Starting phenix.real_space_refine on Fri Sep 11 15:35:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6tqe_10549/09_2026/6tqe_10549.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tqe_10549/09_2026/6tqe_10549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tqe_10549/09_2026/6tqe_10549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tqe_10549/09_2026/6tqe_10549.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tqe_10549/09_2026/6tqe_10549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tqe_10549/09_2026/6tqe_10549.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6tqe_10549/09_2026/6tqe_10549.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6tqe_10549/09_2026/6tqe_10549.cif" } resolution = 4.3 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= 1.000 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 24 5.16 5 C 6478 2.51 5 N 1766 2.21 5 O 1800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10076 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5006 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 603} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 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} Restraints were copied for chains: B Time building chain proxies: 4.79, per 1000 atoms: 0.48 Number of scatterers: 10076 At special positions: 0 Unit cell: (82.6537, 82.6537, 147.413, 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 24 16.00 P 6 15.00 Mg 2 11.99 O 1800 8.00 N 1766 7.00 C 6478 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: 0.84 Conformation dependent library (CDL) restraints added in 313.2 milliseconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2348 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 6 sheets defined 51.7% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 20 through 44 removed outlier: 4.371A pdb=" N THR A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.679A pdb=" N TRP A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A 55 " --> pdb=" O PHE A 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 55' Processing helix chain 'A' and resid 61 through 65 removed outlier: 3.692A pdb=" N SER A 64 " --> pdb=" O GLY A 61 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 65' Processing helix chain 'A' and resid 66 through 109 removed outlier: 4.020A pdb=" N VAL A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU A 74 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET A 95 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A 100 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.972A pdb=" N PHE A 121 " --> pdb=" O GLY A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 3.812A pdb=" N PHE A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 140 removed outlier: 3.816A pdb=" N VAL A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 139 " --> pdb=" O HIS A 135 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 150 through 166 removed outlier: 4.175A pdb=" N TRP A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.567A pdb=" N LEU A 175 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 177 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.615A pdb=" N GLN A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 209 through 213 removed outlier: 3.624A pdb=" N SER A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 213 " --> pdb=" O THR A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 213' Processing helix chain 'A' and resid 215 through 227 removed outlier: 3.641A pdb=" N VAL A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N VAL A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.677A pdb=" N TRP A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 256 " --> pdb=" O TRP A 252 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.571A pdb=" N LYS A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 removed outlier: 3.865A pdb=" N VAL A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 304 removed outlier: 3.826A pdb=" N VAL A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 removed outlier: 3.605A pdb=" N LEU A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Proline residue: A 319 - end of helix Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.506A pdb=" N GLN A 353 " --> pdb=" O PRO A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.625A pdb=" N PHE A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 359 " --> pdb=" O PRO A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 354 through 359' Processing helix chain 'A' and resid 364 through 382 removed outlier: 4.095A pdb=" N GLY A 368 " --> pdb=" O PHE A 364 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 388 through 396 removed outlier: 4.159A pdb=" N PHE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 406 removed outlier: 4.303A pdb=" N LEU A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.579A pdb=" N LEU A 525 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 531 removed outlier: 3.666A pdb=" N THR A 530 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 526 through 531' Processing helix chain 'A' and resid 532 through 533 No H-bonds generated for 'chain 'A' and resid 532 through 533' Processing helix chain 'A' and resid 534 through 538 removed outlier: 3.831A pdb=" N LEU A 537 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 566 removed outlier: 3.549A pdb=" N LEU A 565 " --> pdb=" O PHE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 597 Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.778A pdb=" N HIS A 615 " --> pdb=" O GLU A 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 44 removed outlier: 4.371A pdb=" N THR B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N CYS B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 55 removed outlier: 3.679A pdb=" N TRP B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 55 " --> pdb=" O PHE B 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 55' Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.692A pdb=" N SER B 64 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 65' Processing helix chain 'B' and resid 66 through 109 removed outlier: 4.020A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU B 74 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 122 removed outlier: 3.971A pdb=" N PHE B 121 " --> pdb=" O GLY B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.813A pdb=" N PHE B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 140 removed outlier: 3.815A pdb=" N VAL B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 139 " --> pdb=" O HIS B 135 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 Processing helix chain 'B' and resid 150 through 166 removed outlier: 4.176A pdb=" N TRP B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS B 159 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 163 " --> pdb=" O HIS B 159 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.569A pdb=" N LEU B 175 " --> pdb=" O TYR B 172 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 177 " --> pdb=" O ASP B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.614A pdb=" N GLN B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 209 through 213 removed outlier: 3.623A pdb=" N SER B 212 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 213 " --> pdb=" O THR B 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 209 through 213' Processing helix chain 'B' and resid 215 through 227 removed outlier: 3.640A pdb=" N VAL B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN B 220 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER B 221 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N VAL B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.678A pdb=" N TRP B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 256 " --> pdb=" O TRP B 252 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.572A pdb=" N LYS B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.866A pdb=" N VAL B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 304 removed outlier: 3.826A pdb=" N VAL B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 323 removed outlier: 3.605A pdb=" N LEU B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 314 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Proline residue: B 319 - end of helix Processing helix chain 'B' and resid 348 through 353 removed outlier: 3.506A pdb=" N GLN B 353 " --> pdb=" O PRO B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 359 removed outlier: 3.625A pdb=" N PHE B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 354 through 359' Processing helix chain 'B' and resid 364 through 382 removed outlier: 4.096A pdb=" N GLY B 368 " --> pdb=" O PHE B 364 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP B 379 " --> pdb=" O GLY B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 388 through 396 removed outlier: 4.159A pdb=" N PHE B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 406 removed outlier: 4.301A pdb=" N LEU B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 473 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.579A pdb=" N LEU B 525 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.666A pdb=" N THR B 530 " --> pdb=" O ARG B 526 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 526 through 531' Processing helix chain 'B' and resid 532 through 533 No H-bonds generated for 'chain 'B' and resid 532 through 533' Processing helix chain 'B' and resid 534 through 538 removed outlier: 3.829A pdb=" N LEU B 537 " --> pdb=" O LEU B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 removed outlier: 3.548A pdb=" N LEU B 565 " --> pdb=" O PHE B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 597 Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.779A pdb=" N HIS B 615 " --> pdb=" O GLU B 612 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 418 through 421 removed outlier: 6.598A pdb=" N LEU A 418 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ARG A 486 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ARG A 420 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 434 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 442 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 429 Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 575 removed outlier: 3.605A pdb=" N VAL A 605 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 456 " --> pdb=" O SER A 604 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER A 455 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 619 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU A 621 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR A 459 " --> pdb=" O LEU A 621 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 418 through 421 removed outlier: 6.597A pdb=" N LEU B 418 " --> pdb=" O LEU B 484 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ARG B 486 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ARG B 420 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL B 434 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 442 " --> pdb=" O VAL B 434 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 427 through 429 Processing sheet with id=AA6, first strand: chain 'B' and resid 573 through 575 removed outlier: 3.605A pdb=" N VAL B 605 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 456 " --> pdb=" O SER B 604 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N SER B 455 " --> pdb=" O ASN B 617 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU B 619 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 457 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU B 621 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR B 459 " --> pdb=" O LEU B 621 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 708 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: 1.37 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3257 1.34 - 1.46: 2248 1.46 - 1.57: 4771 1.57 - 1.69: 10 1.69 - 1.81: 40 Bond restraints: 10326 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.18e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.01e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.94e+01 bond pdb=" C5 ATP B 701 " pdb=" C6 ATP B 701 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.93e+01 bond pdb=" C5 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.27e+01 ... (remaining 10321 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.65: 14006 4.65 - 9.31: 72 9.31 - 13.96: 6 13.96 - 18.62: 0 18.62 - 23.27: 4 Bond angle restraints: 14088 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 116.60 23.27 1.00e+00 1.00e+00 5.42e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 116.62 23.25 1.00e+00 1.00e+00 5.41e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 115.99 20.84 1.00e+00 1.00e+00 4.34e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 116.02 20.81 1.00e+00 1.00e+00 4.33e+02 angle pdb=" C5 ATP B 701 " pdb=" C4 ATP B 701 " pdb=" N3 ATP B 701 " ideal model delta sigma weight residual 126.80 118.05 8.75 1.00e+00 1.00e+00 7.66e+01 ... (remaining 14083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 5339 17.27 - 34.55: 545 34.55 - 51.82: 116 51.82 - 69.10: 18 69.10 - 86.37: 6 Dihedral angle restraints: 6024 sinusoidal: 2374 harmonic: 3650 Sorted by residual: dihedral pdb=" CA SER B 13 " pdb=" C SER B 13 " pdb=" N ARG B 14 " pdb=" CA ARG B 14 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER A 13 " pdb=" C SER A 13 " pdb=" N ARG A 14 " pdb=" CA ARG A 14 " ideal model delta harmonic sigma weight residual -180.00 -153.72 -26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PHE A 358 " pdb=" C PHE A 358 " pdb=" N ALA A 359 " pdb=" CA ALA A 359 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 6021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1085 0.054 - 0.108: 417 0.108 - 0.162: 74 0.162 - 0.216: 12 0.216 - 0.270: 4 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CA THR B 318 " pdb=" N THR B 318 " pdb=" C THR B 318 " pdb=" CB THR B 318 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA THR A 318 " pdb=" N THR A 318 " pdb=" C THR A 318 " pdb=" CB THR A 318 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ASN A 183 " pdb=" N ASN A 183 " pdb=" C ASN A 183 " pdb=" CB ASN A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1589 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 436 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 437 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 437 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 437 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 436 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO B 437 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 437 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 437 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 444 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO B 445 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 445 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 445 " 0.026 5.00e-02 4.00e+02 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 153 2.64 - 3.21: 8506 3.21 - 3.77: 13929 3.77 - 4.34: 18172 4.34 - 4.90: 30145 Nonbonded interactions: 70905 Sorted by model distance: nonbonded pdb=" O2G ATP B 701 " pdb="MG MG B 702 " model vdw 2.077 2.170 nonbonded pdb=" O2G ATP A 701 " pdb="MG MG A 702 " model vdw 2.079 2.170 nonbonded pdb=" O2B ATP A 701 " pdb="MG MG A 702 " model vdw 2.109 2.170 nonbonded pdb=" O2B ATP B 701 " pdb="MG MG B 702 " model vdw 2.109 2.170 nonbonded pdb=" OG1 THR A 467 " pdb="MG MG A 702 " model vdw 2.125 2.170 ... (remaining 70900 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' 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 group one per residue 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.520 Find NCS groups from input model: 0.080 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 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 : 0.007 0.082 10326 Z= 0.357 Angle : 1.043 23.271 14088 Z= 0.664 Chirality : 0.057 0.270 1592 Planarity : 0.006 0.051 1786 Dihedral : 14.588 86.369 3676 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.76 % Allowed : 10.68 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.13 (0.15), residues: 1264 helix: -4.57 (0.09), residues: 654 sheet: -2.07 (0.42), residues: 120 loop : -3.59 (0.21), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.014 0.002 TYR B 327 PHE 0.031 0.002 PHE A 88 TRP 0.014 0.002 TRP B 12 HIS 0.003 0.001 HIS B 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.36 (10326) covalent geometry : angle 1.04315 / 0.66 (14088) hydrogen bonds : bond 0.26467 / 17.04 ( 248) hydrogen bonds : angle 8.67954 / 5.95 ( 708) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8031 (pp) REVERT: A 131 MET cc_start: 0.8589 (mtp) cc_final: 0.8258 (ttm) REVERT: B 5 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8097 (pp) REVERT: B 14 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.7014 (ttp80) outliers start: 8 outliers final: 4 residues processed: 72 average time/residue: 0.1004 time to fit residues: 10.7815 Evaluate side-chains 58 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 338 ASN A 618 GLN B 163 GLN B 204 ASN B 338 ASN B 618 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.076669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.064138 restraints weight = 24837.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.065140 restraints weight = 16709.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.065394 restraints weight = 11621.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.065657 restraints weight = 12219.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.065750 restraints weight = 10280.678| |-----------------------------------------------------------------------------| r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10326 Z= 0.126 Angle : 0.605 7.760 14088 Z= 0.303 Chirality : 0.043 0.169 1592 Planarity : 0.004 0.059 1786 Dihedral : 5.290 36.254 1412 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.28 % Allowed : 3.02 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.03 (0.18), residues: 1264 helix: -3.69 (0.13), residues: 642 sheet: -1.61 (0.43), residues: 120 loop : -3.07 (0.24), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 613 TYR 0.010 0.001 TYR A 257 PHE 0.010 0.001 PHE A 573 TRP 0.007 0.001 TRP B 274 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10326) covalent geometry : angle 0.60545 / 0.30 (14088) hydrogen bonds : bond 0.05066 / 3.19 ( 248) hydrogen bonds : angle 5.18603 / 3.55 ( 708) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.383 Fit side-chains REVERT: A 131 MET cc_start: 0.8506 (mtp) cc_final: 0.8252 (ttm) REVERT: B 14 ARG cc_start: 0.7303 (ttp-110) cc_final: 0.7009 (ttp80) outliers start: 3 outliers final: 1 residues processed: 87 average time/residue: 0.0797 time to fit residues: 10.8811 Evaluate side-chains 57 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 80 optimal weight: 0.0040 chunk 74 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN A 618 GLN B 204 ASN B 353 GLN B 618 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.077257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.065024 restraints weight = 24317.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.065915 restraints weight = 17254.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.066646 restraints weight = 13449.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.067178 restraints weight = 11149.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.067424 restraints weight = 9833.230| |-----------------------------------------------------------------------------| r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10326 Z= 0.111 Angle : 0.560 7.435 14088 Z= 0.279 Chirality : 0.042 0.165 1592 Planarity : 0.004 0.056 1786 Dihedral : 4.763 38.285 1412 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.28 % Allowed : 3.12 % Favored : 96.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.35 (0.20), residues: 1264 helix: -3.05 (0.16), residues: 652 sheet: -0.81 (0.49), residues: 106 loop : -2.94 (0.24), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 613 TYR 0.010 0.001 TYR B 257 PHE 0.016 0.001 PHE A 103 TRP 0.007 0.001 TRP B 274 HIS 0.001 0.000 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (10326) covalent geometry : angle 0.56022 / 0.28 (14088) hydrogen bonds : bond 0.04454 / 2.81 ( 248) hydrogen bonds : angle 4.59644 / 3.17 ( 708) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 0.386 Fit side-chains REVERT: A 131 MET cc_start: 0.8510 (mtp) cc_final: 0.8309 (ttm) outliers start: 3 outliers final: 0 residues processed: 87 average time/residue: 0.0850 time to fit residues: 11.4253 Evaluate side-chains 55 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 121 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN A 515 ASN A 618 GLN B 204 ASN B 353 GLN B 515 ASN B 618 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.073665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2572 r_free = 0.2572 target = 0.061364 restraints weight = 25460.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.062259 restraints weight = 18308.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.062845 restraints weight = 14414.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.063256 restraints weight = 12171.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.063594 restraints weight = 10815.498| |-----------------------------------------------------------------------------| r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 10326 Z= 0.235 Angle : 0.687 8.447 14088 Z= 0.340 Chirality : 0.047 0.174 1592 Planarity : 0.004 0.055 1786 Dihedral : 5.314 38.070 1412 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.28 % Allowed : 3.97 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.21 (0.20), residues: 1264 helix: -2.90 (0.16), residues: 668 sheet: -1.24 (0.47), residues: 120 loop : -2.80 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 115 TYR 0.011 0.002 TYR B 513 PHE 0.022 0.002 PHE B 88 TRP 0.009 0.001 TRP B 274 HIS 0.002 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.23 (10326) covalent geometry : angle 0.68652 / 0.34 (14088) hydrogen bonds : bond 0.05592 / 3.53 ( 248) hydrogen bonds : angle 5.08334 / 3.49 ( 708) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 131 MET cc_start: 0.8486 (mtp) cc_final: 0.8236 (ttm) REVERT: B 303 TYR cc_start: 0.8736 (m-10) cc_final: 0.8521 (m-80) outliers start: 3 outliers final: 0 residues processed: 66 average time/residue: 0.0806 time to fit residues: 8.3765 Evaluate side-chains 46 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.077489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.065282 restraints weight = 24518.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.066106 restraints weight = 17468.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.066772 restraints weight = 13754.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.067279 restraints weight = 11484.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.067394 restraints weight = 10093.684| |-----------------------------------------------------------------------------| r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10326 Z= 0.102 Angle : 0.550 7.274 14088 Z= 0.272 Chirality : 0.042 0.163 1592 Planarity : 0.004 0.054 1786 Dihedral : 4.652 39.464 1412 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.19 % Allowed : 2.46 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.69 (0.21), residues: 1264 helix: -2.48 (0.17), residues: 660 sheet: -0.55 (0.51), residues: 108 loop : -2.65 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 115 TYR 0.008 0.001 TYR B 257 PHE 0.010 0.001 PHE B 573 TRP 0.008 0.001 TRP A 274 HIS 0.001 0.000 HIS B 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (10326) covalent geometry : angle 0.55008 / 0.27 (14088) hydrogen bonds : bond 0.04288 / 2.72 ( 248) hydrogen bonds : angle 4.36640 / 3.01 ( 708) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.344 Fit side-chains REVERT: A 131 MET cc_start: 0.8438 (mtp) cc_final: 0.8183 (ttm) REVERT: B 303 TYR cc_start: 0.8655 (m-10) cc_final: 0.8437 (m-80) outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 0.0800 time to fit residues: 10.2166 Evaluate side-chains 50 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 GLN B 204 ASN B 618 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.075610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.063358 restraints weight = 25045.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.064159 restraints weight = 18008.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.064820 restraints weight = 14213.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.065309 restraints weight = 11897.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.065609 restraints weight = 10461.198| |-----------------------------------------------------------------------------| r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10326 Z= 0.144 Angle : 0.595 8.092 14088 Z= 0.290 Chirality : 0.044 0.166 1592 Planarity : 0.004 0.057 1786 Dihedral : 4.694 40.534 1412 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.09 % Allowed : 1.98 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.50 (0.22), residues: 1264 helix: -2.28 (0.18), residues: 652 sheet: -0.79 (0.49), residues: 120 loop : -2.60 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 115 TYR 0.008 0.001 TYR B 513 PHE 0.014 0.001 PHE B 103 TRP 0.007 0.001 TRP A 274 HIS 0.001 0.000 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (10326) covalent geometry : angle 0.59529 / 0.29 (14088) hydrogen bonds : bond 0.04593 / 2.91 ( 248) hydrogen bonds : angle 4.47042 / 3.07 ( 708) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.416 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.0663 time to fit residues: 7.8656 Evaluate side-chains 48 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 86 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN B 204 ASN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.076018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.063817 restraints weight = 24698.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.064724 restraints weight = 17680.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.065384 restraints weight = 13824.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.065725 restraints weight = 11554.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.065925 restraints weight = 10380.811| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10326 Z= 0.136 Angle : 0.591 7.519 14088 Z= 0.287 Chirality : 0.044 0.167 1592 Planarity : 0.004 0.057 1786 Dihedral : 4.645 42.524 1412 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.28 % Allowed : 1.42 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.32 (0.22), residues: 1264 helix: -2.13 (0.18), residues: 652 sheet: -0.73 (0.49), residues: 122 loop : -2.52 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 115 TYR 0.006 0.001 TYR B 388 PHE 0.016 0.001 PHE A 103 TRP 0.008 0.001 TRP A 274 HIS 0.001 0.000 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (10326) covalent geometry : angle 0.59124 / 0.29 (14088) hydrogen bonds : bond 0.04527 / 2.86 ( 248) hydrogen bonds : angle 4.41418 / 3.04 ( 708) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.354 Fit side-chains REVERT: B 129 SER cc_start: 0.8964 (m) cc_final: 0.8196 (p) outliers start: 3 outliers final: 0 residues processed: 75 average time/residue: 0.0678 time to fit residues: 8.7470 Evaluate side-chains 53 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 60 optimal weight: 0.0040 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 618 GLN B 618 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.078788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.066344 restraints weight = 23857.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.067370 restraints weight = 16529.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.068088 restraints weight = 12615.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.068549 restraints weight = 10383.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.068919 restraints weight = 9116.107| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10326 Z= 0.092 Angle : 0.539 7.304 14088 Z= 0.259 Chirality : 0.041 0.159 1592 Planarity : 0.003 0.060 1786 Dihedral : 4.234 40.485 1412 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.19 % Allowed : 0.09 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.07 (0.22), residues: 1264 helix: -1.87 (0.19), residues: 652 sheet: -0.24 (0.53), residues: 108 loop : -2.53 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 115 TYR 0.014 0.001 TYR A 257 PHE 0.008 0.001 PHE A 573 TRP 0.008 0.001 TRP A 47 HIS 0.001 0.000 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 (10326) covalent geometry : angle 0.53899 / 0.26 (14088) hydrogen bonds : bond 0.03723 / 2.34 ( 248) hydrogen bonds : angle 4.02103 / 2.77 ( 708) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.375 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 84 average time/residue: 0.0665 time to fit residues: 9.5509 Evaluate side-chains 55 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN A 618 GLN B 353 GLN B 618 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.073804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.061634 restraints weight = 25198.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.062423 restraints weight = 18375.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.063096 restraints weight = 14612.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.063462 restraints weight = 12328.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.063781 restraints weight = 11001.838| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10326 Z= 0.230 Angle : 0.690 8.401 14088 Z= 0.337 Chirality : 0.048 0.173 1592 Planarity : 0.004 0.062 1786 Dihedral : 4.985 45.776 1412 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.19 % Allowed : 1.42 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.32 (0.22), residues: 1264 helix: -2.10 (0.18), residues: 668 sheet: -0.81 (0.49), residues: 120 loop : -2.52 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 115 TYR 0.022 0.002 TYR A 257 PHE 0.014 0.002 PHE A 195 TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (10326) covalent geometry : angle 0.69033 / 0.34 (14088) hydrogen bonds : bond 0.05449 / 3.41 ( 248) hydrogen bonds : angle 4.90155 / 3.36 ( 708) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.275 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.0537 time to fit residues: 6.1642 Evaluate side-chains 46 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.074935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.062907 restraints weight = 24686.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.063773 restraints weight = 17790.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.064283 restraints weight = 14003.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.064767 restraints weight = 11952.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.065116 restraints weight = 10691.708| |-----------------------------------------------------------------------------| r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10326 Z= 0.171 Angle : 0.631 7.531 14088 Z= 0.308 Chirality : 0.046 0.168 1592 Planarity : 0.004 0.062 1786 Dihedral : 4.936 47.727 1412 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.18 (0.22), residues: 1264 helix: -1.98 (0.18), residues: 668 sheet: -0.86 (0.49), residues: 122 loop : -2.44 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 115 TYR 0.018 0.001 TYR A 257 PHE 0.029 0.002 PHE B 88 TRP 0.008 0.001 TRP A 274 HIS 0.001 0.000 HIS B 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (10326) covalent geometry : angle 0.63117 / 0.31 (14088) hydrogen bonds : bond 0.05041 / 3.17 ( 248) hydrogen bonds : angle 4.68476 / 3.25 ( 708) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.377 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.0640 time to fit residues: 7.6040 Evaluate side-chains 47 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 47 optimal weight: 0.0270 chunk 124 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN A 618 GLN B 353 GLN B 618 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.076538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.064414 restraints weight = 24486.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.065329 restraints weight = 17562.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.065892 restraints weight = 13706.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.066377 restraints weight = 11581.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.066571 restraints weight = 10287.558| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10326 Z= 0.116 Angle : 0.573 7.715 14088 Z= 0.278 Chirality : 0.043 0.163 1592 Planarity : 0.004 0.063 1786 Dihedral : 4.576 46.127 1412 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.38 % Allowed : 0.09 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.89 (0.23), residues: 1264 helix: -1.70 (0.19), residues: 666 sheet: -0.71 (0.50), residues: 122 loop : -2.37 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 115 TYR 0.017 0.001 TYR B 257 PHE 0.027 0.001 PHE A 88 TRP 0.007 0.001 TRP A 274 HIS 0.001 0.000 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10326) covalent geometry : angle 0.57345 / 0.28 (14088) hydrogen bonds : bond 0.04385 / 2.75 ( 248) hydrogen bonds : angle 4.33568 / 3.02 ( 708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1305.87 seconds wall clock time: 23 minutes 19.45 seconds (1399.45 seconds total)