Starting phenix.real_space_refine on Mon May 12 04:34:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jol_36459/05_2025/8jol_36459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jol_36459/05_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_36459/05_2025/8jol_36459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jol_36459/05_2025/8jol_36459.map" model { file = "/net/cci-nas-00/data/ceres_data/8jol_36459/05_2025/8jol_36459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jol_36459/05_2025/8jol_36459.cif" } resolution = 3.0 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 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 10} 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: 5.52, per 1000 atoms: 0.65 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: 2.45 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.01 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: 2.25 Time building geometry restraints manager: 2.79 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 \ 543 or resid 601 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: 0.800 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.580 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.010 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (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 TRP 0.024 0.005 TRP B 189 HIS 0.003 0.001 HIS B 225 PHE 0.018 0.003 PHE A 156 TYR 0.022 0.004 TYR B 184 ARG 0.003 0.001 ARG B 265 Details of bonding type rmsd hydrogen bonds : bond 0.25275 ( 399) hydrogen bonds : angle 9.24245 ( 1128) covalent geometry : bond 0.00918 ( 8660) covalent geometry : angle 1.46194 (11731) *********************** 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 : 0.953 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: 0.8474 (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: 0.8906 time to fit residues: 304.8890 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 : 1.017 ------------------------------------------------------------------------------- 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 91 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 40 HIS 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 Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.082814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.065179 restraints weight = 35588.575| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.29 r_work: 0.3289 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8660 Z= 0.158 Angle : 0.781 12.457 11731 Z= 0.389 Chirality : 0.043 0.193 1360 Planarity : 0.006 0.060 1502 Dihedral : 11.476 79.344 1269 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 7.17 % Allowed : 23.04 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.33 (0.24), residues: 1071 helix: -1.34 (0.18), residues: 678 sheet: -2.33 (0.57), residues: 58 loop : -1.43 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 260 HIS 0.008 0.001 HIS A 225 PHE 0.021 0.002 PHE B 220 TYR 0.017 0.002 TYR A 77 ARG 0.011 0.001 ARG A 483 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 399) hydrogen bonds : angle 4.93245 ( 1128) covalent geometry : bond 0.00360 ( 8660) covalent geometry : angle 0.78140 (11731) *********************** 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: 65 poor density : 120 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.9097 (m) cc_final: 0.8787 (p) REVERT: A 47 MET cc_start: 0.7225 (mmm) cc_final: 0.5417 (mmm) REVERT: A 206 ASP cc_start: 0.8892 (m-30) cc_final: 0.8629 (m-30) REVERT: A 218 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8772 (pt) REVERT: A 263 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7920 (mp0) REVERT: A 360 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8771 (mt) REVERT: A 361 VAL cc_start: 0.9548 (OUTLIER) cc_final: 0.9087 (t) REVERT: A 364 GLU cc_start: 0.8712 (pm20) cc_final: 0.8312 (pm20) REVERT: A 486 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: B 123 ASN cc_start: 0.9005 (t0) cc_final: 0.8717 (t0) REVERT: B 185 ASP cc_start: 0.8859 (m-30) cc_final: 0.8582 (m-30) REVERT: B 334 MET cc_start: 0.7447 (mmm) cc_final: 0.7195 (mmm) REVERT: B 376 MET cc_start: 0.8847 (mpm) cc_final: 0.8644 (mpm) REVERT: B 468 VAL cc_start: 0.6741 (m) cc_final: 0.6505 (p) REVERT: B 469 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: B 533 MET cc_start: 0.7912 (ppp) cc_final: 0.6891 (ppp) outliers start: 65 outliers final: 17 residues processed: 171 average time/residue: 0.8861 time to fit residues: 164.7853 Evaluate side-chains 125 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 459 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 381 CYS 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 1 optimal weight: 0.0770 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN B 536 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.074094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.056484 restraints weight = 35818.303| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.17 r_work: 0.3070 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.6992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8660 Z= 0.147 Angle : 0.717 10.030 11731 Z= 0.354 Chirality : 0.042 0.156 1360 Planarity : 0.005 0.048 1502 Dihedral : 9.605 85.817 1238 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 5.84 % Allowed : 23.15 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.76 (0.25), residues: 1071 helix: -0.09 (0.20), residues: 668 sheet: -1.65 (0.58), residues: 58 loop : -0.86 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 260 HIS 0.003 0.001 HIS B 225 PHE 0.016 0.001 PHE A 204 TYR 0.015 0.001 TYR A 77 ARG 0.006 0.001 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 399) hydrogen bonds : angle 4.26364 ( 1128) covalent geometry : bond 0.00332 ( 8660) covalent geometry : angle 0.71715 (11731) *********************** 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 155 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 102 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.9273 (m) cc_final: 0.8936 (p) REVERT: A 49 THR cc_start: 0.9144 (m) cc_final: 0.8916 (p) REVERT: A 128 MET cc_start: 0.9337 (mtp) cc_final: 0.9053 (mtp) REVERT: A 206 ASP cc_start: 0.8953 (m-30) cc_final: 0.8662 (m-30) REVERT: A 217 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8195 (mm) REVERT: A 218 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8248 (pt) REVERT: A 307 MET cc_start: 0.8681 (tpp) cc_final: 0.8188 (tpt) REVERT: A 361 VAL cc_start: 0.9586 (OUTLIER) cc_final: 0.9144 (t) REVERT: A 364 GLU cc_start: 0.8756 (pm20) cc_final: 0.8295 (pm20) REVERT: A 486 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: B 185 ASP cc_start: 0.9053 (m-30) cc_final: 0.8729 (m-30) REVERT: B 224 GLU cc_start: 0.9316 (mp0) cc_final: 0.8921 (pm20) REVERT: B 334 MET cc_start: 0.8462 (mmm) cc_final: 0.8041 (mmm) REVERT: B 338 LYS cc_start: 0.6411 (mptp) cc_final: 0.5870 (mmtt) REVERT: B 383 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8947 (mm-30) REVERT: B 432 ASP cc_start: 0.8748 (m-30) cc_final: 0.8487 (t0) outliers start: 53 outliers final: 15 residues processed: 144 average time/residue: 0.9497 time to fit residues: 148.3499 Evaluate side-chains 109 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 217 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 235 ILE 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 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 229 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 285 CYS 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 40 optimal weight: 0.6980 chunk 3 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 0.0030 chunk 86 optimal weight: 0.1980 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.064409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.048124 restraints weight = 35336.819| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 4.39 r_work: 0.2800 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.9579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8660 Z= 0.175 Angle : 0.741 11.320 11731 Z= 0.366 Chirality : 0.044 0.187 1360 Planarity : 0.005 0.053 1502 Dihedral : 9.650 82.186 1234 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.84 % Allowed : 23.93 % 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 (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: -0.08 (0.26), residues: 1071 helix: 0.45 (0.21), residues: 678 sheet: -1.08 (0.65), residues: 46 loop : -0.71 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 410 HIS 0.007 0.001 HIS A 19 PHE 0.015 0.002 PHE A 204 TYR 0.015 0.002 TYR B 369 ARG 0.007 0.001 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 399) hydrogen bonds : angle 4.23720 ( 1128) covalent geometry : bond 0.00411 ( 8660) covalent geometry : angle 0.74082 (11731) *********************** 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 136 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 83 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.9424 (OUTLIER) cc_final: 0.9074 (t) REVERT: A 49 THR cc_start: 0.9526 (m) cc_final: 0.9265 (p) REVERT: A 206 ASP cc_start: 0.9074 (m-30) cc_final: 0.8764 (m-30) REVERT: A 307 MET cc_start: 0.9171 (tpp) cc_final: 0.8949 (tmm) REVERT: A 360 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9116 (mt) REVERT: A 361 VAL cc_start: 0.9504 (OUTLIER) cc_final: 0.9225 (t) REVERT: A 364 GLU cc_start: 0.8850 (pm20) cc_final: 0.8378 (pm20) REVERT: A 376 MET cc_start: 0.9533 (mmp) cc_final: 0.9284 (mpm) REVERT: A 399 MET cc_start: 0.9479 (mmp) cc_final: 0.9245 (mmm) REVERT: A 486 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7745 (tm-30) REVERT: B 114 MET cc_start: 0.8756 (mpt) cc_final: 0.8493 (mpp) REVERT: B 185 ASP cc_start: 0.9328 (m-30) cc_final: 0.8892 (m-30) REVERT: B 316 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8508 (pp20) REVERT: B 351 LEU cc_start: 0.8943 (mt) cc_final: 0.8682 (mt) REVERT: B 383 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8884 (mm-30) outliers start: 53 outliers final: 12 residues processed: 128 average time/residue: 1.0437 time to fit residues: 143.9084 Evaluate side-chains 88 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 229 VAL 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 430 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 83 LEU 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 381 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 283 GLN A 475 ASN B 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.061946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.045895 restraints weight = 36119.994| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.53 r_work: 0.2733 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 1.0169 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= 0.171 Angle : 0.683 10.102 11731 Z= 0.337 Chirality : 0.042 0.158 1360 Planarity : 0.005 0.056 1502 Dihedral : 9.438 87.279 1230 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.74 % Allowed : 25.36 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.25 (0.26), residues: 1071 helix: 0.72 (0.21), residues: 682 sheet: -0.64 (0.68), residues: 46 loop : -0.69 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 189 HIS 0.004 0.001 HIS A 19 PHE 0.019 0.001 PHE B 337 TYR 0.017 0.001 TYR B 369 ARG 0.005 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.03408 ( 399) hydrogen bonds : angle 4.11119 ( 1128) covalent geometry : bond 0.00404 ( 8660) covalent geometry : angle 0.68311 (11731) *********************** 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 116 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 73 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 SER cc_start: 0.9575 (OUTLIER) cc_final: 0.9251 (p) REVERT: A 206 ASP cc_start: 0.9096 (m-30) cc_final: 0.8807 (m-30) REVERT: A 360 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9052 (mt) REVERT: A 361 VAL cc_start: 0.9501 (OUTLIER) cc_final: 0.9187 (t) REVERT: A 364 GLU cc_start: 0.8887 (pm20) cc_final: 0.8390 (pm20) REVERT: A 376 MET cc_start: 0.9521 (mmp) cc_final: 0.9298 (mmm) REVERT: A 486 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: B 47 MET cc_start: 0.6646 (ptm) cc_final: 0.6242 (ppp) REVERT: B 114 MET cc_start: 0.8907 (mpt) cc_final: 0.8639 (mpp) REVERT: B 147 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.8788 (mtp) REVERT: B 185 ASP cc_start: 0.9348 (m-30) cc_final: 0.8919 (m-30) REVERT: B 316 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8562 (pp20) REVERT: B 348 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8578 (ptp) REVERT: B 351 LEU cc_start: 0.9232 (mt) cc_final: 0.9007 (mt) REVERT: B 364 GLU cc_start: 0.9004 (pm20) cc_final: 0.8409 (pm20) REVERT: B 383 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8880 (mm-30) REVERT: B 408 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8662 (mppt) REVERT: B 533 MET cc_start: 0.8455 (ppp) cc_final: 0.8208 (ptt) REVERT: B 534 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8695 (pp30) outliers start: 43 outliers final: 14 residues processed: 109 average time/residue: 0.9544 time to fit residues: 112.9758 Evaluate side-chains 91 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 68 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 229 VAL 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 393 LEU Chi-restraints excluded: chain A residue 430 VAL 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 141 ILE Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 534 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 283 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.061925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.046024 restraints weight = 35768.047| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.96 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 1.0619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8660 Z= 0.124 Angle : 0.663 13.928 11731 Z= 0.318 Chirality : 0.040 0.151 1360 Planarity : 0.004 0.057 1502 Dihedral : 9.075 85.327 1228 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.41 % Allowed : 25.91 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.42 (0.26), residues: 1071 helix: 0.89 (0.21), residues: 683 sheet: -0.48 (0.70), residues: 46 loop : -0.72 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 189 HIS 0.004 0.001 HIS B 536 PHE 0.017 0.001 PHE B 337 TYR 0.011 0.001 TYR B 135 ARG 0.003 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 399) hydrogen bonds : angle 3.92056 ( 1128) covalent geometry : bond 0.00298 ( 8660) covalent geometry : angle 0.66287 (11731) *********************** 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 110 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 70 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.8863 (m-30) cc_final: 0.8505 (m-30) REVERT: A 360 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8934 (mt) REVERT: A 361 VAL cc_start: 0.9424 (OUTLIER) cc_final: 0.8999 (t) REVERT: A 364 GLU cc_start: 0.8252 (pm20) cc_final: 0.7817 (pm20) REVERT: A 486 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: B 114 MET cc_start: 0.8759 (mpt) cc_final: 0.8525 (mpp) REVERT: B 147 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8620 (mtp) REVERT: B 185 ASP cc_start: 0.9044 (m-30) cc_final: 0.8650 (m-30) REVERT: B 316 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8512 (pp20) REVERT: B 338 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7316 (mmtt) REVERT: B 348 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8493 (ptp) REVERT: B 351 LEU cc_start: 0.9287 (mt) cc_final: 0.9048 (mp) REVERT: B 364 GLU cc_start: 0.8634 (pm20) cc_final: 0.7986 (pm20) REVERT: B 383 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8589 (mm-30) REVERT: B 408 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8756 (mppt) outliers start: 40 outliers final: 9 residues processed: 102 average time/residue: 0.9585 time to fit residues: 106.2072 Evaluate side-chains 85 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 229 VAL 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 430 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 460 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 0.0040 chunk 56 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 88 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- 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 = 0.3342 r_free = 0.3342 target = 0.059826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.044169 restraints weight = 36398.577| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 4.30 r_work: 0.2689 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 1.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8660 Z= 0.159 Angle : 0.693 11.689 11731 Z= 0.336 Chirality : 0.042 0.210 1360 Planarity : 0.005 0.057 1502 Dihedral : 9.209 86.914 1228 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.08 % Allowed : 27.45 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.51 (0.26), residues: 1071 helix: 0.95 (0.21), residues: 682 sheet: -0.28 (0.73), residues: 46 loop : -0.68 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 189 HIS 0.005 0.001 HIS B 82 PHE 0.025 0.002 PHE A 220 TYR 0.016 0.001 TYR B 369 ARG 0.003 0.001 ARG B 53 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 399) hydrogen bonds : angle 4.03362 ( 1128) covalent geometry : bond 0.00376 ( 8660) covalent geometry : angle 0.69256 (11731) *********************** 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 105 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 68 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8676 (pp20) REVERT: A 47 MET cc_start: 0.9079 (mmm) cc_final: 0.8798 (mtm) REVERT: A 307 MET cc_start: 0.9233 (mmm) cc_final: 0.8436 (tpp) REVERT: A 360 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9103 (mt) REVERT: A 361 VAL cc_start: 0.9459 (OUTLIER) cc_final: 0.9107 (t) REVERT: A 364 GLU cc_start: 0.8892 (pm20) cc_final: 0.8438 (pm20) REVERT: A 376 MET cc_start: 0.9334 (mpm) cc_final: 0.9068 (mpp) REVERT: A 486 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: A 533 MET cc_start: 0.8841 (ppp) cc_final: 0.8516 (ppp) REVERT: B 47 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7431 (ppp) REVERT: B 147 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.9036 (mtp) REVERT: B 185 ASP cc_start: 0.9391 (m-30) cc_final: 0.8960 (m-30) REVERT: B 316 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8629 (pp20) REVERT: B 338 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7932 (mmtt) REVERT: B 348 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8673 (ptp) REVERT: B 383 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8918 (mm-30) REVERT: B 408 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8886 (mppt) REVERT: B 459 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8952 (tt) outliers start: 37 outliers final: 9 residues processed: 95 average time/residue: 1.1363 time to fit residues: 115.9271 Evaluate side-chains 83 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 185 ASP 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 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 47 MET Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 316 GLU Chi-restraints excluded: chain B residue 338 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 5 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 21 optimal weight: 9.9990 chunk 3 optimal weight: 0.4980 chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 0.0370 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.5060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.061270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045276 restraints weight = 36223.417| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.80 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 1.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8660 Z= 0.114 Angle : 0.687 15.578 11731 Z= 0.326 Chirality : 0.041 0.206 1360 Planarity : 0.005 0.055 1502 Dihedral : 8.859 83.012 1228 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.43 % Allowed : 29.44 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.67 (0.26), residues: 1071 helix: 1.08 (0.21), residues: 674 sheet: -0.31 (0.74), residues: 46 loop : -0.57 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 189 HIS 0.005 0.001 HIS B 82 PHE 0.022 0.001 PHE A 539 TYR 0.011 0.001 TYR B 135 ARG 0.003 0.000 ARG A 8 Details of bonding type rmsd hydrogen bonds : bond 0.02808 ( 399) hydrogen bonds : angle 3.85271 ( 1128) covalent geometry : bond 0.00277 ( 8660) covalent geometry : angle 0.68704 (11731) *********************** 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 89 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8481 (pp20) REVERT: A 47 MET cc_start: 0.8758 (mmm) cc_final: 0.8536 (mtm) REVERT: A 147 MET cc_start: 0.9197 (mtp) cc_final: 0.8817 (ptp) REVERT: A 225 HIS cc_start: 0.8437 (p-80) cc_final: 0.8193 (p-80) REVERT: A 307 MET cc_start: 0.9080 (mmm) cc_final: 0.8285 (tpp) REVERT: A 360 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8858 (mt) REVERT: A 361 VAL cc_start: 0.9396 (OUTLIER) cc_final: 0.8997 (t) REVERT: A 364 GLU cc_start: 0.8220 (pm20) cc_final: 0.7826 (pm20) REVERT: A 376 MET cc_start: 0.8893 (mpm) cc_final: 0.8687 (mpm) REVERT: A 486 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7341 (tm-30) REVERT: A 533 MET cc_start: 0.8618 (ppp) cc_final: 0.8392 (ppp) REVERT: B 47 MET cc_start: 0.7745 (ppp) cc_final: 0.7205 (ppp) REVERT: B 114 MET cc_start: 0.8923 (mpp) cc_final: 0.8635 (mpp) REVERT: B 147 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8636 (mtp) REVERT: B 185 ASP cc_start: 0.9073 (m-30) cc_final: 0.8684 (m-30) REVERT: B 343 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8414 (tppt) REVERT: B 348 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8323 (ptp) REVERT: B 351 LEU cc_start: 0.9426 (mt) cc_final: 0.9205 (mp) REVERT: B 383 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8575 (mm-30) outliers start: 22 outliers final: 7 residues processed: 85 average time/residue: 1.0814 time to fit residues: 99.3405 Evaluate side-chains 79 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.0870 chunk 84 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 102 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 HIS ** 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 = 0.3357 r_free = 0.3357 target = 0.060264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.044450 restraints weight = 36443.180| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 4.76 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 1.1594 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= 0.129 Angle : 0.694 15.249 11731 Z= 0.331 Chirality : 0.042 0.239 1360 Planarity : 0.005 0.056 1502 Dihedral : 8.805 85.357 1228 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.98 % Allowed : 30.43 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.57 (0.26), residues: 1071 helix: 0.97 (0.21), residues: 687 sheet: -0.31 (0.73), residues: 46 loop : -0.59 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 189 HIS 0.005 0.001 HIS B 82 PHE 0.023 0.001 PHE B 539 TYR 0.012 0.001 TYR B 540 ARG 0.002 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03033 ( 399) hydrogen bonds : angle 3.92523 ( 1128) covalent geometry : bond 0.00316 ( 8660) covalent geometry : angle 0.69440 (11731) *********************** 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 84 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8512 (pp20) REVERT: A 307 MET cc_start: 0.9094 (mmm) cc_final: 0.8402 (tpp) REVERT: A 360 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8946 (mt) REVERT: A 361 VAL cc_start: 0.9427 (OUTLIER) cc_final: 0.9136 (t) REVERT: A 364 GLU cc_start: 0.8224 (pm20) cc_final: 0.7840 (pm20) REVERT: A 376 MET cc_start: 0.8921 (mpm) cc_final: 0.8693 (mpm) REVERT: A 486 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: A 533 MET cc_start: 0.8637 (ppp) cc_final: 0.8358 (ppp) REVERT: B 185 ASP cc_start: 0.9069 (m-30) cc_final: 0.8688 (m-30) REVERT: B 348 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8449 (ptp) REVERT: B 351 LEU cc_start: 0.9447 (mt) cc_final: 0.9235 (mp) REVERT: B 383 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8579 (mm-30) outliers start: 18 outliers final: 7 residues processed: 80 average time/residue: 1.1078 time to fit residues: 95.3874 Evaluate side-chains 76 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 110 PHE 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 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 82 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 59 optimal weight: 10.0000 chunk 73 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 54 optimal weight: 0.0870 overall best weight: 1.4364 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.060078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.044568 restraints weight = 35784.437| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 4.57 r_work: 0.2703 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 1.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8660 Z= 0.130 Angle : 0.700 14.190 11731 Z= 0.336 Chirality : 0.042 0.262 1360 Planarity : 0.005 0.056 1502 Dihedral : 8.865 85.312 1228 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.65 % Allowed : 30.87 % Favored : 67.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.67 (0.26), residues: 1071 helix: 1.03 (0.21), residues: 680 sheet: -0.32 (0.73), residues: 46 loop : -0.48 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 189 HIS 0.005 0.001 HIS B 82 PHE 0.017 0.001 PHE B 539 TYR 0.011 0.001 TYR B 369 ARG 0.002 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 399) hydrogen bonds : angle 3.92465 ( 1128) covalent geometry : bond 0.00318 ( 8660) covalent geometry : angle 0.69959 (11731) ********************** 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 80 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8683 (pp20) REVERT: A 316 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8516 (pm20) REVERT: A 360 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9030 (mt) REVERT: A 361 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9189 (t) REVERT: A 364 GLU cc_start: 0.8875 (pm20) cc_final: 0.8454 (pm20) REVERT: A 376 MET cc_start: 0.9322 (mpm) cc_final: 0.8977 (mpp) REVERT: A 486 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: A 533 MET cc_start: 0.8681 (ppp) cc_final: 0.8356 (ppp) REVERT: B 114 MET cc_start: 0.9485 (mtm) cc_final: 0.9172 (mpp) REVERT: B 185 ASP cc_start: 0.9418 (m-30) cc_final: 0.8985 (m-30) REVERT: B 348 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8632 (ptp) REVERT: B 383 GLU cc_start: 0.9295 (mm-30) cc_final: 0.9020 (mm-30) outliers start: 15 outliers final: 8 residues processed: 77 average time/residue: 1.2074 time to fit residues: 99.9417 Evaluate side-chains 77 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 262 GLN 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 456 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 69 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 40.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 HIS ** 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 = 0.3365 r_free = 0.3365 target = 0.060583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.045234 restraints weight = 36526.946| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.33 r_work: 0.2733 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 1.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8660 Z= 0.120 Angle : 0.734 16.135 11731 Z= 0.346 Chirality : 0.041 0.260 1360 Planarity : 0.004 0.055 1502 Dihedral : 8.686 84.080 1228 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.65 % Allowed : 31.20 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.73 (0.27), residues: 1071 helix: 1.07 (0.21), residues: 680 sheet: -0.31 (0.73), residues: 46 loop : -0.43 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 189 HIS 0.005 0.001 HIS B 82 PHE 0.032 0.001 PHE B 220 TYR 0.010 0.001 TYR B 135 ARG 0.002 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.02822 ( 399) hydrogen bonds : angle 3.83212 ( 1128) covalent geometry : bond 0.00296 ( 8660) covalent geometry : angle 0.73402 (11731) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5649.96 seconds wall clock time: 98 minutes 3.59 seconds (5883.59 seconds total)