Starting phenix.real_space_refine on Sat Dec 28 23:00:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gnq_51477/12_2024/9gnq_51477.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gnq_51477/12_2024/9gnq_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_51477/12_2024/9gnq_51477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gnq_51477/12_2024/9gnq_51477.map" model { file = "/net/cci-nas-00/data/ceres_data/9gnq_51477/12_2024/9gnq_51477.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gnq_51477/12_2024/9gnq_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.90, per 1000 atoms: 0.63 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: 2.71 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: 0.97 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: 2.57 Time building geometry restraints manager: 3.04 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: 1.980 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.580 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: 0.000 Load rotamer database and sin/cos tables:14.640 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.930 ------------------------------------------------------------------------------- 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 : 1.037 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: 1.6184 time to fit residues: 369.7540 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 : 0.997 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 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 : 1.041 Fit side-chains revert: symmetry clash REVERT: A 326 LYS cc_start: 0.6061 (mttt) cc_final: 0.5582 (mttt) outliers start: 25 outliers final: 8 residues processed: 138 average time/residue: 1.4879 time to fit residues: 218.0579 Evaluate side-chains 115 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 107 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 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 314 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.0770 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.0470 chunk 71 optimal weight: 10.0000 chunk 28 optimal weight: 0.3980 chunk 104 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 overall best weight: 2.3040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 HIS A 50 ASN ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9510 Z= 0.224 Angle : 0.577 6.472 12906 Z= 0.289 Chirality : 0.046 0.376 1419 Planarity : 0.004 0.065 1668 Dihedral : 10.777 168.708 1409 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.49 % Allowed : 16.90 % Favored : 80.62 % 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: 1.09 (0.25), residues: 1156 helix: 1.86 (0.25), residues: 484 sheet: 1.08 (0.34), residues: 216 loop : -0.70 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS B 229 PHE 0.008 0.001 PHE K 116 TYR 0.009 0.001 TYR K 62 ARG 0.010 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: 25 poor density : 107 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7189 (tmm) cc_final: 0.6593 (tmm) REVERT: A 50 ASN cc_start: 0.8466 (t0) cc_final: 0.8163 (t0) REVERT: A 326 LYS cc_start: 0.6233 (mttt) cc_final: 0.5570 (mttt) outliers start: 25 outliers final: 17 residues processed: 127 average time/residue: 1.4218 time to fit residues: 191.9593 Evaluate side-chains 109 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 353 THR 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 183 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 139 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 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 : 0.005 0.082 9510 Z= 0.343 Angle : 0.613 5.985 12906 Z= 0.310 Chirality : 0.047 0.301 1419 Planarity : 0.004 0.065 1668 Dihedral : 10.686 170.780 1409 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.08 % Allowed : 17.50 % 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: 1.03 (0.25), residues: 1156 helix: 1.72 (0.24), residues: 491 sheet: 1.08 (0.33), residues: 216 loop : -0.66 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.004 0.001 HIS A 266 PHE 0.009 0.001 PHE B 395 TYR 0.015 0.001 TYR K 118 ARG 0.013 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 124 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: A 302 MET cc_start: 0.8863 (mmm) cc_final: 0.8659 (mtm) REVERT: A 326 LYS cc_start: 0.5912 (mttt) cc_final: 0.5063 (mttt) outliers start: 31 outliers final: 16 residues processed: 116 average time/residue: 1.4340 time to fit residues: 176.8795 Evaluate side-chains 104 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 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 435 VAL Chi-restraints excluded: chain K residue 87 THR 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 63 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 28 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 253 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9510 Z= 0.250 Angle : 0.577 7.303 12906 Z= 0.290 Chirality : 0.045 0.237 1419 Planarity : 0.004 0.064 1668 Dihedral : 10.408 168.426 1409 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.48 % Allowed : 17.00 % Favored : 79.52 % 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: 1.05 (0.25), residues: 1156 helix: 1.75 (0.24), residues: 491 sheet: 0.97 (0.33), residues: 222 loop : -0.63 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 21 HIS 0.002 0.001 HIS A 283 PHE 0.007 0.001 PHE K 116 TYR 0.015 0.001 TYR K 118 ARG 0.009 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 135 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 100 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 295 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8709 (mtp) REVERT: A 1 MET cc_start: 0.7278 (tmm) cc_final: 0.6908 (tmm) REVERT: A 50 ASN cc_start: 0.8417 (t0) cc_final: 0.8155 (t0) REVERT: A 302 MET cc_start: 0.8916 (mmm) cc_final: 0.8641 (mtm) REVERT: A 326 LYS cc_start: 0.5876 (mttt) cc_final: 0.5480 (mttt) outliers start: 35 outliers final: 17 residues processed: 126 average time/residue: 1.4442 time to fit residues: 193.9114 Evaluate side-chains 110 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 295 MET 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 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 141 LYS 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 100 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 chunk 92 optimal weight: 0.0170 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9510 Z= 0.260 Angle : 0.587 6.801 12906 Z= 0.295 Chirality : 0.045 0.223 1419 Planarity : 0.004 0.064 1668 Dihedral : 10.211 168.228 1409 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.88 % Allowed : 18.19 % 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: 1.06 (0.25), residues: 1156 helix: 1.74 (0.24), residues: 491 sheet: 1.08 (0.34), residues: 217 loop : -0.63 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.003 0.001 HIS B 266 PHE 0.007 0.001 PHE K 135 TYR 0.008 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 128 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: B 295 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8683 (mtp) REVERT: A 50 ASN cc_start: 0.8496 (t0) cc_final: 0.8247 (t0) REVERT: A 302 MET cc_start: 0.8934 (mmm) cc_final: 0.8603 (mtm) REVERT: A 326 LYS cc_start: 0.5923 (mttt) cc_final: 0.5514 (mttt) outliers start: 29 outliers final: 15 residues processed: 116 average time/residue: 1.5216 time to fit residues: 187.1200 Evaluate side-chains 109 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 295 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 69 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 68 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3101 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= 0.169 Angle : 0.586 8.904 12906 Z= 0.293 Chirality : 0.044 0.208 1419 Planarity : 0.004 0.063 1668 Dihedral : 9.876 164.832 1409 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.99 % Allowed : 20.08 % 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: 1.08 (0.25), residues: 1156 helix: 1.75 (0.24), residues: 497 sheet: 1.23 (0.34), residues: 211 loop : -0.71 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 21 HIS 0.002 0.000 HIS B 266 PHE 0.007 0.001 PHE B 377 TYR 0.010 0.001 TYR A 108 ARG 0.019 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 130 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7476 (tmm) cc_final: 0.6934 (tmm) REVERT: A 50 ASN cc_start: 0.8292 (t0) cc_final: 0.7891 (t0) REVERT: A 302 MET cc_start: 0.8872 (mmm) cc_final: 0.8519 (mtm) REVERT: A 326 LYS cc_start: 0.5863 (mttt) cc_final: 0.5204 (mttt) outliers start: 20 outliers final: 11 residues processed: 123 average time/residue: 1.4353 time to fit residues: 187.9412 Evaluate side-chains 109 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 SER Chi-restraints excluded: chain B residue 238 VAL 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 87 THR Chi-restraints excluded: chain K residue 132 VAL Chi-restraints excluded: chain K residue 183 ILE Chi-restraints excluded: chain K residue 302 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 70 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9510 Z= 0.289 Angle : 0.625 7.838 12906 Z= 0.315 Chirality : 0.046 0.217 1419 Planarity : 0.004 0.063 1668 Dihedral : 9.889 165.330 1409 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.59 % Allowed : 20.78 % Favored : 77.63 % 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: 1.12 (0.25), residues: 1156 helix: 1.79 (0.25), residues: 491 sheet: 1.11 (0.34), residues: 216 loop : -0.61 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.004 0.001 HIS B 139 PHE 0.007 0.001 PHE K 135 TYR 0.011 0.001 TYR K 118 ARG 0.013 0.001 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 116 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7607 (tmm) cc_final: 0.7232 (tmm) REVERT: A 50 ASN cc_start: 0.8452 (t0) cc_final: 0.8179 (t0) REVERT: A 302 MET cc_start: 0.8951 (mmm) cc_final: 0.8558 (mtm) REVERT: A 326 LYS cc_start: 0.5959 (mttt) cc_final: 0.5479 (mttt) outliers start: 16 outliers final: 11 residues processed: 111 average time/residue: 1.4127 time to fit residues: 167.1733 Evaluate side-chains 108 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 238 VAL 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 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 103 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 109 optimal weight: 0.0870 overall best weight: 0.9962 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3218 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= 0.175 Angle : 0.616 8.269 12906 Z= 0.310 Chirality : 0.044 0.205 1419 Planarity : 0.004 0.063 1668 Dihedral : 9.632 162.020 1409 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.59 % Allowed : 21.17 % 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 (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: 1.10 (0.25), residues: 1156 helix: 1.74 (0.24), residues: 496 sheet: 1.21 (0.35), residues: 210 loop : -0.64 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 0.015 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 119 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 50 ASN cc_start: 0.8348 (t0) cc_final: 0.8110 (t0) REVERT: A 302 MET cc_start: 0.8865 (mmm) cc_final: 0.8456 (mtm) REVERT: A 326 LYS cc_start: 0.5876 (mttt) cc_final: 0.5211 (mttt) outliers start: 16 outliers final: 13 residues processed: 115 average time/residue: 1.4615 time to fit residues: 180.0506 Evaluate side-chains 109 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 238 VAL 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 183 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 66 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 75 optimal weight: 0.0970 chunk 114 optimal weight: 0.9980 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 9 optimal weight: 0.3980 chunk 70 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 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 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3237 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= 0.198 Angle : 0.636 10.056 12906 Z= 0.318 Chirality : 0.044 0.210 1419 Planarity : 0.004 0.065 1668 Dihedral : 9.492 159.710 1409 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.29 % Allowed : 21.27 % Favored : 77.44 % 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: 1.11 (0.25), residues: 1156 helix: 1.76 (0.24), residues: 496 sheet: 1.11 (0.34), residues: 216 loop : -0.61 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 21 HIS 0.003 0.001 HIS B 139 PHE 0.007 0.001 PHE K 116 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 112 residues out of total 1007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.7563 (tmm) cc_final: 0.7186 (tmm) REVERT: A 50 ASN cc_start: 0.8216 (t0) cc_final: 0.7981 (t0) REVERT: A 302 MET cc_start: 0.8869 (mmm) cc_final: 0.8446 (mtm) REVERT: A 326 LYS cc_start: 0.5816 (mttt) cc_final: 0.5415 (mttt) outliers start: 13 outliers final: 13 residues processed: 109 average time/residue: 1.4167 time to fit residues: 164.8240 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 : 1.189 ------------------------------------------------------------------------------- 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 238 VAL 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 126 LEU Chi-restraints excluded: chain K residue 132 VAL 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 27 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 25 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.084166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.067600 restraints weight = 17777.577| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.90 r_work: 0.2709 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9510 Z= 0.165 Angle : 0.621 10.120 12906 Z= 0.308 Chirality : 0.044 0.202 1419 Planarity : 0.004 0.063 1668 Dihedral : 9.181 154.683 1409 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.39 % Allowed : 20.97 % Favored : 77.63 % 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: 1.18 (0.25), residues: 1156 helix: 1.79 (0.24), residues: 496 sheet: 1.30 (0.35), residues: 211 loop : -0.61 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 21 HIS 0.002 0.000 HIS B 139 PHE 0.007 0.001 PHE B 377 TYR 0.010 0.001 TYR A 108 ARG 0.015 0.000 ARG K 161 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3516.16 seconds wall clock time: 65 minutes 0.27 seconds (3900.27 seconds total)