GLU Chi-restraints excluded: chain K residue 218 GLN 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 3 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.079701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.063228 restraints weight = 17502.624| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.96 r_work: 0.2625 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9510 Z= 0.183 Angle : 0.540 8.901 12906 Z= 0.268 Chirality : 0.044 0.242 1419 Planarity : 0.004 0.064 1668 Dihedral : 10.287 168.184 1409 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.39 % Allowed : 17.79 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1156 helix: 1.89 (0.24), residues: 493 sheet: 1.12 (0.34), residues: 221 loop : -0.60 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.003 0.001 HIS B 139 PHE 0.007 0.001 PHE B 377 TYR 0.010 0.001 TYR A 108 ARG 0.010 0.000 ARG K 161 *********************** 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: 24 poor density : 107 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 ASN cc_start: 0.8941 (m-40) cc_final: 0.8617 (m-40) REVERT: B 113 GLU cc_start: 0.8677 (mp0) cc_final: 0.8362 (mp0) REVERT: B 205 ASP cc_start: 0.8932 (p0) cc_final: 0.8645 (p0) REVERT: B 295 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8471 (mtp) REVERT: B 299 LYS cc_start: 0.9300 (ptpp) cc_final: 0.9067 (ptmt) REVERT: B 416 MET cc_start: 0.8495 (mmm) cc_final: 0.8120 (mmm) REVERT: B 417 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8204 (mt-10) REVERT: A 1 MET cc_start: 0.7030 (tmm) cc_final: 0.6552 (tmm) REVERT: A 50 ASN cc_start: 0.8498 (t0) cc_final: 0.7530 (t0) REVERT: A 90 GLU cc_start: 0.8749 (tp30) cc_final: 0.8437 (tm-30) REVERT: A 279 GLU cc_start: 0.8816 (mp0) cc_final: 0.8573 (mp0) REVERT: A 326 LYS cc_start: 0.5245 (mttt) cc_final: 0.4920 (mttt) REVERT: A 339 ARG cc_start: 0.8710 (mmm160) cc_final: 0.8403 (mmp80) REVERT: A 414 GLU cc_start: 0.8801 (tt0) cc_final: 0.8459 (tp30) REVERT: A 420 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8264 (mt-10) REVERT: A 433 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8610 (pp20) REVERT: K 72 ASP cc_start: 0.8812 (m-30) cc_final: 0.8424 (t0) REVERT: K 122 MET cc_start: 0.8600 (tpp) cc_final: 0.8098 (tpp) REVERT: K 177 ASP cc_start: 0.8453 (p0) cc_final: 0.7941 (p0) REVERT: K 178 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: K 181 ASP cc_start: 0.9025 (m-30) cc_final: 0.8809 (m-30) REVERT: K 231 ASP cc_start: 0.8482 (t0) cc_final: 0.8142 (t0) outliers start: 24 outliers final: 14 residues processed: 122 average time/residue: 1.4479 time to fit residues: 187.8603 Evaluate side-chains 116 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 B residue 353 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 425 MET 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 178 GLU Chi-restraints excluded: chain K residue 218 GLN Chi-restraints excluded: chain K residue 302 CYS Chi-restraints excluded: chain K residue 314 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 85 optimal weight: 0.0870 chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 0.0870 chunk 42 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 91 GLN ** A 101 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 = 0.3098 r_free = 0.3098 target = 0.078389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.061995 restraints weight = 17684.749| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 2.96 r_work: 0.2600 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9510 Z= 0.257 Angle : 0.564 6.851 12906 Z= 0.283 Chirality : 0.045 0.230 1419 Planarity : 0.004 0.064 1668 Dihedral : 10.181 168.476 1409 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.58 % Allowed : 17.99 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1156 helix: 1.88 (0.24), residues: 493 sheet: 1.16 (0.34), residues: 216 loop : -0.57 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 21 HIS 0.003 0.001 HIS B 139 PHE 0.007 0.001 PHE K 135 TYR 0.009 0.001 TYR A 108 ARG 0.011 0.000 ARG K 161 *********************** 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 131 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 ASN cc_start: 0.8987 (m-40) cc_final: 0.8680 (m-40) REVERT: B 113 GLU cc_start: 0.8731 (mp0) cc_final: 0.8416 (mp0) REVERT: B 205 ASP cc_start: 0.8933 (p0) cc_final: 0.8649 (p0) REVERT: B 295 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8485 (mtp) REVERT: B 299 LYS cc_start: 0.9324 (ptpp) cc_final: 0.9117 (ptmt) REVERT: B 416 MET cc_start: 0.8591 (mmm) cc_final: 0.8231 (mmm) REVERT: B 417 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8276 (mt-10) REVERT: A 50 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.7752 (t0) REVERT: A 90 GLU cc_start: 0.8778 (tp30) cc_final: 0.8536 (tm-30) REVERT: A 279 GLU cc_start: 0.8815 (mp0) cc_final: 0.8545 (mp0) REVERT: A 302 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8897 (mtm) REVERT: A 326 LYS cc_start: 0.5361 (mttt) cc_final: 0.4682 (mttt) REVERT: A 414 GLU cc_start: 0.8813 (tt0) cc_final: 0.8466 (tp30) REVERT: A 420 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8307 (mt-10) REVERT: A 433 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8660 (pp20) REVERT: K 122 MET cc_start: 0.8658 (tpp) cc_final: 0.8199 (tpp) REVERT: K 177 ASP cc_start: 0.8474 (p0) cc_final: 0.7994 (p0) REVERT: K 178 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: K 181 ASP cc_start: 0.9027 (m-30) cc_final: 0.8810 (m-30) REVERT: K 231 ASP cc_start: 0.8510 (t0) cc_final: 0.8150 (t0) outliers start: 26 outliers final: 14 residues processed: 119 average time/residue: 1.4189 time to fit residues: 179.6876 Evaluate side-chains 119 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 68 VAL 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 B residue 393 GLU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain A residue 50 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 302 MET 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 K residue 126 LEU Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 178 GLU Chi-restraints excluded: chain K residue 218 GLN 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 42 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 66 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 113 optimal weight: 0.0050 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3147 r_free = 0.3147 target = 0.080951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.064543 restraints weight = 17752.970| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 2.99 r_work: 0.2660 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9510 Z= 0.143 Angle : 0.546 8.188 12906 Z= 0.271 Chirality : 0.043 0.210 1419 Planarity : 0.004 0.063 1668 Dihedral : 9.817 164.314 1409 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.19 % Allowed : 18.89 % 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 (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: 1.24 (0.26), residues: 1156 helix: 1.88 (0.25), residues: 497 sheet: 1.23 (0.35), residues: 214 loop : -0.59 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 21 HIS 0.002 0.000 HIS B 139 PHE 0.010 0.001 PHE A 49 TYR 0.011 0.001 TYR A 108 ARG 0.017 0.001 ARG A 339 *********************** 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 137 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.8996 (tpp) cc_final: 0.8795 (tpp) REVERT: B 59 ASN cc_start: 0.8966 (m-40) cc_final: 0.8660 (m-40) REVERT: B 113 GLU cc_start: 0.8745 (mp0) cc_final: 0.8406 (mp0) REVERT: B 205 ASP cc_start: 0.8915 (p0) cc_final: 0.8625 (p0) REVERT: B 295 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8515 (mtp) REVERT: B 299 LYS cc_start: 0.9289 (ptpp) cc_final: 0.9071 (ptmt) REVERT: B 416 MET cc_start: 0.8429 (mmm) cc_final: 0.8036 (mmm) REVERT: A 1 MET cc_start: 0.7585 (tmm) cc_final: 0.6848 (tmm) REVERT: A 50 ASN cc_start: 0.8403 (t0) cc_final: 0.7639 (t0) REVERT: A 90 GLU cc_start: 0.8776 (tp30) cc_final: 0.8543 (tm-30) REVERT: A 91 GLN cc_start: 0.8460 (mt0) cc_final: 0.8239 (tt0) REVERT: A 154 MET cc_start: 0.9007 (mmm) cc_final: 0.8668 (mtm) REVERT: A 279 GLU cc_start: 0.8773 (mp0) cc_final: 0.8494 (mp0) REVERT: A 326 LYS cc_start: 0.5265 (mttt) cc_final: 0.4979 (mttt) REVERT: A 414 GLU cc_start: 0.8789 (tt0) cc_final: 0.8478 (tp30) REVERT: A 420 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8217 (mt-10) REVERT: A 433 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8582 (pp20) REVERT: K 122 MET cc_start: 0.8603 (tpp) cc_final: 0.8211 (tpp) REVERT: K 177 ASP cc_start: 0.8443 (p0) cc_final: 0.7956 (p0) REVERT: K 178 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: K 218 GLN cc_start: 0.9380 (OUTLIER) cc_final: 0.9026 (mp10) REVERT: K 231 ASP cc_start: 0.8439 (t0) cc_final: 0.8106 (t0) outliers start: 22 outliers final: 10 residues processed: 127 average time/residue: 1.4215 time to fit residues: 191.9198 Evaluate side-chains 116 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 353 THR 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 367 ASP Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 178 GLU Chi-restraints excluded: chain K residue 218 GLN Chi-restraints excluded: chain K residue 265 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 82 optimal weight: 0.0670 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.4124 ------------------------------------------------------------------------------- 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 = 0.3105 r_free = 0.3105 target = 0.078933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.062575 restraints weight = 18042.097| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.99 r_work: 0.2612 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9510 Z= 0.234 Angle : 0.594 8.311 12906 Z= 0.298 Chirality : 0.045 0.220 1419 Planarity : 0.004 0.063 1668 Dihedral : 9.763 163.729 1409 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.09 % Allowed : 20.08 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1156 helix: 1.92 (0.25), residues: 497 sheet: 1.25 (0.34), residues: 215 loop : -0.57 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.003 0.001 HIS A 266 PHE 0.007 0.001 PHE B 377 TYR 0.008 0.001 TYR A 108 ARG 0.013 0.000 ARG K 161 *********************** 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 128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: B 59 ASN cc_start: 0.9019 (m-40) cc_final: 0.8696 (m-40) REVERT: B 113 GLU cc_start: 0.8786 (mp0) cc_final: 0.8453 (mp0) REVERT: B 205 ASP cc_start: 0.8906 (p0) cc_final: 0.8632 (p0) REVERT: B 295 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8439 (mtp) REVERT: B 416 MET cc_start: 0.8554 (mmm) cc_final: 0.8174 (mmm) REVERT: B 417 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8274 (mt-10) REVERT: A 1 MET cc_start: 0.7564 (tmm) cc_final: 0.6917 (tmm) REVERT: A 50 ASN cc_start: 0.8483 (t0) cc_final: 0.7712 (t0) REVERT: A 90 GLU cc_start: 0.8787 (tp30) cc_final: 0.8555 (tm-30) REVERT: A 326 LYS cc_start: 0.5325 (mttt) cc_final: 0.5018 (mttt) REVERT: A 392 ASP cc_start: 0.8780 (m-30) cc_final: 0.8542 (p0) REVERT: A 414 GLU cc_start: 0.8813 (tt0) cc_final: 0.8484 (tp30) REVERT: A 420 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8258 (mt-10) REVERT: A 433 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8654 (pp20) REVERT: K 122 MET cc_start: 0.8625 (tpp) cc_final: 0.8265 (tpp) REVERT: K 218 GLN cc_start: 0.9382 (OUTLIER) cc_final: 0.9040 (mp10) REVERT: K 231 ASP cc_start: 0.8446 (t0) cc_final: 0.8084 (t0) outliers start: 21 outliers final: 9 residues processed: 121 average time/residue: 1.5208 time to fit residues: 195.2520 Evaluate side-chains 110 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 238 VAL 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 K residue 87 THR Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 218 GLN Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 85 optimal weight: 0.1980 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 95 optimal weight: 0.0270 chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- 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 = 0.3166 r_free = 0.3166 target = 0.080912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.064468 restraints weight = 17532.332| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.93 r_work: 0.2676 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9510 Z= 0.166 Angle : 0.581 8.381 12906 Z= 0.290 Chirality : 0.044 0.208 1419 Planarity : 0.004 0.063 1668 Dihedral : 9.500 159.869 1409 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.89 % Allowed : 20.18 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.25), residues: 1156 helix: 1.95 (0.25), residues: 497 sheet: 1.33 (0.35), residues: 209 loop : -0.56 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.002 0.001 HIS B 139 PHE 0.007 0.001 PHE B 377 TYR 0.010 0.001 TYR A 108 ARG 0.014 0.000 ARG K 161 *********************** 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 122 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 ASN cc_start: 0.8954 (m-40) cc_final: 0.8677 (m-40) REVERT: B 113 GLU cc_start: 0.8750 (mp0) cc_final: 0.8428 (mp0) REVERT: B 205 ASP cc_start: 0.8811 (p0) cc_final: 0.8578 (p0) REVERT: B 295 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8567 (mtp) REVERT: B 416 MET cc_start: 0.8492 (mmm) cc_final: 0.8134 (mmm) REVERT: B 417 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8157 (mt-10) REVERT: A 1 MET cc_start: 0.7788 (tmm) cc_final: 0.7227 (tmm) REVERT: A 50 ASN cc_start: 0.8450 (t0) cc_final: 0.7784 (t0) REVERT: A 91 GLN cc_start: 0.8496 (mt0) cc_final: 0.8283 (tt0) REVERT: A 326 LYS cc_start: 0.5364 (mttt) cc_final: 0.5098 (mttt) REVERT: A 414 GLU cc_start: 0.8764 (tt0) cc_final: 0.8520 (tp30) REVERT: A 433 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8581 (pp20) REVERT: K 231 ASP cc_start: 0.8415 (t0) cc_final: 0.8077 (t0) outliers start: 19 outliers final: 13 residues processed: 116 average time/residue: 1.4291 time to fit residues: 176.6350 Evaluate side-chains 115 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 238 VAL 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 335 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 218 GLN Chi-restraints excluded: chain K residue 265 ILE 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 20 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 50 optimal weight: 0.0020 chunk 91 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.7794 ------------------------------------------------------------------------------- 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 = 0.3146 r_free = 0.3146 target = 0.080301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.063833 restraints weight = 17879.161| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.97 r_work: 0.2653 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9510 Z= 0.205 Angle : 0.600 8.183 12906 Z= 0.302 Chirality : 0.044 0.212 1419 Planarity : 0.004 0.066 1668 Dihedral : 9.401 157.271 1409 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.69 % Allowed : 20.08 % 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 (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: 1.31 (0.25), residues: 1156 helix: 1.95 (0.24), residues: 496 sheet: 1.33 (0.35), residues: 209 loop : -0.58 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.003 0.001 HIS A 393 PHE 0.007 0.001 PHE B 377 TYR 0.010 0.001 TYR K 118 ARG 0.015 0.000 ARG K 161 ********************** 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 114 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 ASN cc_start: 0.9021 (m-40) cc_final: 0.8712 (m-40) REVERT: B 113 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8452 (mp0) REVERT: B 205 ASP cc_start: 0.8887 (p0) cc_final: 0.8604 (p0) REVERT: B 295 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8501 (mtp) REVERT: B 416 MET cc_start: 0.8548 (mmm) cc_final: 0.8175 (mmm) REVERT: B 417 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8247 (mt-10) REVERT: A 1 MET cc_start: 0.7800 (tmm) cc_final: 0.7209 (tmm) REVERT: A 50 ASN cc_start: 0.8478 (t0) cc_final: 0.7780 (t0) REVERT: A 326 LYS cc_start: 0.5274 (mttt) cc_final: 0.4951 (mttt) REVERT: A 414 GLU cc_start: 0.8799 (tt0) cc_final: 0.8502 (tp30) REVERT: A 433 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8498 (pp20) REVERT: K 99 LEU cc_start: 0.9460 (mm) cc_final: 0.9131 (tm) REVERT: K 231 ASP cc_start: 0.8412 (t0) cc_final: 0.8068 (t0) outliers start: 17 outliers final: 13 residues processed: 109 average time/residue: 1.5075 time to fit residues: 174.3811 Evaluate side-chains 113 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 353 THR 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 335 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 218 GLN 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 23 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 110 optimal weight: 0.0030 chunk 96 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 overall best weight: 2.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 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 = 0.3115 r_free = 0.3115 target = 0.078885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.062347 restraints weight = 17916.109| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.95 r_work: 0.2619 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9510 Z= 0.275 Angle : 0.625 8.132 12906 Z= 0.316 Chirality : 0.046 0.215 1419 Planarity : 0.004 0.069 1668 Dihedral : 9.435 155.857 1409 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.59 % Allowed : 20.48 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.29 (0.25), residues: 1156 helix: 1.95 (0.24), residues: 492 sheet: 1.22 (0.34), residues: 215 loop : -0.55 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 21 HIS 0.003 0.001 HIS B 139 PHE 0.007 0.001 PHE B 395 TYR 0.009 0.001 TYR K 118 ARG 0.015 0.001 ARG K 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5630.08 seconds wall clock time: 100 minutes 24.51 seconds (6024.51 seconds total)