Starting phenix.real_space_refine on Thu Jul 2 12:38:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jol_36459/07_2026/8jol_36459.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jol_36459/07_2026/8jol_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 { model { file = "/net/cci-nas-00/data/ceres_data/8jol_36459/07_2026/8jol_36459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jol_36459/07_2026/8jol_36459.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jol_36459/07_2026/8jol_36459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jol_36459/07_2026/8jol_36459.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jol_36459/07_2026/8jol_36459.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jol_36459/07_2026/8jol_36459.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 58 5.16 5 C 5388 2.51 5 N 1439 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8513 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 4039 Classifications: {'peptide': 503} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 481} Chain breaks: 2 Chain: "B" Number of atoms: 3965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3965 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 473} Chain breaks: 3 Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 445 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 278 Unresolved non-hydrogen angles: 349 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ARG:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 7, 'GLU:plan': 8, 'ASN:plan1': 4, 'PHE:plan': 3, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 162 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.13, per 1000 atoms: 0.25 Number of scatterers: 8513 At special positions: 0 Unit cell: (95.04, 114.84, 137.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 2 11.99 O 1620 8.00 N 1439 7.00 C 5388 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 504.4 milliseconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2096 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 65.5% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 18 removed outlier: 3.563A pdb=" N LEU A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.758A pdb=" N ALA A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N TYR A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 46 Processing helix chain 'A' and resid 49 through 65 removed outlier: 3.557A pdb=" N ARG A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 65 " --> pdb=" O TYR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.620A pdb=" N ALA A 84 " --> pdb=" O GLN A 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 86 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 106 through 110 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.523A pdb=" N ILE A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 212 removed outlier: 4.023A pdb=" N PHE A 204 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 240 removed outlier: 3.692A pdb=" N ALA A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 264 removed outlier: 3.653A pdb=" N ALA A 261 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A 262 " --> pdb=" O ILE A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.915A pdb=" N ILE A 277 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 305 removed outlier: 3.648A pdb=" N TYR A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 327 removed outlier: 4.885A pdb=" N VAL A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 344 through 355 Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ARG A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 396 removed outlier: 3.738A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 428 through 440 Processing helix chain 'A' and resid 458 through 468 removed outlier: 3.654A pdb=" N PHE A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 485 removed outlier: 3.768A pdb=" N ALA A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.851A pdb=" N LEU A 535 " --> pdb=" O PHE A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 removed outlier: 3.938A pdb=" N SER A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 removed outlier: 3.630A pdb=" N LEU B 10 " --> pdb=" O GLU B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 20 removed outlier: 3.560A pdb=" N LEU B 17 " --> pdb=" O ALA B 13 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS B 19 " --> pdb=" O THR B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 33 removed outlier: 3.773A pdb=" N ALA B 26 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 46 Processing helix chain 'B' and resid 49 through 65 removed outlier: 3.553A pdb=" N ARG B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 removed outlier: 3.656A pdb=" N ILE B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 removed outlier: 3.618A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 86 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 removed outlier: 3.891A pdb=" N MET B 114 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 164 through 173 removed outlier: 3.507A pdb=" N ILE B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 212 removed outlier: 4.015A pdb=" N PHE B 204 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 208 " --> pdb=" O PHE B 204 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 209 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 242 removed outlier: 3.929A pdb=" N ASP B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 264 removed outlier: 4.189A pdb=" N ILE B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 281 removed outlier: 4.001A pdb=" N ILE B 277 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 305 removed outlier: 3.591A pdb=" N TYR B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 327 removed outlier: 4.890A pdb=" N VAL B 318 " --> pdb=" O LYS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.791A pdb=" N GLU B 356 " --> pdb=" O ASN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 363 Processing helix chain 'B' and resid 373 through 384 removed outlier: 3.891A pdb=" N ALA B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARG B 380 " --> pdb=" O MET B 376 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N CYS B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 395 Processing helix chain 'B' and resid 396 through 399 Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 469 through 484 removed outlier: 3.793A pdb=" N ALA B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.850A pdb=" N LEU B 535 " --> pdb=" O PHE B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 removed outlier: 3.925A pdb=" N SER B 542 " --> pdb=" O LYS B 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 13 through 18 removed outlier: 3.750A pdb=" N PHE C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 33 removed outlier: 3.773A pdb=" N ILE C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL C 29 " --> pdb=" O GLU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 46 Processing helix chain 'C' and resid 49 through 64 removed outlier: 3.552A pdb=" N LYS C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 80 through 92 removed outlier: 3.617A pdb=" N LEU C 84 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU C 86 " --> pdb=" O GLU C 82 " (cutoff:3.500A) Proline residue: C 90 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 7.093A pdb=" N THR A 245 " --> pdb=" O ARG A 267 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU A 269 " --> pdb=" O THR A 245 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N PHE A 247 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR A 271 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N PHE A 249 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE A 153 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL A 270 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU A 155 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 272 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 157 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE A 154 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE A 288 " --> pdb=" O PHE A 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N PHE A 156 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 290 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N HIS A 158 " --> pdb=" O VAL A 290 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA3, first strand: chain 'B' and resid 186 through 191 removed outlier: 6.820A pdb=" N THR B 245 " --> pdb=" O ARG B 267 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU B 269 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE B 247 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N THR B 271 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE B 249 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 272 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 159 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE B 154 " --> pdb=" O GLU B 286 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE B 288 " --> pdb=" O PHE B 154 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 156 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 290 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS B 158 " --> pdb=" O VAL B 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 405 through 406 399 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2514 1.33 - 1.46: 1796 1.46 - 1.59: 4252 1.59 - 1.72: 6 1.72 - 1.85: 92 Bond restraints: 8660 Sorted by residual: bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.483 -0.095 1.00e-02 1.00e+04 8.95e+01 bond pdb=" C4 ATP B 602 " pdb=" C5 ATP B 602 " ideal model delta sigma weight residual 1.388 1.480 -0.092 1.00e-02 1.00e+04 8.53e+01 bond pdb=" C5 ATP A 602 " pdb=" C6 ATP A 602 " ideal model delta sigma weight residual 1.409 1.492 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C5 ATP B 602 " pdb=" N7 ATP B 602 " ideal model delta sigma weight residual 1.387 1.332 0.055 1.00e-02 1.00e+04 3.01e+01 bond pdb=" C8 ATP A 602 " pdb=" N7 ATP A 602 " ideal model delta sigma weight residual 1.310 1.356 -0.046 1.00e-02 1.00e+04 2.09e+01 ... (remaining 8655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 11612 5.15 - 10.29: 112 10.29 - 15.44: 4 15.44 - 20.59: 2 20.59 - 25.73: 1 Bond angle restraints: 11731 Sorted by residual: angle pdb=" PB ATP A 602 " pdb=" O3B ATP A 602 " pdb=" PG ATP A 602 " ideal model delta sigma weight residual 139.87 114.14 25.73 1.00e+00 1.00e+00 6.62e+02 angle pdb=" PA ATP B 602 " pdb=" O3A ATP B 602 " pdb=" PB ATP B 602 " ideal model delta sigma weight residual 136.83 119.12 17.71 1.00e+00 1.00e+00 3.14e+02 angle pdb=" PB ATP B 602 " pdb=" O3B ATP B 602 " pdb=" PG ATP B 602 " ideal model delta sigma weight residual 139.87 122.83 17.04 1.00e+00 1.00e+00 2.90e+02 angle pdb=" PA ATP A 602 " pdb=" O3A ATP A 602 " pdb=" PB ATP A 602 " ideal model delta sigma weight residual 136.83 121.64 15.19 1.00e+00 1.00e+00 2.31e+02 angle pdb=" N3 ATP B 602 " pdb=" C4 ATP B 602 " pdb=" N9 ATP B 602 " ideal model delta sigma weight residual 127.04 136.39 -9.35 1.15e+00 7.59e-01 6.64e+01 ... (remaining 11726 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 4597 17.39 - 34.79: 463 34.79 - 52.18: 149 52.18 - 69.58: 61 69.58 - 86.97: 7 Dihedral angle restraints: 5277 sinusoidal: 2078 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 5274 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 960 0.070 - 0.140: 301 0.140 - 0.210: 76 0.210 - 0.279: 19 0.279 - 0.349: 4 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CA PHE A 532 " pdb=" N PHE A 532 " pdb=" C PHE A 532 " pdb=" CB PHE A 532 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA LYS A 212 " pdb=" N LYS A 212 " pdb=" C LYS A 212 " pdb=" CB LYS A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA PHE B 532 " pdb=" N PHE B 532 " pdb=" C PHE B 532 " pdb=" CB PHE B 532 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 1357 not shown) Planarity restraints: 1502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 87 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C VAL C 87 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL C 87 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU C 88 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 253 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C VAL A 253 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL A 253 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN A 254 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 220 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO B 221 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 221 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 221 " -0.032 5.00e-02 4.00e+02 ... (remaining 1499 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1343 2.75 - 3.29: 9096 3.29 - 3.83: 14060 3.83 - 4.36: 18222 4.36 - 4.90: 27779 Nonbonded interactions: 70500 Sorted by model distance: nonbonded pdb=" O1B ATP A 602 " pdb=" O2G ATP A 602 " model vdw 2.214 3.040 nonbonded pdb=" O ARG A 259 " pdb=" N GLN A 262 " model vdw 2.275 3.120 nonbonded pdb=" O4' ATP A 602 " pdb=" O5' ATP A 602 " model vdw 2.319 2.432 nonbonded pdb=" OG SER B 166 " pdb="MG MG B 601 " model vdw 2.341 2.170 nonbonded pdb=" O LEU B 120 " pdb=" N ASN B 123 " model vdw 2.349 3.120 ... (remaining 70495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 98 or resid 106 through 416 or resid 426 through \ 602)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.460 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 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 : 17.244 86.969 3181 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 35.79 Ramachandran Plot: Outliers : 0.84 % Allowed : 12.32 % Favored : 86.83 % Rotamer: Outliers : 16.43 % Allowed : 15.21 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.77 (0.21), residues: 1071 helix: -3.29 (0.15), residues: 632 sheet: -2.60 (0.61), residues: 60 loop : -2.63 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 265 TYR 0.022 0.004 TYR B 184 PHE 0.018 0.003 PHE A 156 TRP 0.024 0.005 TRP B 189 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00918 / 0.60 ( 8660) covalent geometry : angle 1.46194 / 1.02 (11731) hydrogen bonds : bond 0.25275 / 17.31 ( 399) hydrogen bonds : angle 9.24245 / 6.37 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 215 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 SER cc_start: 0.8962 (m) cc_final: 0.8522 (p) REVERT: A 47 MET cc_start: 0.6707 (mmm) cc_final: 0.6151 (mmm) REVERT: A 123 ASN cc_start: 0.8269 (m110) cc_final: 0.7650 (t0) REVERT: A 128 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7943 (tpp) REVERT: A 144 LEU cc_start: 0.8740 (mt) cc_final: 0.8503 (mt) REVERT: A 185 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7666 (t0) REVERT: A 205 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8843 (m) REVERT: A 206 ASP cc_start: 0.8609 (m-30) cc_final: 0.8231 (m-30) REVERT: A 218 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8387 (pt) REVERT: A 228 SER cc_start: 0.9145 (m) cc_final: 0.8888 (t) REVERT: A 233 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7569 (ttp-170) REVERT: A 286 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7454 (mm-30) REVERT: A 290 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7993 (t) REVERT: A 443 LEU cc_start: 0.9052 (mt) cc_final: 0.8667 (mp) REVERT: B 45 SER cc_start: 0.4096 (OUTLIER) cc_final: 0.3860 (p) REVERT: B 128 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7837 (OUTLIER) REVERT: B 185 ASP cc_start: 0.8675 (OUTLIER) cc_final: 0.8356 (m-30) REVERT: B 190 LEU cc_start: 0.8856 (mt) cc_final: 0.8473 (mt) REVERT: B 218 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7944 (pt) REVERT: B 361 VAL cc_start: 0.8410 (t) cc_final: 0.7470 (p) REVERT: B 382 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7187 (t) outliers start: 149 outliers final: 10 residues processed: 317 average time/residue: 0.3894 time to fit residues: 133.6075 Evaluate side-chains 148 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 542 SER Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 542 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.4980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 38 optimal weight: 3.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN A 123 ASN A 219 ASN A 244 ASN A 329 ASN A 461 HIS A 471 GLN A 482 GLN A 534 GLN B 34 ASN B 64 GLN B 113 GLN B 244 ASN B 482 GLN B 534 GLN B 536 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.080028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.062315 restraints weight = 35520.487| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 4.24 r_work: 0.3219 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8660 Z= 0.180 Angle : 0.786 12.714 11731 Z= 0.393 Chirality : 0.044 0.196 1360 Planarity : 0.006 0.061 1502 Dihedral : 8.258 68.701 1207 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 7.39 % Allowed : 23.37 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.24), residues: 1071 helix: -1.38 (0.18), residues: 682 sheet: -2.24 (0.57), residues: 58 loop : -1.40 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 483 TYR 0.017 0.002 TYR A 77 PHE 0.018 0.002 PHE B 220 TRP 0.008 0.001 TRP B 410 HIS 0.007 0.001 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 8660) covalent geometry : angle 0.78581 / 0.39 (11731) hydrogen bonds : bond 0.04209 / 2.73 ( 399) hydrogen bonds : angle 4.91093 / 3.46 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 113 time to evaluate : 0.318 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: 0.9193 (m) cc_final: 0.8811 (p) REVERT: A 52 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7622 (mp0) REVERT: A 202 ASP cc_start: 0.9452 (m-30) cc_final: 0.8913 (m-30) REVERT: A 206 ASP cc_start: 0.8943 (m-30) cc_final: 0.8680 (m-30) REVERT: A 218 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8738 (pt) REVERT: A 360 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8789 (mt) REVERT: A 361 VAL cc_start: 0.9555 (OUTLIER) cc_final: 0.9112 (t) REVERT: A 364 GLU cc_start: 0.8743 (pm20) cc_final: 0.8362 (pm20) REVERT: A 486 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7697 (tm-30) REVERT: B 123 ASN cc_start: 0.9185 (t0) cc_final: 0.8919 (t0) REVERT: B 185 ASP cc_start: 0.8910 (m-30) cc_final: 0.8579 (m-30) REVERT: B 334 MET cc_start: 0.7727 (mmm) cc_final: 0.7415 (mmm) REVERT: B 462 MET cc_start: 0.9023 (mpm) cc_final: 0.8823 (mpp) REVERT: B 468 VAL cc_start: 0.7029 (m) cc_final: 0.6812 (p) REVERT: B 533 MET cc_start: 0.7954 (ppp) cc_final: 0.6970 (ppp) outliers start: 67 outliers final: 17 residues processed: 166 average time/residue: 0.4294 time to fit residues: 76.8953 Evaluate side-chains 118 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 285 CYS Chi-restraints excluded: chain B residue 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 88 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 103 optimal weight: 50.0000 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 97 optimal weight: 20.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 HIS A 56 ASN B 40 HIS B 64 GLN B 158 HIS B 262 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.067029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.050573 restraints weight = 35576.149| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.43 r_work: 0.2873 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.8610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8660 Z= 0.184 Angle : 0.758 9.210 11731 Z= 0.379 Chirality : 0.043 0.189 1360 Planarity : 0.006 0.053 1502 Dihedral : 6.080 72.449 1176 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 5.95 % Allowed : 23.26 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.25), residues: 1071 helix: -0.02 (0.20), residues: 671 sheet: -1.34 (0.61), residues: 56 loop : -0.84 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 390 TYR 0.016 0.002 TYR A 77 PHE 0.016 0.002 PHE B 74 TRP 0.009 0.001 TRP B 260 HIS 0.004 0.001 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 8660) covalent geometry : angle 0.75825 / 0.38 (11731) hydrogen bonds : bond 0.04241 / 2.81 ( 399) hydrogen bonds : angle 4.44678 / 3.13 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 84 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.8434 (mmm) cc_final: 0.6408 (mmm) REVERT: A 206 ASP cc_start: 0.9035 (m-30) cc_final: 0.8732 (m-30) REVERT: A 209 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9126 (mm) REVERT: A 218 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8431 (pt) REVERT: A 307 MET cc_start: 0.8828 (tpp) cc_final: 0.8281 (tpt) REVERT: A 360 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9113 (mt) REVERT: A 361 VAL cc_start: 0.9561 (OUTLIER) cc_final: 0.9124 (t) REVERT: A 364 GLU cc_start: 0.8854 (pm20) cc_final: 0.8343 (pm20) REVERT: A 376 MET cc_start: 0.9470 (mmp) cc_final: 0.9118 (mpm) REVERT: A 486 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: B 97 GLU cc_start: 0.2406 (OUTLIER) cc_final: 0.2114 (pp20) REVERT: B 185 ASP cc_start: 0.9278 (m-30) cc_final: 0.8850 (m-30) REVERT: B 302 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8843 (mt) REVERT: B 316 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8362 (pp20) REVERT: B 351 LEU cc_start: 0.8888 (mt) cc_final: 0.8667 (mt) REVERT: B 383 GLU cc_start: 0.9185 (mm-30) cc_final: 0.8893 (mm-30) REVERT: B 432 ASP cc_start: 0.8975 (m-30) cc_final: 0.8601 (t0) outliers start: 54 outliers final: 11 residues processed: 128 average time/residue: 0.4299 time to fit residues: 58.9924 Evaluate side-chains 96 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 218 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 486 GLU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 302 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 459 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 HIS A 56 ASN A 262 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.061979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045924 restraints weight = 36443.557| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 4.44 r_work: 0.2744 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 1.0181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8660 Z= 0.190 Angle : 0.718 9.668 11731 Z= 0.355 Chirality : 0.043 0.150 1360 Planarity : 0.005 0.055 1502 Dihedral : 5.750 64.925 1172 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.40 % Allowed : 23.04 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 1071 helix: 0.49 (0.20), residues: 681 sheet: -1.10 (0.68), residues: 46 loop : -0.83 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 358 TYR 0.017 0.002 TYR B 369 PHE 0.025 0.002 PHE B 337 TRP 0.012 0.002 TRP A 410 HIS 0.007 0.001 HIS A 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 8660) covalent geometry : angle 0.71817 / 0.35 (11731) hydrogen bonds : bond 0.03651 / 2.41 ( 399) hydrogen bonds : angle 4.18739 / 2.97 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 80 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4619 (ttt) cc_final: 0.4396 (ttt) REVERT: A 114 MET cc_start: 0.9173 (mtm) cc_final: 0.8887 (ptt) REVERT: A 206 ASP cc_start: 0.9106 (m-30) cc_final: 0.8787 (m-30) REVERT: A 212 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8420 (ttmm) REVERT: A 360 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9104 (mt) REVERT: A 361 VAL cc_start: 0.9488 (OUTLIER) cc_final: 0.9173 (t) REVERT: A 364 GLU cc_start: 0.8899 (pm20) cc_final: 0.8407 (pm20) REVERT: A 376 MET cc_start: 0.9512 (mmp) cc_final: 0.9294 (mmm) REVERT: A 486 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7589 (tm-30) REVERT: B 147 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8904 (mtp) REVERT: B 185 ASP cc_start: 0.9350 (m-30) cc_final: 0.8915 (m-30) REVERT: B 338 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7541 (mmtt) REVERT: B 351 LEU cc_start: 0.9252 (mt) cc_final: 0.9030 (mt) REVERT: B 383 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8748 (mm-30) outliers start: 49 outliers final: 13 residues processed: 121 average time/residue: 0.4325 time to fit residues: 56.1766 Evaluate side-chains 85 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 212 LYS 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 10 LEU 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 239 LEU Chi-restraints excluded: chain B residue 338 LYS 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 25 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN A 425 GLN A 475 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.061863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.046195 restraints weight = 36233.994| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 4.23 r_work: 0.2752 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 1.0481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8660 Z= 0.121 Angle : 0.654 12.804 11731 Z= 0.314 Chirality : 0.041 0.198 1360 Planarity : 0.004 0.056 1502 Dihedral : 5.152 60.388 1168 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.97 % Allowed : 25.91 % Favored : 70.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.26), residues: 1071 helix: 0.93 (0.21), residues: 677 sheet: -0.79 (0.70), residues: 46 loop : -0.90 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 358 TYR 0.010 0.001 TYR B 135 PHE 0.018 0.001 PHE A 220 TRP 0.010 0.001 TRP A 189 HIS 0.004 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 8660) covalent geometry : angle 0.65390 / 0.31 (11731) hydrogen bonds : bond 0.03100 / 2.04 ( 399) hydrogen bonds : angle 3.90111 / 2.81 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 68 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.9150 (mtp) cc_final: 0.8724 (ptp) REVERT: A 206 ASP cc_start: 0.9078 (m-30) cc_final: 0.8732 (m-30) REVERT: A 224 GLU cc_start: 0.9084 (pp20) cc_final: 0.8855 (pm20) REVERT: A 307 MET cc_start: 0.9047 (mmm) cc_final: 0.8499 (tpp) REVERT: A 316 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8495 (pm20) REVERT: A 360 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8978 (mt) REVERT: A 361 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9136 (t) REVERT: A 364 GLU cc_start: 0.8841 (pm20) cc_final: 0.8344 (pm20) REVERT: A 486 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: B 97 GLU cc_start: 0.2925 (OUTLIER) cc_final: 0.2615 (pp20) REVERT: B 185 ASP cc_start: 0.9344 (m-30) cc_final: 0.8907 (m-30) REVERT: B 351 LEU cc_start: 0.9315 (mt) cc_final: 0.9100 (mt) REVERT: B 364 GLU cc_start: 0.8992 (pm20) cc_final: 0.8320 (pm20) REVERT: B 383 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8828 (mm-30) REVERT: B 408 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8751 (mppt) outliers start: 36 outliers final: 9 residues processed: 98 average time/residue: 0.4230 time to fit residues: 44.6893 Evaluate side-chains 82 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 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 393 LEU 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 15 THR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 262 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS B 534 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.058399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.042895 restraints weight = 35880.610| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 4.33 r_work: 0.2641 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 1.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 8660 Z= 0.204 Angle : 0.709 12.071 11731 Z= 0.347 Chirality : 0.043 0.189 1360 Planarity : 0.005 0.056 1502 Dihedral : 5.560 70.910 1168 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.63 % Allowed : 25.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.26), residues: 1071 helix: 0.95 (0.21), residues: 676 sheet: -0.38 (0.74), residues: 46 loop : -0.89 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 24 TYR 0.012 0.001 TYR B 369 PHE 0.021 0.002 PHE A 204 TRP 0.009 0.002 TRP A 410 HIS 0.004 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 ( 8660) covalent geometry : angle 0.70937 / 0.35 (11731) hydrogen bonds : bond 0.03931 / 2.53 ( 399) hydrogen bonds : angle 4.16432 / 2.96 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 64 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 114 MET cc_start: 0.9329 (ptp) cc_final: 0.9106 (ptt) REVERT: A 316 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8474 (pm20) REVERT: A 376 MET cc_start: 0.9346 (mpm) cc_final: 0.9074 (mpp) REVERT: A 486 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: A 533 MET cc_start: 0.8852 (ppp) cc_final: 0.8605 (ppp) REVERT: B 97 GLU cc_start: 0.3972 (OUTLIER) cc_final: 0.3708 (pp20) REVERT: B 114 MET cc_start: 0.9131 (mpp) cc_final: 0.8828 (pmm) REVERT: B 408 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8879 (mppt) REVERT: B 459 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9082 (tt) outliers start: 42 outliers final: 14 residues processed: 98 average time/residue: 0.4444 time to fit residues: 46.6816 Evaluate side-chains 75 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 408 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.060047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.044637 restraints weight = 36294.277| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 4.32 r_work: 0.2700 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 1.1555 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= 0.113 Angle : 0.674 13.636 11731 Z= 0.320 Chirality : 0.040 0.174 1360 Planarity : 0.005 0.055 1502 Dihedral : 5.184 61.712 1168 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.87 % Allowed : 27.89 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1071 helix: 1.19 (0.21), residues: 676 sheet: -0.37 (0.74), residues: 46 loop : -0.72 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 8 TYR 0.011 0.001 TYR B 135 PHE 0.021 0.001 PHE A 220 TRP 0.010 0.001 TRP A 189 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.11 ( 8660) covalent geometry : angle 0.67358 / 0.32 (11731) hydrogen bonds : bond 0.02910 / 1.92 ( 399) hydrogen bonds : angle 3.78888 / 2.74 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.9214 (mtp) cc_final: 0.8808 (ptp) REVERT: A 307 MET cc_start: 0.9129 (mmm) cc_final: 0.8472 (tpp) REVERT: A 316 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8486 (pm20) REVERT: A 376 MET cc_start: 0.9293 (mpm) cc_final: 0.9082 (mpm) REVERT: A 486 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: B 185 ASP cc_start: 0.9356 (m-30) cc_final: 0.8951 (m-30) REVERT: B 348 MET cc_start: 0.8918 (ptp) cc_final: 0.8544 (ptp) REVERT: B 351 LEU cc_start: 0.9518 (mt) cc_final: 0.9253 (mp) REVERT: B 459 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9015 (tt) outliers start: 17 outliers final: 5 residues processed: 74 average time/residue: 0.5320 time to fit residues: 42.3252 Evaluate side-chains 66 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain B residue 128 MET Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 430 VAL 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 58 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 0.0670 chunk 74 optimal weight: 0.0970 chunk 7 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 ASN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.060531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.044946 restraints weight = 35882.274| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 4.44 r_work: 0.2714 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 1.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8660 Z= 0.110 Angle : 0.678 12.177 11731 Z= 0.319 Chirality : 0.040 0.211 1360 Planarity : 0.004 0.055 1502 Dihedral : 4.849 57.140 1166 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.54 % Allowed : 28.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1071 helix: 1.24 (0.21), residues: 671 sheet: -0.21 (0.74), residues: 46 loop : -0.43 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 358 TYR 0.010 0.001 TYR B 135 PHE 0.017 0.001 PHE A 204 TRP 0.009 0.001 TRP A 189 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 ( 8660) covalent geometry : angle 0.67788 / 0.32 (11731) hydrogen bonds : bond 0.02800 / 1.82 ( 399) hydrogen bonds : angle 3.70670 / 2.70 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 MET cc_start: 0.9198 (mtp) cc_final: 0.8861 (ptm) REVERT: A 307 MET cc_start: 0.9129 (mmm) cc_final: 0.8448 (tpp) REVERT: A 316 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8484 (pm20) REVERT: A 376 MET cc_start: 0.9297 (mpm) cc_final: 0.9078 (mpm) REVERT: A 399 MET cc_start: 0.9419 (tpp) cc_final: 0.8946 (mmm) REVERT: A 533 MET cc_start: 0.8809 (ppp) cc_final: 0.8533 (ppp) REVERT: B 47 MET cc_start: 0.7237 (ppp) cc_final: 0.6630 (pp-130) REVERT: B 114 MET cc_start: 0.9396 (mtm) cc_final: 0.8997 (pmm) REVERT: B 185 ASP cc_start: 0.9366 (m-30) cc_final: 0.8971 (m-30) REVERT: B 348 MET cc_start: 0.8964 (ptp) cc_final: 0.8550 (ptp) REVERT: B 351 LEU cc_start: 0.9469 (mt) cc_final: 0.9222 (mp) REVERT: B 459 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9024 (tt) outliers start: 14 outliers final: 5 residues processed: 71 average time/residue: 0.4355 time to fit residues: 33.2671 Evaluate side-chains 67 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 459 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.058246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.043012 restraints weight = 35926.420| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 4.24 r_work: 0.2657 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 1.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8660 Z= 0.178 Angle : 0.704 13.021 11731 Z= 0.340 Chirality : 0.042 0.240 1360 Planarity : 0.004 0.054 1502 Dihedral : 5.145 67.307 1166 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.54 % Allowed : 28.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.26), residues: 1071 helix: 1.09 (0.21), residues: 683 sheet: -0.14 (0.73), residues: 46 loop : -0.37 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 242 TYR 0.010 0.001 TYR B 369 PHE 0.031 0.002 PHE A 220 TRP 0.012 0.002 TRP A 410 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 8660) covalent geometry : angle 0.70386 / 0.34 (11731) hydrogen bonds : bond 0.03496 / 2.27 ( 399) hydrogen bonds : angle 3.93112 / 2.83 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.8551 (ttm170) REVERT: A 307 MET cc_start: 0.9187 (mmm) cc_final: 0.8475 (tpp) REVERT: A 316 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8488 (pm20) REVERT: A 376 MET cc_start: 0.9332 (mpm) cc_final: 0.8976 (mpp) REVERT: A 533 MET cc_start: 0.8786 (ppp) cc_final: 0.8441 (ppp) REVERT: B 47 MET cc_start: 0.6995 (ppp) cc_final: 0.6305 (pp-130) REVERT: B 348 MET cc_start: 0.9015 (ptp) cc_final: 0.8639 (ptp) outliers start: 14 outliers final: 5 residues processed: 70 average time/residue: 0.5207 time to fit residues: 39.0797 Evaluate side-chains 65 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 15 THR Chi-restraints excluded: chain B residue 229 VAL 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 46 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 0.0970 chunk 61 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.059642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.044350 restraints weight = 36048.661| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 4.47 r_work: 0.2693 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 1.1970 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= 0.117 Angle : 0.700 15.429 11731 Z= 0.330 Chirality : 0.041 0.249 1360 Planarity : 0.004 0.054 1502 Dihedral : 5.082 66.587 1166 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.66 % Allowed : 29.33 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.27), residues: 1071 helix: 1.19 (0.21), residues: 684 sheet: -0.15 (0.72), residues: 46 loop : -0.42 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 358 TYR 0.010 0.001 TYR B 135 PHE 0.016 0.001 PHE A 204 TRP 0.010 0.001 TRP A 189 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 8660) covalent geometry : angle 0.70019 / 0.33 (11731) hydrogen bonds : bond 0.02978 / 1.94 ( 399) hydrogen bonds : angle 3.75997 / 2.73 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.9122 (mmm) cc_final: 0.8302 (mtm) REVERT: A 316 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8513 (mp0) REVERT: A 376 MET cc_start: 0.9324 (mpm) cc_final: 0.9091 (mpm) REVERT: A 533 MET cc_start: 0.8698 (ppp) cc_final: 0.8344 (ppp) REVERT: B 114 MET cc_start: 0.9454 (mtm) cc_final: 0.8951 (pmm) REVERT: B 185 ASP cc_start: 0.9384 (m-30) cc_final: 0.8986 (m-30) outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.5335 time to fit residues: 36.0592 Evaluate side-chains 62 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 GLU Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 430 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.059634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.044367 restraints weight = 35861.060| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 4.33 r_work: 0.2697 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 1.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8660 Z= 0.120 Angle : 0.715 15.526 11731 Z= 0.334 Chirality : 0.041 0.248 1360 Planarity : 0.004 0.054 1502 Dihedral : 5.088 69.649 1166 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.77 % Allowed : 29.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 1071 helix: 1.25 (0.21), residues: 680 sheet: -0.13 (0.72), residues: 46 loop : -0.28 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 242 TYR 0.010 0.001 TYR B 135 PHE 0.016 0.001 PHE A 204 TRP 0.009 0.001 TRP A 189 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 ( 8660) covalent geometry : angle 0.71533 / 0.33 (11731) hydrogen bonds : bond 0.02949 / 1.91 ( 399) hydrogen bonds : angle 3.72908 / 2.71 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2698.21 seconds wall clock time: 46 minutes 41.32 seconds (2801.32 seconds total)