Starting phenix.real_space_refine on Sat Aug 23 00:14:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jol_36459/08_2025/8jol_36459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jol_36459/08_2025/8jol_36459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jol_36459/08_2025/8jol_36459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jol_36459/08_2025/8jol_36459.map" model { file = "/net/cci-nas-00/data/ceres_data/8jol_36459/08_2025/8jol_36459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jol_36459/08_2025/8jol_36459.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5388 2.51 5 N 1439 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8513 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "B" Number of atoms: 3965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3965 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 3 Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 445 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ARG:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 8, 'ASN:plan1': 4, 'PHE:plan': 3, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.93, per 1000 atoms: 0.23 Number of scatterers: 8513 At special positions: 0 Unit cell: (95.04, 114.84, 137.28, 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 58 16.00 P 6 15.00 Mg 2 11.99 O 1620 8.00 N 1439 7.00 C 5388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 314.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 65.5% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.563A pdb=" N LEU A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.758A pdb=" N ALA A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 49 through 65 removed outlier: 3.557A pdb=" N ARG A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.620A pdb=" N ALA A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.523A pdb=" N ILE A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 4.023A pdb=" N PHE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.692A pdb=" N ALA A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.653A pdb=" N ALA A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.915A pdb=" N ILE A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.648A pdb=" N TYR A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 327 removed outlier: 4.885A pdb=" N VAL A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.738A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.654A pdb=" N PHE A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.768A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.851A pdb=" N LEU A 535 " --> pdb=" O PHE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.560A pdb=" N LEU B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 33 removed outlier: 3.773A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 49 through 65 removed outlier: 3.553A pdb=" N ARG B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 removed outlier: 3.656A pdb=" N ILE B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 removed outlier: 3.891A pdb=" N MET B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 164 through 173 removed outlier: 3.507A pdb=" N ILE B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 4.015A pdb=" N PHE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 242 removed outlier: 3.929A pdb=" N ASP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 4.189A pdb=" N ILE B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 removed outlier: 4.001A pdb=" N ILE B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 removed outlier: 3.591A pdb=" N TYR B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 327 removed outlier: 4.890A pdb=" N VAL B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.791A pdb=" N GLU B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 396 through 399 Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 469 through 484 removed outlier: 3.793A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.850A pdb=" N LEU B 535 " --> pdb=" O PHE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.925A pdb=" N SER B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.750A pdb=" N PHE C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.773A pdb=" N ILE C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 46 Processing helix chain 'C' and resid 49 through 64 removed outlier: 3.552A pdb=" N LYS C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 80 through 92 removed outlier: 3.617A pdb=" N LEU C 84 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Proline residue: C 90 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 7.093A pdb=" N THR A 245 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU A 269 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE A 247 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR A 271 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 249 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 153 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL A 270 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 155 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 272 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 157 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 154 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE A 288 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE A 156 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 290 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N HIS A 158 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 191 removed outlier: 6.820A pdb=" N THR B 245 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU B 269 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE B 247 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR B 271 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE B 249 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 272 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 159 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE B 154 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE B 288 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 156 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 290 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS B 158 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 405 through 406 399 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.31 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2514 1.33 - 1.46: 1796 1.46 - 1.59: 4252 1.59 - 1.72: 6 1.72 - 1.85: 92 Bond restraints: 8660 Sorted by residual: bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 8.95e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.480 -0.092 1.00e-02 1.00e+04 8.53e+01 bond pdb=" C5 ATP A 602 " pdb=" C6 ATP A 602 " ideal model delta sigma weight residual 1.409 1.492 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C5 ATP B 602 " pdb=" N7 ATP B 602 " ideal model delta sigma weight residual 1.387 1.332 0.055 1.00e-02 1.00e+04 3.01e+01 bond pdb=" C8 ATP A 602 " pdb=" N7 ATP A 602 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.09e+01 ... (remaining 8655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 11612 5.15 - 10.29: 112 10.29 - 15.44: 4 15.44 - 20.59: 2 20.59 - 25.73: 1 Bond angle restraints: 11731 Sorted by residual: angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 114.14 25.73 1.00e+00 1.00e+00 6.62e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 119.12 17.71 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 122.83 17.04 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP A 602 " pdb=" O3A ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 136.83 121.64 15.19 1.00e+00 1.00e+00 2.31e+02 angle pdb=" N3 ATP B 602 " pdb=" C4 ATP B 602 " pdb=" N9 ATP B 602 " ideal model delta sigma weight residual 127.04 136.39 -9.35 1.15e+00 7.59e-01 6.64e+01 ... (remaining 11726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 4606 17.39 - 34.79: 480 34.79 - 52.18: 162 52.18 - 69.58: 78 69.58 - 86.97: 13 Dihedral angle restraints: 5339 sinusoidal: 2140 harmonic: 3199 Sorted by residual: dihedral pdb=" CA ASP B 216 " pdb=" C ASP B 216 " pdb=" N LEU B 217 " pdb=" CA LEU B 217 " ideal model delta harmonic sigma weight residual 180.00 153.89 26.11 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA ASP A 216 " pdb=" C ASP A 216 " pdb=" N LEU A 217 " pdb=" CA LEU A 217 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA CYS A 268 " pdb=" C CYS A 268 " pdb=" N LEU A 269 " pdb=" CA LEU A 269 " ideal model delta harmonic sigma weight residual 180.00 158.55 21.45 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 5336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 960 0.070 - 0.140: 301 0.140 - 0.210: 76 0.210 - 0.279: 19 0.279 - 0.349: 4 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CA PHE A 532 " pdb=" N PHE A 532 " pdb=" C PHE A 532 " pdb=" CB PHE A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA LYS A 212 " pdb=" N LYS A 212 " pdb=" C LYS A 212 " pdb=" CB LYS A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA PHE B 532 " pdb=" N PHE B 532 " pdb=" C PHE B 532 " pdb=" CB PHE B 532 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1357 not shown) Planarity restraints: 1502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 87 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C VAL C 87 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL C 87 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU C 88 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 253 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C VAL A 253 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL A 253 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN A 254 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 220 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO B 221 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 221 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 221 " -0.032 5.00e-02 4.00e+02 ... (remaining 1499 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1343 2.75 - 3.29: 9096 3.29 - 3.83: 14060 3.83 - 4.36: 18222 4.36 - 4.90: 27779 Nonbonded interactions: 70500 Sorted by model distance: nonbonded pdb=" O1B ATP A 602 " pdb=" O2G ATP A 602 " model vdw 2.214 3.040 nonbonded pdb=" O ARG A 259 " pdb=" N GLN A 262 " model vdw 2.275 3.120 nonbonded pdb=" O4' ATP A 602 " pdb=" O5' ATP A 602 " model vdw 2.319 2.432 nonbonded pdb=" OG SER B 166 " pdb="MG MG B 601 " model vdw 2.341 2.170 nonbonded pdb=" O LEU B 120 " pdb=" N ASN B 123 " model vdw 2.349 3.120 ... (remaining 70495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 98 or resid 106 through 416 or resid 426 through \ 602)) selection = chain 'B' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.880 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 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 : 0.009 0.095 8660 Z= 0.601 Angle : 1.462 25.735 11731 Z= 1.023 Chirality : 0.074 0.349 1360 Planarity : 0.005 0.060 1502 Dihedral : 18.200 86.969 3243 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 35.79 Ramachandran Plot: Outliers : 0.84 % Allowed : 12.32 % Favored : 86.83 % Rotamer: Outliers : 16.43 % Allowed : 15.21 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.77 (0.21), residues: 1071 helix: -3.29 (0.15), residues: 632 sheet: -2.60 (0.61), residues: 60 loop : -2.63 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 265 TYR 0.022 0.004 TYR B 184 PHE 0.018 0.003 PHE A 156 TRP 0.024 0.005 TRP B 189 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00918 ( 8660) covalent geometry : angle 1.46194 (11731) hydrogen bonds : bond 0.25275 ( 399) hydrogen bonds : angle 9.24245 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 215 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8962 (m) cc_final: 0.8522 (p) REVERT: A 47 MET cc_start: 0.6707 (mmm) cc_final: 0.6151 (mmm) REVERT: A 123 ASN cc_start: 0.8269 (m110) cc_final: 0.7650 (t0) REVERT: A 128 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7943 (tpp) REVERT: A 144 LEU cc_start: 0.8740 (mt) cc_final: 0.8503 (mt) REVERT: A 185 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7666 (t0) REVERT: A 205 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8843 (m) REVERT: A 206 ASP cc_start: 0.8609 (m-30) cc_final: 0.8231 (m-30) REVERT: A 218 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8387 (pt) REVERT: A 228 SER cc_start: 0.9145 (m) cc_final: 0.8888 (t) REVERT: A 233 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7569 (ttp-170) REVERT: A 286 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: A 290 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7993 (t) REVERT: A 443 LEU cc_start: 0.9052 (mt) cc_final: 0.8667 (mp) REVERT: B 45 SER cc_start: 0.4096 (OUTLIER) cc_final: 0.3860 (p) REVERT: B 128 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7837 (OUTLIER) REVERT: B 185 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: B 190 LEU cc_start: 0.8856 (mt) cc_final: 0.8473 (mt) REVERT: B 218 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7944 (pt) REVERT: B 361 VAL cc_start: 0.8410 (t) cc_final: 0.7470 (p) REVERT: B 382 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7187 (t) outliers start: 149 outliers final: 10 residues processed: 317 average time/residue: 0.4456 time to fit residues: 152.1077 Evaluate side-chains 148 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 542 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 123 ASN A 219 ASN A 244 ASN A 329 ASN A 461 HIS A 471 GLN A 482 GLN A 534 GLN B 34 ASN B 64 GLN B 113 GLN B 244 ASN B 482 GLN B 534 GLN B 536 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.079941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.062177 restraints weight = 35606.971| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 4.25 r_work: 0.3219 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8660 Z= 0.174 Angle : 0.802 12.787 11731 Z= 0.399 Chirality : 0.044 0.194 1360 Planarity : 0.006 0.062 1502 Dihedral : 11.399 78.575 1269 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 8.05 % Allowed : 22.49 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.24), residues: 1071 helix: -1.31 (0.18), residues: 677 sheet: -2.26 (0.57), residues: 58 loop : -1.40 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 483 TYR 0.018 0.002 TYR A 77 PHE 0.018 0.002 PHE B 220 TRP 0.006 0.001 TRP B 260 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8660) covalent geometry : angle 0.80189 (11731) hydrogen bonds : bond 0.04135 ( 399) hydrogen bonds : angle 4.88871 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 112 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.9199 (m) cc_final: 0.8828 (p) REVERT: A 52 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7592 (mp0) REVERT: A 206 ASP cc_start: 0.8938 (m-30) cc_final: 0.8671 (m-30) REVERT: A 218 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8732 (pt) REVERT: A 360 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8776 (mt) REVERT: A 361 VAL cc_start: 0.9546 (OUTLIER) cc_final: 0.9118 (t) REVERT: A 364 GLU cc_start: 0.8751 (pm20) cc_final: 0.8346 (pm20) REVERT: A 486 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: B 123 ASN cc_start: 0.9205 (t0) cc_final: 0.8934 (t0) REVERT: B 185 ASP cc_start: 0.8922 (m-30) cc_final: 0.8585 (m-30) REVERT: B 334 MET cc_start: 0.7689 (mmm) cc_final: 0.7410 (mmm) REVERT: B 376 MET cc_start: 0.8936 (mpm) cc_final: 0.8720 (mpm) REVERT: B 533 MET cc_start: 0.7953 (ppp) cc_final: 0.6957 (ppp) outliers start: 73 outliers final: 19 residues processed: 171 average time/residue: 0.4202 time to fit residues: 77.7581 Evaluate side-chains 118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 469 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 103 optimal weight: 30.0000 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 0.0470 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS B 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.071305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054692 restraints weight = 35477.790| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 4.78 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8660 Z= 0.153 Angle : 0.703 9.883 11731 Z= 0.350 Chirality : 0.042 0.154 1360 Planarity : 0.005 0.052 1502 Dihedral : 9.606 84.740 1238 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.40 % Allowed : 23.81 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.26), residues: 1071 helix: -0.03 (0.20), residues: 671 sheet: -1.57 (0.60), residues: 56 loop : -0.85 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 390 TYR 0.015 0.001 TYR A 77 PHE 0.015 0.002 PHE A 204 TRP 0.008 0.001 TRP B 260 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8660) covalent geometry : angle 0.70299 (11731) hydrogen bonds : bond 0.03703 ( 399) hydrogen bonds : angle 4.27234 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 93 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.9367 (m) cc_final: 0.8997 (p) REVERT: A 47 MET cc_start: 0.7894 (mmm) cc_final: 0.5492 (mmm) REVERT: A 48 SER cc_start: 0.8666 (m) cc_final: 0.8444 (m) REVERT: A 206 ASP cc_start: 0.8789 (m-30) cc_final: 0.8505 (m-30) REVERT: A 209 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9013 (mm) REVERT: A 307 MET cc_start: 0.8594 (tpp) cc_final: 0.8128 (tpt) REVERT: A 361 VAL cc_start: 0.9531 (OUTLIER) cc_final: 0.9029 (t) REVERT: A 364 GLU cc_start: 0.8293 (pm20) cc_final: 0.7867 (pm20) REVERT: A 486 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7576 (tm-30) REVERT: B 114 MET cc_start: 0.8231 (mpt) cc_final: 0.8004 (mpt) REVERT: B 185 ASP cc_start: 0.8754 (m-30) cc_final: 0.8505 (m-30) REVERT: B 307 MET cc_start: 0.6910 (tpt) cc_final: 0.6257 (tpp) REVERT: B 334 MET cc_start: 0.8748 (mmm) cc_final: 0.8319 (mmm) REVERT: B 383 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8690 (mm-30) REVERT: B 432 ASP cc_start: 0.8700 (m-30) cc_final: 0.8394 (t0) outliers start: 49 outliers final: 12 residues processed: 131 average time/residue: 0.4366 time to fit residues: 61.8235 Evaluate side-chains 100 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 381 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 70 optimal weight: 0.0970 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 262 GLN A 425 GLN B 40 HIS B 158 HIS B 466 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.062362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.046275 restraints weight = 36519.312| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 4.30 r_work: 0.2746 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 1.0081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 8660 Z= 0.214 Angle : 0.756 10.345 11731 Z= 0.373 Chirality : 0.044 0.155 1360 Planarity : 0.005 0.054 1502 Dihedral : 9.839 87.352 1232 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 6.28 % Allowed : 23.48 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.26), residues: 1071 helix: 0.35 (0.20), residues: 680 sheet: -0.83 (0.62), residues: 56 loop : -0.67 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 390 TYR 0.018 0.002 TYR B 369 PHE 0.018 0.002 PHE A 204 TRP 0.009 0.002 TRP A 410 HIS 0.005 0.001 HIS A 225 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 8660) covalent geometry : angle 0.75575 (11731) hydrogen bonds : bond 0.04004 ( 399) hydrogen bonds : angle 4.41529 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 80 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9175 (mtm) cc_final: 0.8962 (ptt) REVERT: A 147 MET cc_start: 0.9091 (mtp) cc_final: 0.8825 (ptm) REVERT: A 206 ASP cc_start: 0.9074 (m-30) cc_final: 0.8794 (m-30) REVERT: A 224 GLU cc_start: 0.9082 (pp20) cc_final: 0.8802 (pm20) REVERT: A 376 MET cc_start: 0.9500 (mmp) cc_final: 0.9277 (mpm) REVERT: A 399 MET cc_start: 0.9541 (mmp) cc_final: 0.9281 (mmm) REVERT: A 486 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: B 185 ASP cc_start: 0.9331 (m-30) cc_final: 0.8897 (m-30) REVERT: B 316 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8501 (pp20) REVERT: B 383 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8800 (mm-30) outliers start: 57 outliers final: 13 residues processed: 128 average time/residue: 0.5272 time to fit residues: 72.4332 Evaluate side-chains 82 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 473 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 25 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 283 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN B 64 GLN B 283 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.061171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045535 restraints weight = 36224.139| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 4.47 r_work: 0.2716 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 1.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8660 Z= 0.152 Angle : 0.683 12.812 11731 Z= 0.330 Chirality : 0.041 0.203 1360 Planarity : 0.005 0.057 1502 Dihedral : 9.476 87.621 1230 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.53 % Allowed : 26.24 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.26), residues: 1071 helix: 0.79 (0.21), residues: 681 sheet: -0.87 (0.67), residues: 46 loop : -0.97 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 8 TYR 0.010 0.001 TYR B 369 PHE 0.017 0.001 PHE A 204 TRP 0.011 0.002 TRP A 189 HIS 0.003 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8660) covalent geometry : angle 0.68336 (11731) hydrogen bonds : bond 0.03383 ( 399) hydrogen bonds : angle 4.07537 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.9110 (m-30) cc_final: 0.8788 (m-30) REVERT: A 486 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: B 114 MET cc_start: 0.9102 (mpp) cc_final: 0.8872 (mpp) REVERT: B 147 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.9023 (mtp) REVERT: B 185 ASP cc_start: 0.9363 (m-30) cc_final: 0.8922 (m-30) REVERT: B 316 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8496 (pp20) REVERT: B 338 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7522 (mmtt) REVERT: B 348 MET cc_start: 0.8988 (ptp) cc_final: 0.8638 (ptp) REVERT: B 373 SER cc_start: 0.8137 (OUTLIER) cc_final: 0.7689 (t) REVERT: B 383 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8758 (mm-30) REVERT: B 408 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8766 (mppt) REVERT: B 435 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8747 (mtmm) REVERT: B 459 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8816 (tt) outliers start: 32 outliers final: 8 residues processed: 93 average time/residue: 0.5925 time to fit residues: 58.8194 Evaluate side-chains 78 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 70 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.058088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.042754 restraints weight = 36025.192| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 4.27 r_work: 0.2633 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 1.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8660 Z= 0.222 Angle : 0.737 13.053 11731 Z= 0.362 Chirality : 0.043 0.189 1360 Planarity : 0.005 0.057 1502 Dihedral : 9.598 88.201 1230 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 4.41 % Allowed : 26.46 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.26), residues: 1071 helix: 0.87 (0.21), residues: 675 sheet: -0.72 (0.73), residues: 44 loop : -0.96 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 112 TYR 0.011 0.002 TYR A 540 PHE 0.021 0.002 PHE A 204 TRP 0.009 0.002 TRP A 189 HIS 0.006 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00521 ( 8660) covalent geometry : angle 0.73677 (11731) hydrogen bonds : bond 0.04020 ( 399) hydrogen bonds : angle 4.33031 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 65 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.9364 (mpm) cc_final: 0.9067 (mpp) REVERT: A 399 MET cc_start: 0.9666 (tpp) cc_final: 0.9400 (mmm) REVERT: A 486 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: B 383 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8714 (mm-30) REVERT: B 408 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8990 (mppt) REVERT: B 435 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8824 (mtmt) outliers start: 40 outliers final: 15 residues processed: 96 average time/residue: 0.5833 time to fit residues: 59.8602 Evaluate side-chains 76 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 239 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.059903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.044273 restraints weight = 36303.285| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 4.60 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 1.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8660 Z= 0.117 Angle : 0.690 13.365 11731 Z= 0.327 Chirality : 0.041 0.191 1360 Planarity : 0.005 0.053 1502 Dihedral : 9.184 81.824 1230 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.43 % Allowed : 28.78 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.26), residues: 1071 helix: 1.08 (0.21), residues: 675 sheet: -0.53 (0.71), residues: 46 loop : -0.80 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 50 TYR 0.011 0.001 TYR B 135 PHE 0.022 0.001 PHE A 220 TRP 0.011 0.001 TRP A 189 HIS 0.003 0.000 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8660) covalent geometry : angle 0.69006 (11731) hydrogen bonds : bond 0.03028 ( 399) hydrogen bonds : angle 3.90592 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.8938 (mpm) cc_final: 0.8668 (mpp) REVERT: A 486 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7312 (tm-30) REVERT: A 533 MET cc_start: 0.8641 (ppp) cc_final: 0.8394 (ppp) REVERT: B 114 MET cc_start: 0.9242 (mtm) cc_final: 0.8776 (pmm) REVERT: B 185 ASP cc_start: 0.9011 (m-30) cc_final: 0.8681 (m-30) REVERT: B 316 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8515 (pp20) REVERT: B 348 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8549 (ptp) REVERT: B 383 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8451 (mm-30) REVERT: B 435 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8557 (mtmm) outliers start: 22 outliers final: 6 residues processed: 79 average time/residue: 0.5475 time to fit residues: 46.4341 Evaluate side-chains 71 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 58 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 63 optimal weight: 0.0970 chunk 95 optimal weight: 0.0010 chunk 74 optimal weight: 0.0040 chunk 7 optimal weight: 4.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 425 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.059283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.043817 restraints weight = 35763.326| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 4.46 r_work: 0.2693 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 1.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8660 Z= 0.123 Angle : 0.704 14.375 11731 Z= 0.331 Chirality : 0.041 0.203 1360 Planarity : 0.004 0.054 1502 Dihedral : 9.000 83.434 1230 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.09 % Allowed : 29.11 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.26), residues: 1071 helix: 1.04 (0.21), residues: 677 sheet: -0.25 (0.73), residues: 46 loop : -0.66 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 50 TYR 0.009 0.001 TYR B 135 PHE 0.019 0.001 PHE A 204 TRP 0.009 0.001 TRP A 189 HIS 0.004 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8660) covalent geometry : angle 0.70428 (11731) hydrogen bonds : bond 0.03187 ( 399) hydrogen bonds : angle 3.88144 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.9337 (mpm) cc_final: 0.9119 (mpm) REVERT: A 533 MET cc_start: 0.8851 (ppp) cc_final: 0.8566 (ppp) REVERT: B 114 MET cc_start: 0.9437 (mtm) cc_final: 0.8947 (pmm) REVERT: B 348 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8726 (ptp) REVERT: B 383 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8857 (mm-30) REVERT: B 435 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8837 (mtmm) outliers start: 19 outliers final: 10 residues processed: 77 average time/residue: 0.5389 time to fit residues: 44.4935 Evaluate side-chains 73 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 456 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.4980 chunk 34 optimal weight: 0.4980 chunk 97 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 104 optimal weight: 40.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.059470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.044141 restraints weight = 35845.516| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 4.68 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 1.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8660 Z= 0.123 Angle : 0.715 12.818 11731 Z= 0.336 Chirality : 0.041 0.200 1360 Planarity : 0.004 0.053 1502 Dihedral : 8.935 81.982 1230 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.65 % Allowed : 29.77 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.26), residues: 1071 helix: 1.09 (0.21), residues: 680 sheet: -0.20 (0.73), residues: 46 loop : -0.55 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 50 TYR 0.010 0.001 TYR B 135 PHE 0.017 0.001 PHE A 204 TRP 0.010 0.001 TRP A 189 HIS 0.004 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8660) covalent geometry : angle 0.71521 (11731) hydrogen bonds : bond 0.03022 ( 399) hydrogen bonds : angle 3.78115 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 376 MET cc_start: 0.8984 (mpm) cc_final: 0.8731 (mpm) REVERT: A 533 MET cc_start: 0.8770 (ppp) cc_final: 0.8431 (ppp) REVERT: B 185 ASP cc_start: 0.9030 (m-30) cc_final: 0.8649 (m-30) REVERT: B 348 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8521 (ptp) REVERT: B 383 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8467 (mm-30) REVERT: B 435 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8564 (mtmm) outliers start: 15 outliers final: 9 residues processed: 74 average time/residue: 0.5170 time to fit residues: 41.1046 Evaluate side-chains 73 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 70 optimal weight: 0.0470 chunk 74 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.059848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.044359 restraints weight = 35711.098| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 4.84 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 1.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8660 Z= 0.118 Angle : 0.704 12.997 11731 Z= 0.333 Chirality : 0.041 0.170 1360 Planarity : 0.004 0.054 1502 Dihedral : 8.750 81.670 1230 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.32 % Allowed : 30.43 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.27), residues: 1071 helix: 1.13 (0.21), residues: 682 sheet: -0.27 (0.72), residues: 46 loop : -0.48 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 50 TYR 0.010 0.001 TYR B 135 PHE 0.016 0.001 PHE A 204 TRP 0.010 0.001 TRP A 189 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8660) covalent geometry : angle 0.70413 (11731) hydrogen bonds : bond 0.02916 ( 399) hydrogen bonds : angle 3.72250 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.9374 (mppt) cc_final: 0.9096 (mmtp) REVERT: A 225 HIS cc_start: 0.8515 (p-80) cc_final: 0.8314 (p-80) REVERT: A 316 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: A 533 MET cc_start: 0.8716 (ppp) cc_final: 0.8382 (ppp) REVERT: B 114 MET cc_start: 0.9209 (mtm) cc_final: 0.8728 (pmm) REVERT: B 185 ASP cc_start: 0.9069 (m-30) cc_final: 0.8717 (m-30) REVERT: B 348 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8492 (ptp) REVERT: B 435 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8563 (mtmm) outliers start: 12 outliers final: 6 residues processed: 71 average time/residue: 0.5581 time to fit residues: 42.2910 Evaluate side-chains 70 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 435 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 0.4980 chunk 107 optimal weight: 0.0070 chunk 33 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.3004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.059499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.043867 restraints weight = 35786.225| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 4.67 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 1.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8660 Z= 0.127 Angle : 0.733 15.956 11731 Z= 0.342 Chirality : 0.041 0.177 1360 Planarity : 0.004 0.055 1502 Dihedral : 8.728 83.052 1230 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.99 % Allowed : 30.76 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.27), residues: 1071 helix: 1.15 (0.21), residues: 683 sheet: -0.23 (0.72), residues: 46 loop : -0.46 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 50 TYR 0.009 0.001 TYR B 135 PHE 0.033 0.001 PHE A 220 TRP 0.010 0.001 TRP A 189 HIS 0.004 0.001 HIS B 82 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8660) covalent geometry : angle 0.73331 (11731) hydrogen bonds : bond 0.03012 ( 399) hydrogen bonds : angle 3.78162 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2612.43 seconds wall clock time: 45 minutes 16.28 seconds (2716.28 seconds total)