Starting phenix.real_space_refine on Fri Oct 23 19:36:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25mi_80202/10_2026/25mi_80202.cif Found real_map, /net/cci-nas-00/data/ceres_data/25mi_80202/10_2026/25mi_80202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25mi_80202/10_2026/25mi_80202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25mi_80202/10_2026/25mi_80202.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25mi_80202/10_2026/25mi_80202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25mi_80202/10_2026/25mi_80202.map" } resolution = 3.28 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= 0.003 sd= 0.052 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 K 2 8.98 5 P 4 5.49 5 S 60 5.16 5 C 6946 2.51 5 N 1698 2.21 5 O 1890 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10600 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5266 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Chain: "B" Number of atoms: 5266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 664, 5266 Classifications: {'peptide': 664} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 643} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' K': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.80, per 1000 atoms: 0.26 Number of scatterers: 10600 At special positions: 0 Unit cell: (122.831, 91.308, 109.787, 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) K 2 19.00 S 60 16.00 P 4 15.00 O 1890 8.00 N 1698 7.00 C 6946 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 313.2 milliseconds 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2480 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 2 sheets defined 45.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 56 through 64 removed outlier: 3.656A pdb=" N SER A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 75 through 79 removed outlier: 3.806A pdb=" N LEU A 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 102 Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.735A pdb=" N ALA A 121 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 removed outlier: 3.702A pdb=" N VAL A 153 " --> pdb=" O PRO A 150 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU A 154 " --> pdb=" O GLU A 151 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 155 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 178 removed outlier: 3.609A pdb=" N LYS A 176 " --> pdb=" O MET A 172 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 200 removed outlier: 3.550A pdb=" N PHE A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.751A pdb=" N LEU A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Proline residue: A 206 - end of helix Processing helix chain 'A' and resid 212 through 213 No H-bonds generated for 'chain 'A' and resid 212 through 213' Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.842A pdb=" N ILE A 217 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LYS A 218 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N SER A 219 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 269 removed outlier: 3.764A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.629A pdb=" N LEU A 278 " --> pdb=" O ILE A 275 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 280 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU A 281 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 4.253A pdb=" N ILE A 287 " --> pdb=" O PRO A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 335 through 343 removed outlier: 4.419A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 removed outlier: 3.599A pdb=" N TYR A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.713A pdb=" N ASP A 362 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 382 removed outlier: 3.710A pdb=" N VAL A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL A 375 " --> pdb=" O PRO A 371 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A 380 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 429 through 434 Processing helix chain 'A' and resid 445 through 453 removed outlier: 4.051A pdb=" N ALA A 449 " --> pdb=" O LYS A 445 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 472 removed outlier: 3.565A pdb=" N VAL A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 498 removed outlier: 3.675A pdb=" N PHE A 483 " --> pdb=" O TRP A 479 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 491 " --> pdb=" O PHE A 487 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TYR A 494 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.587A pdb=" N GLY A 505 " --> pdb=" O LYS A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 Processing helix chain 'A' and resid 519 through 524 removed outlier: 3.980A pdb=" N TRP A 523 " --> pdb=" O MET A 519 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 519 through 524' Processing helix chain 'A' and resid 527 through 537 removed outlier: 3.987A pdb=" N TYR A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.744A pdb=" N ILE A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 653 removed outlier: 3.849A pdb=" N GLU A 639 " --> pdb=" O PRO A 635 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ARG A 640 " --> pdb=" O ASP A 636 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 645 " --> pdb=" O HIS A 641 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 751 Processing helix chain 'A' and resid 754 through 762 removed outlier: 3.708A pdb=" N LYS A 760 " --> pdb=" O ASN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 769 removed outlier: 3.580A pdb=" N LEU A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 774 No H-bonds generated for 'chain 'A' and resid 772 through 774' Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 64 through 67 removed outlier: 3.772A pdb=" N GLY B 67 " --> pdb=" O GLN B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.757A pdb=" N THR B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHE B 85 " --> pdb=" O TYR B 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 80 through 85' Processing helix chain 'B' and resid 100 through 105 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 149 through 155 removed outlier: 3.782A pdb=" N VAL B 153 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU B 154 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 removed outlier: 3.936A pdb=" N MET B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 removed outlier: 3.565A pdb=" N VAL B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.793A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 217 removed outlier: 3.984A pdb=" N GLY B 216 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 217 " --> pdb=" O VAL B 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 213 through 217' Processing helix chain 'B' and resid 226 through 234 removed outlier: 3.560A pdb=" N VAL B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE B 232 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 269 removed outlier: 3.695A pdb=" N LEU B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.550A pdb=" N ALA B 280 " --> pdb=" O VAL B 277 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 281 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 294 through 300 Processing helix chain 'B' and resid 303 through 308 removed outlier: 3.785A pdb=" N CYS B 307 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 343 removed outlier: 3.590A pdb=" N THR B 340 " --> pdb=" O PRO B 336 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 364 removed outlier: 3.730A pdb=" N ILE B 364 " --> pdb=" O PHE B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 4.071A pdb=" N VAL B 375 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.984A pdb=" N ALA B 449 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 472 removed outlier: 4.018A pdb=" N THR B 461 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR B 462 " --> pdb=" O MET B 458 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 487 removed outlier: 3.667A pdb=" N ILE B 480 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 485 " --> pdb=" O ALA B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 499 removed outlier: 3.701A pdb=" N SER B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 537 removed outlier: 4.533A pdb=" N VAL B 528 " --> pdb=" O GLN B 524 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR B 531 " --> pdb=" O ARG B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.559A pdb=" N ILE B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 653 removed outlier: 3.779A pdb=" N GLU B 639 " --> pdb=" O PRO B 635 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ARG B 640 " --> pdb=" O ASP B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 727 removed outlier: 3.760A pdb=" N LYS B 726 " --> pdb=" O LYS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 753 Processing helix chain 'B' and resid 754 through 759 removed outlier: 3.581A pdb=" N LEU B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 769 removed outlier: 3.946A pdb=" N LEU B 769 " --> pdb=" O GLY B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 774 No H-bonds generated for 'chain 'B' and resid 772 through 774' Processing sheet with id=AA1, first strand: chain 'A' and resid 410 through 411 Processing sheet with id=AA2, first strand: chain 'A' and resid 608 through 611 removed outlier: 4.374A pdb=" N SER A 583 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL A 556 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HIS A 585 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY A 558 " --> pdb=" O HIS A 585 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLY A 733 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N LEU A 777 " --> pdb=" O MET A 728 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR A 730 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL A 779 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET A 732 " --> pdb=" O VAL A 779 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N MET A 781 " --> pdb=" O MET A 732 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU A 734 " --> pdb=" O MET A 781 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N TYR A 783 " --> pdb=" O GLU A 734 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLU A 736 " --> pdb=" O TYR A 783 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU A 776 " --> pdb=" O GLY B 780 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU B 776 " --> pdb=" O GLY A 780 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLY B 733 " --> pdb=" O TYR B 563 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE B 588 " --> pdb=" O PHE B 620 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N CYS B 622 " --> pdb=" O PHE B 588 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU B 590 " --> pdb=" O CYS B 622 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL B 624 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER B 592 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N TYR B 626 " --> pdb=" O SER B 592 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS B 594 " --> pdb=" O TYR B 626 " (cutoff:3.500A) 283 hydrogen bonds defined for protein. 783 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: 1.33 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: 1866 1.33 - 1.45: 2882 1.45 - 1.58: 5978 1.58 - 1.70: 6 1.70 - 1.82: 104 Bond restraints: 10836 Sorted by residual: bond pdb=" CG HIS B 759 " pdb=" CD2 HIS B 759 " ideal model delta sigma weight residual 1.354 1.323 0.031 1.10e-02 8.26e+03 8.09e+00 bond pdb=" N ARG A 527 " pdb=" CA ARG A 527 " ideal model delta sigma weight residual 1.456 1.491 -0.036 1.36e-02 5.41e+03 6.97e+00 bond pdb=" N HIS A 759 " pdb=" CA HIS A 759 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.31e-02 5.83e+03 6.64e+00 bond pdb=" C ARG B 527 " pdb=" O ARG B 527 " ideal model delta sigma weight residual 1.236 1.204 0.033 1.32e-02 5.74e+03 6.07e+00 bond pdb=" N HIS B 759 " pdb=" CA HIS B 759 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.32e-02 5.74e+03 5.55e+00 ... (remaining 10831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 14308 2.74 - 5.48: 357 5.48 - 8.22: 42 8.22 - 10.96: 6 10.96 - 13.69: 5 Bond angle restraints: 14718 Sorted by residual: angle pdb=" N ARG A 527 " pdb=" CA ARG A 527 " pdb=" C ARG A 527 " ideal model delta sigma weight residual 114.04 105.11 8.93 1.24e+00 6.50e-01 5.19e+01 angle pdb=" N SER B 209 " pdb=" CA SER B 209 " pdb=" C SER B 209 " ideal model delta sigma weight residual 114.75 105.75 9.00 1.26e+00 6.30e-01 5.10e+01 angle pdb=" N ILE B 381 " pdb=" CA ILE B 381 " pdb=" C ILE B 381 " ideal model delta sigma weight residual 112.17 105.54 6.63 9.50e-01 1.11e+00 4.87e+01 angle pdb=" N VAL A 514 " pdb=" CA VAL A 514 " pdb=" C VAL A 514 " ideal model delta sigma weight residual 113.71 107.20 6.51 9.50e-01 1.11e+00 4.69e+01 angle pdb=" N SER A 380 " pdb=" CA SER A 380 " pdb=" C SER A 380 " ideal model delta sigma weight residual 114.75 106.63 8.12 1.26e+00 6.30e-01 4.16e+01 ... (remaining 14713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.38: 5738 26.38 - 52.76: 539 52.76 - 79.14: 54 79.14 - 105.51: 6 105.51 - 131.89: 1 Dihedral angle restraints: 6338 sinusoidal: 2462 harmonic: 3876 Sorted by residual: dihedral pdb=" CD ARG B 527 " pdb=" NE ARG B 527 " pdb=" CZ ARG B 527 " pdb=" NH1 ARG B 527 " ideal model delta sinusoidal sigma weight residual 0.00 -74.20 74.20 1 1.00e+01 1.00e-02 6.99e+01 dihedral pdb=" CD ARG A 527 " pdb=" NE ARG A 527 " pdb=" CZ ARG A 527 " pdb=" NH1 ARG A 527 " ideal model delta sinusoidal sigma weight residual 0.00 57.98 -57.98 1 1.00e+01 1.00e-02 4.51e+01 dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 71.89 -131.89 1 2.00e+01 2.50e-03 4.00e+01 ... (remaining 6335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1178 0.045 - 0.089: 420 0.089 - 0.134: 117 0.134 - 0.179: 9 0.179 - 0.224: 2 Chirality restraints: 1726 Sorted by residual: chirality pdb=" CA VAL A 526 " pdb=" N VAL A 526 " pdb=" C VAL A 526 " pdb=" CB VAL A 526 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR A 717 " pdb=" CA THR A 717 " pdb=" OG1 THR A 717 " pdb=" CG2 THR A 717 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.75e-01 chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.65e-01 ... (remaining 1723 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 527 " 1.058 9.50e-02 1.11e+02 4.74e-01 1.36e+02 pdb=" NE ARG B 527 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 527 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 527 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 527 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 527 " -0.913 9.50e-02 1.11e+02 4.09e-01 1.02e+02 pdb=" NE ARG A 527 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 527 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 527 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 527 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 76 " 0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO B 77 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO B 77 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 77 " 0.048 5.00e-02 4.00e+02 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 3863 2.85 - 3.42: 9993 3.42 - 4.00: 18263 4.00 - 4.57: 26653 4.57 - 5.14: 40995 Nonbonded interactions: 99767 Sorted by model distance: nonbonded pdb=" O HIS B 759 " pdb=" ND1 HIS B 759 " model vdw 2.280 3.120 nonbonded pdb=" NE2 HIS B 759 " pdb=" O1B ADP B 901 " model vdw 2.291 3.120 nonbonded pdb=" O HIS A 759 " pdb=" ND1 HIS A 759 " model vdw 2.374 3.120 nonbonded pdb=" NH2 ARG B 527 " pdb=" OH TYR B 755 " model vdw 2.394 3.120 nonbonded pdb=" O2' ADP B 901 " pdb=" O3' ADP B 901 " model vdw 2.449 2.432 ... (remaining 99762 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 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.810 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 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 : 0.004 0.040 10836 Z= 0.219 Angle : 1.030 13.695 14718 Z= 0.674 Chirality : 0.047 0.224 1726 Planarity : 0.016 0.474 1786 Dihedral : 18.846 131.893 3858 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.33 % Favored : 89.29 % Rotamer: Outliers : 3.89 % Allowed : 39.10 % Favored : 57.01 % 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: -5.37 (0.19), residues: 1316 helix: -4.04 (0.13), residues: 760 sheet: -1.03 (0.54), residues: 106 loop : -2.90 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 324 TYR 0.039 0.001 TYR B 450 PHE 0.026 0.001 PHE B 502 TRP 0.006 0.001 TRP A 258 HIS 0.007 0.001 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.22 (10836) covalent geometry : angle 1.03019 / 0.67 (14718) hydrogen bonds : bond 0.25968 / 17.02 ( 283) hydrogen bonds : angle 9.14342 / 6.21 ( 783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 151 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.6166 (mp0) REVERT: A 239 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.6190 (m-80) REVERT: A 358 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7928 (m110) REVERT: A 767 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6215 (mtmt) REVERT: B 114 TYR cc_start: 0.8449 (m-80) cc_final: 0.7522 (m-80) REVERT: B 126 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6307 (tm-30) REVERT: B 178 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6394 (tp30) REVERT: B 312 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5951 (pp20) REVERT: B 464 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.4740 (mpp) REVERT: B 724 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6344 (tmm-80) outliers start: 45 outliers final: 27 residues processed: 204 average time/residue: 0.0909 time to fit residues: 27.2666 Evaluate side-chains 194 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 527 ARG Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 576 HIS Chi-restraints excluded: chain A residue 767 LYS Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 527 ARG Chi-restraints excluded: chain B residue 536 ARG Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 724 ARG Chi-restraints excluded: chain B residue 759 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS B 124 ASN B 761 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.167428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140042 restraints weight = 13162.296| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.06 r_work: 0.3491 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10836 Z= 0.198 Angle : 0.734 8.447 14718 Z= 0.385 Chirality : 0.047 0.158 1726 Planarity : 0.005 0.080 1786 Dihedral : 10.308 120.092 1553 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.70 % Favored : 88.07 % Rotamer: Outliers : 8.13 % Allowed : 33.04 % Favored : 58.82 % 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: -5.04 (0.20), residues: 1316 helix: -3.71 (0.14), residues: 782 sheet: -0.99 (0.52), residues: 106 loop : -2.74 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 324 TYR 0.023 0.002 TYR B 421 PHE 0.020 0.001 PHE B 237 TRP 0.010 0.001 TRP A 258 HIS 0.008 0.001 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (10836) covalent geometry : angle 0.73416 / 0.38 (14718) hydrogen bonds : bond 0.04673 / 3.04 ( 283) hydrogen bonds : angle 5.81089 / 4.00 ( 783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 163 time to evaluate : 0.364 Fit side-chains REVERT: A 205 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8727 (t) REVERT: A 239 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7612 (m-80) REVERT: A 246 LYS cc_start: 0.6949 (pttt) cc_final: 0.5834 (mttt) REVERT: A 512 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7932 (pt) REVERT: A 648 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 767 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8273 (ptpp) REVERT: B 159 THR cc_start: 0.7004 (OUTLIER) cc_final: 0.6656 (p) REVERT: B 178 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6482 (tp30) REVERT: B 312 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.5934 (pp20) REVERT: B 464 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7218 (mtp) REVERT: B 581 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7485 (tt) REVERT: B 600 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7217 (mtt90) REVERT: B 615 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7990 (tptp) REVERT: B 718 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.4742 (mt-10) outliers start: 94 outliers final: 41 residues processed: 235 average time/residue: 0.0928 time to fit residues: 31.7860 Evaluate side-chains 207 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 767 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain B residue 615 LYS Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [106, 52, 62, 10, 130, 34, 70, 92, 56, 67, 4] chunk 106 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.169414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.141255 restraints weight = 13005.667| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.13 r_work: 0.3520 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10836 Z= 0.128 Angle : 0.653 8.818 14718 Z= 0.343 Chirality : 0.044 0.153 1726 Planarity : 0.005 0.082 1786 Dihedral : 8.616 117.511 1499 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.56 % Favored : 89.21 % Rotamer: Outliers : 7.01 % Allowed : 32.27 % Favored : 60.73 % 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: -4.65 (0.21), residues: 1316 helix: -3.40 (0.15), residues: 780 sheet: -0.79 (0.54), residues: 106 loop : -2.61 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.020 0.001 TYR B 421 PHE 0.016 0.001 PHE B 237 TRP 0.010 0.001 TRP A 258 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10836) covalent geometry : angle 0.65334 / 0.34 (14718) hydrogen bonds : bond 0.03688 / 2.38 ( 283) hydrogen bonds : angle 5.29026 / 3.64 ( 783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 169 time to evaluate : 0.382 Fit side-chains REVERT: A 124 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8262 (m-40) REVERT: A 239 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: A 246 LYS cc_start: 0.6922 (pttt) cc_final: 0.5869 (mttt) REVERT: A 636 ASP cc_start: 0.7964 (t0) cc_final: 0.7733 (t0) REVERT: A 767 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7987 (ptpp) REVERT: B 92 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7771 (mtpt) REVERT: B 126 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: B 159 THR cc_start: 0.7037 (OUTLIER) cc_final: 0.6611 (p) REVERT: B 275 ILE cc_start: 0.8724 (pp) cc_final: 0.8159 (mm) REVERT: B 312 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.5799 (pp20) REVERT: B 464 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7085 (mpp) REVERT: B 581 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7424 (tt) REVERT: B 718 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.4517 (mt-10) outliers start: 81 outliers final: 41 residues processed: 229 average time/residue: 0.0980 time to fit residues: 32.4969 Evaluate side-chains 202 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 151 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 239 PHE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 767 LYS Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [82, 62, 94, 56, 6, 61, 23, 45, 37, 128, 127] chunk 82 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 94 optimal weight: 0.1980 chunk 56 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.170066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141969 restraints weight = 13047.771| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.14 r_work: 0.3524 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10836 Z= 0.124 Angle : 0.636 9.226 14718 Z= 0.331 Chirality : 0.043 0.154 1726 Planarity : 0.004 0.074 1786 Dihedral : 8.254 115.740 1496 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.73 % Favored : 90.05 % Rotamer: Outliers : 7.35 % Allowed : 30.97 % Favored : 61.68 % 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: -4.38 (0.21), residues: 1316 helix: -3.20 (0.15), residues: 788 sheet: -0.62 (0.53), residues: 106 loop : -2.46 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 324 TYR 0.021 0.001 TYR B 421 PHE 0.014 0.001 PHE B 237 TRP 0.009 0.001 TRP A 258 HIS 0.002 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (10836) covalent geometry : angle 0.63578 / 0.33 (14718) hydrogen bonds : bond 0.03379 / 2.17 ( 283) hydrogen bonds : angle 5.03535 / 3.47 ( 783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 166 time to evaluate : 0.409 Fit side-chains REVERT: A 96 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8645 (t) REVERT: A 246 LYS cc_start: 0.6959 (pttt) cc_final: 0.6066 (mttt) REVERT: A 767 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7783 (ptpp) REVERT: B 92 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7735 (mtpt) REVERT: B 126 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7419 (tm-30) REVERT: B 151 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6598 (mt-10) REVERT: B 159 THR cc_start: 0.7001 (OUTLIER) cc_final: 0.6712 (p) REVERT: B 275 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8240 (mm) REVERT: B 312 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.5721 (pp20) REVERT: B 469 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6828 (ptp) REVERT: B 517 MET cc_start: 0.8577 (ttt) cc_final: 0.8363 (ttm) REVERT: B 541 ARG cc_start: 0.7699 (mtm180) cc_final: 0.6179 (mtt90) REVERT: B 581 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7421 (tt) REVERT: B 718 GLU cc_start: 0.5725 (OUTLIER) cc_final: 0.4650 (mt-10) outliers start: 85 outliers final: 53 residues processed: 231 average time/residue: 0.0923 time to fit residues: 31.0873 Evaluate side-chains 222 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 158 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 767 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 420 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 717 THR Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [86, 71, 53, 9, 39, 83, 24, 109, 42, 95, 4] chunk 86 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN B 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.171690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.143711 restraints weight = 12842.784| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.03 r_work: 0.3512 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10836 Z= 0.111 Angle : 0.614 9.101 14718 Z= 0.318 Chirality : 0.043 0.158 1726 Planarity : 0.004 0.076 1786 Dihedral : 7.886 115.055 1494 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.57 % Favored : 90.20 % Rotamer: Outliers : 6.57 % Allowed : 31.40 % Favored : 62.02 % 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: -4.15 (0.22), residues: 1316 helix: -3.02 (0.16), residues: 796 sheet: -0.45 (0.54), residues: 106 loop : -2.36 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 324 TYR 0.019 0.001 TYR B 421 PHE 0.013 0.001 PHE B 237 TRP 0.008 0.001 TRP A 258 HIS 0.002 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (10836) covalent geometry : angle 0.61386 / 0.32 (14718) hydrogen bonds : bond 0.03131 / 2.00 ( 283) hydrogen bonds : angle 4.83386 / 3.31 ( 783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 169 time to evaluate : 0.273 Fit side-chains REVERT: A 96 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8708 (t) REVERT: A 124 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8306 (m-40) REVERT: A 246 LYS cc_start: 0.7066 (pttt) cc_final: 0.6111 (mttt) REVERT: B 92 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7687 (mtpt) REVERT: B 126 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: B 151 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.6580 (mt-10) REVERT: B 159 THR cc_start: 0.6858 (OUTLIER) cc_final: 0.6427 (p) REVERT: B 275 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8250 (mm) REVERT: B 312 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5588 (pp20) REVERT: B 469 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6807 (ptp) REVERT: B 482 ILE cc_start: 0.7489 (OUTLIER) cc_final: 0.7278 (mp) REVERT: B 541 ARG cc_start: 0.7664 (mtm180) cc_final: 0.6154 (mtt90) REVERT: B 581 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7360 (tt) REVERT: B 718 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.4700 (mt-10) outliers start: 76 outliers final: 47 residues processed: 228 average time/residue: 0.0834 time to fit residues: 28.0303 Evaluate side-chains 215 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 156 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ASN Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 209 SER Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [114, 129, 41, 116, 77, 93, 127, 55, 7, 12, 98] chunk 114 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 7 optimal weight: 0.0170 chunk 12 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 90 ASN B 124 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.143498 restraints weight = 12919.030| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.01 r_work: 0.3542 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10836 Z= 0.116 Angle : 0.618 9.524 14718 Z= 0.318 Chirality : 0.044 0.155 1726 Planarity : 0.004 0.070 1786 Dihedral : 7.473 114.119 1487 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.19 % Favored : 90.58 % Rotamer: Outliers : 7.09 % Allowed : 30.62 % Favored : 62.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.83 (0.22), residues: 1316 helix: -2.77 (0.17), residues: 764 sheet: -0.36 (0.54), residues: 106 loop : -2.29 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 324 TYR 0.019 0.001 TYR B 421 PHE 0.017 0.001 PHE B 502 TRP 0.008 0.001 TRP A 258 HIS 0.002 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10836) covalent geometry : angle 0.61797 / 0.32 (14718) hydrogen bonds : bond 0.03145 / 2.01 ( 283) hydrogen bonds : angle 4.75172 / 3.24 ( 783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 161 time to evaluate : 0.392 Fit side-chains REVERT: A 124 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8375 (m-40) REVERT: A 246 LYS cc_start: 0.7197 (pttt) cc_final: 0.6265 (mttt) REVERT: A 401 MET cc_start: 0.8437 (mmm) cc_final: 0.8077 (mmm) REVERT: A 720 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8181 (t) REVERT: A 724 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6755 (tpp80) REVERT: B 57 THR cc_start: 0.7396 (p) cc_final: 0.7050 (t) REVERT: B 92 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7686 (mtpt) REVERT: B 126 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: B 159 THR cc_start: 0.6821 (OUTLIER) cc_final: 0.6345 (p) REVERT: B 178 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6570 (tp30) REVERT: B 275 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8223 (mm) REVERT: B 312 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5695 (pp20) REVERT: B 464 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7394 (mpp) REVERT: B 469 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6905 (ptp) REVERT: B 541 ARG cc_start: 0.7677 (mtm180) cc_final: 0.6119 (mtt90) REVERT: B 581 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7399 (tt) REVERT: B 718 GLU cc_start: 0.5832 (OUTLIER) cc_final: 0.4845 (mt-10) outliers start: 82 outliers final: 51 residues processed: 224 average time/residue: 0.0900 time to fit residues: 29.5044 Evaluate side-chains 222 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 158 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 724 ARG Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 469 MET Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 556 VAL Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [92, 75, 115, 121, 35, 58, 9, 114, 11, 130, 62] chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 121 optimal weight: 7.9990 chunk 35 optimal weight: 0.0170 chunk 58 optimal weight: 0.9990 chunk 9 optimal weight: 0.0670 chunk 114 optimal weight: 0.0470 chunk 11 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN ** B 269 ASN ** 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 = 0.4040 r_free = 0.4040 target = 0.176360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.149171 restraints weight = 12914.131| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.97 r_work: 0.3599 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.002 0.034 10836 Z= 0.095 Angle : 0.590 8.293 14718 Z= 0.303 Chirality : 0.042 0.157 1726 Planarity : 0.004 0.073 1786 Dihedral : 7.157 113.704 1486 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.59 % Favored : 91.19 % Rotamer: Outliers : 4.84 % Allowed : 32.79 % Favored : 62.37 % 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: -3.46 (0.23), residues: 1316 helix: -2.46 (0.17), residues: 756 sheet: -0.22 (0.55), residues: 106 loop : -2.16 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 324 TYR 0.018 0.001 TYR B 421 PHE 0.011 0.001 PHE A 483 TRP 0.008 0.000 TRP A 258 HIS 0.002 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.09 (10836) covalent geometry : angle 0.59010 / 0.30 (14718) hydrogen bonds : bond 0.02723 / 1.73 ( 283) hydrogen bonds : angle 4.52962 / 3.08 ( 783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 175 time to evaluate : 0.242 Fit side-chains REVERT: A 124 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8319 (m-40) REVERT: A 246 LYS cc_start: 0.7269 (pttt) cc_final: 0.6350 (mttt) REVERT: A 401 MET cc_start: 0.8445 (mmm) cc_final: 0.8055 (mmm) REVERT: A 441 ARG cc_start: 0.7625 (ptt90) cc_final: 0.7290 (ptp90) REVERT: A 724 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7363 (tpt-90) REVERT: B 57 THR cc_start: 0.7432 (p) cc_final: 0.7094 (t) REVERT: B 92 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7751 (mtpt) REVERT: B 151 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6650 (mt-10) REVERT: B 159 THR cc_start: 0.6822 (OUTLIER) cc_final: 0.6217 (p) REVERT: B 168 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5860 (ttt-90) REVERT: B 275 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8229 (mm) REVERT: B 312 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5599 (pp20) REVERT: B 427 TYR cc_start: 0.7998 (m-80) cc_final: 0.7627 (m-80) REVERT: B 464 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7610 (mpp) REVERT: B 469 MET cc_start: 0.7232 (ttm) cc_final: 0.6887 (ptp) REVERT: B 541 ARG cc_start: 0.7629 (mtm180) cc_final: 0.6181 (mtt90) REVERT: B 581 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7355 (tt) REVERT: B 645 TYR cc_start: 0.7565 (m-80) cc_final: 0.7245 (m-80) REVERT: B 718 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.4910 (mt-10) outliers start: 56 outliers final: 36 residues processed: 217 average time/residue: 0.0939 time to fit residues: 29.5460 Evaluate side-chains 211 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 364 ILE Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 724 ARG Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 151 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 718 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [16, 85, 76, 129, 104, 55, 93, 121, 90, 30, 64] chunk 16 optimal weight: 0.2980 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 30 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN ** B 269 ASN ** 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 = 0.3971 r_free = 0.3971 target = 0.169863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.141445 restraints weight = 12803.445| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.12 r_work: 0.3514 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10836 Z= 0.150 Angle : 0.638 7.859 14718 Z= 0.327 Chirality : 0.045 0.150 1726 Planarity : 0.004 0.069 1786 Dihedral : 7.253 110.360 1484 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.57 % Favored : 90.27 % Rotamer: Outliers : 5.54 % Allowed : 31.83 % Favored : 62.63 % 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: -3.49 (0.23), residues: 1316 helix: -2.44 (0.17), residues: 758 sheet: -0.43 (0.54), residues: 106 loop : -2.23 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.021 0.001 TYR B 421 PHE 0.018 0.001 PHE B 502 TRP 0.008 0.001 TRP A 258 HIS 0.003 0.000 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (10836) covalent geometry : angle 0.63788 / 0.33 (14718) hydrogen bonds : bond 0.03526 / 2.28 ( 283) hydrogen bonds : angle 4.78813 / 3.26 ( 783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 159 time to evaluate : 0.391 Fit side-chains REVERT: A 246 LYS cc_start: 0.7191 (pttt) cc_final: 0.6221 (mttt) REVERT: A 441 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7375 (ptp90) REVERT: A 519 MET cc_start: 0.8876 (ptt) cc_final: 0.8670 (ptt) REVERT: A 724 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7309 (tpt-90) REVERT: B 57 THR cc_start: 0.7538 (p) cc_final: 0.7201 (t) REVERT: B 92 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7772 (mtpt) REVERT: B 159 THR cc_start: 0.6819 (OUTLIER) cc_final: 0.6325 (p) REVERT: B 168 ARG cc_start: 0.6208 (OUTLIER) cc_final: 0.5816 (ttt-90) REVERT: B 178 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6431 (tp30) REVERT: B 275 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8243 (mm) REVERT: B 312 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5552 (pp20) REVERT: B 430 MET cc_start: 0.7617 (ttp) cc_final: 0.7372 (mtm) REVERT: B 464 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.6960 (mpp) REVERT: B 499 MET cc_start: 0.7864 (mmm) cc_final: 0.7418 (mmp) REVERT: B 541 ARG cc_start: 0.7663 (mtm180) cc_final: 0.6153 (mtt90) REVERT: B 581 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7454 (tt) outliers start: 64 outliers final: 42 residues processed: 209 average time/residue: 0.0904 time to fit residues: 27.5460 Evaluate side-chains 205 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 441 ARG Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 724 ARG Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 93 ASP Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 271 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 324 ARG Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 464 MET Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [107, 93, 33, 75, 92, 122, 130, 72, 16, 70, 58] chunk 107 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 130 optimal weight: 0.0670 chunk 72 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 0.0050 overall best weight: 0.3132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.175164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.147129 restraints weight = 12804.845| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.06 r_work: 0.3588 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 10836 Z= 0.097 Angle : 0.592 8.291 14718 Z= 0.302 Chirality : 0.042 0.158 1726 Planarity : 0.004 0.076 1786 Dihedral : 6.934 111.269 1484 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.66 % Favored : 91.19 % Rotamer: Outliers : 4.07 % Allowed : 33.13 % Favored : 62.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.17 (0.23), residues: 1316 helix: -2.18 (0.18), residues: 750 sheet: -0.32 (0.55), residues: 106 loop : -2.10 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 324 TYR 0.020 0.001 TYR B 421 PHE 0.023 0.001 PHE A 502 TRP 0.008 0.001 TRP A 258 HIS 0.002 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (10836) covalent geometry : angle 0.59223 / 0.30 (14718) hydrogen bonds : bond 0.02834 / 1.79 ( 283) hydrogen bonds : angle 4.51824 / 3.07 ( 783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 161 time to evaluate : 0.286 Fit side-chains REVERT: A 124 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8195 (m-40) REVERT: A 246 LYS cc_start: 0.7133 (pttt) cc_final: 0.6213 (mttt) REVERT: A 358 ASN cc_start: 0.8430 (t0) cc_final: 0.8152 (t0) REVERT: A 401 MET cc_start: 0.8286 (mmm) cc_final: 0.7856 (mmm) REVERT: A 441 ARG cc_start: 0.7456 (ptt90) cc_final: 0.7180 (ptp90) REVERT: A 724 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7249 (tpt-90) REVERT: B 57 THR cc_start: 0.7525 (p) cc_final: 0.7186 (t) REVERT: B 92 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7732 (mtpt) REVERT: B 126 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: B 154 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7605 (mt-10) REVERT: B 159 THR cc_start: 0.6786 (OUTLIER) cc_final: 0.6241 (p) REVERT: B 168 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5931 (ttt-90) REVERT: B 275 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8297 (mm) REVERT: B 312 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5497 (pp20) REVERT: B 430 MET cc_start: 0.7519 (ttp) cc_final: 0.7244 (mtm) REVERT: B 469 MET cc_start: 0.7140 (ttm) cc_final: 0.6793 (ptp) REVERT: B 499 MET cc_start: 0.7797 (mmm) cc_final: 0.7324 (mmp) REVERT: B 541 ARG cc_start: 0.7583 (mtm180) cc_final: 0.6203 (mtt90) REVERT: B 581 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7435 (tt) REVERT: B 636 ASP cc_start: 0.7189 (m-30) cc_final: 0.6833 (m-30) outliers start: 47 outliers final: 30 residues processed: 199 average time/residue: 0.0962 time to fit residues: 27.7576 Evaluate side-chains 191 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 724 ARG Chi-restraints excluded: chain B residue 55 TRP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 740 GLU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [46, 11, 16, 40, 131, 33, 130, 41, 28, 36, 59] chunk 46 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 59 optimal weight: 0.0770 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN ** B 269 ASN ** 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 = 0.4029 r_free = 0.4029 target = 0.175412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146932 restraints weight = 12755.786| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.06 r_work: 0.3577 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10836 Z= 0.102 Angle : 0.600 8.532 14718 Z= 0.305 Chirality : 0.043 0.164 1726 Planarity : 0.004 0.066 1786 Dihedral : 6.838 110.131 1484 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.59 % Favored : 91.26 % Rotamer: Outliers : 3.72 % Allowed : 33.13 % Favored : 63.15 % 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: -3.04 (0.23), residues: 1316 helix: -2.04 (0.18), residues: 752 sheet: -0.31 (0.54), residues: 106 loop : -2.08 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 324 TYR 0.019 0.001 TYR B 421 PHE 0.020 0.001 PHE B 502 TRP 0.007 0.001 TRP A 258 HIS 0.002 0.000 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (10836) covalent geometry : angle 0.59965 / 0.30 (14718) hydrogen bonds : bond 0.02892 / 1.83 ( 283) hydrogen bonds : angle 4.51964 / 3.06 ( 783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2632 Ramachandran restraints generated. 1316 Oldfield, 0 Emsley, 1316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.339 Fit side-chains REVERT: A 124 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8221 (m-40) REVERT: A 246 LYS cc_start: 0.7248 (pttt) cc_final: 0.6247 (mttt) REVERT: A 358 ASN cc_start: 0.8426 (t0) cc_final: 0.8107 (t0) REVERT: A 401 MET cc_start: 0.8366 (mmm) cc_final: 0.7915 (mmm) REVERT: A 441 ARG cc_start: 0.7446 (ptt90) cc_final: 0.7151 (ptp90) REVERT: A 724 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.7231 (tpt-90) REVERT: B 57 THR cc_start: 0.7475 (p) cc_final: 0.7150 (t) REVERT: B 92 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7698 (mtpt) REVERT: B 126 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: B 154 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7600 (mt-10) REVERT: B 159 THR cc_start: 0.6709 (OUTLIER) cc_final: 0.6164 (p) REVERT: B 168 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5857 (ttt-90) REVERT: B 275 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8341 (mm) REVERT: B 312 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5632 (pp20) REVERT: B 430 MET cc_start: 0.7491 (ttp) cc_final: 0.7221 (mtm) REVERT: B 469 MET cc_start: 0.7157 (ttm) cc_final: 0.6949 (ptp) REVERT: B 499 MET cc_start: 0.7793 (mmm) cc_final: 0.7363 (mmp) REVERT: B 541 ARG cc_start: 0.7547 (mtm180) cc_final: 0.6161 (mtt90) REVERT: B 636 ASP cc_start: 0.7204 (m-30) cc_final: 0.6843 (m-30) outliers start: 43 outliers final: 30 residues processed: 196 average time/residue: 0.0906 time to fit residues: 25.9955 Evaluate side-chains 196 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 616 ASP Chi-restraints excluded: chain A residue 724 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 129 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 168 ARG Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 251 PHE Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 312 GLU Chi-restraints excluded: chain B residue 366 ASP Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 565 GLU Chi-restraints excluded: chain B residue 576 HIS Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 633 GLU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 777 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [52, 103, 110, 13, 65, 122, 61, 58, 31, 129, 131] chunk 52 optimal weight: 0.0060 chunk 103 optimal weight: 0.0070 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 overall best weight: 0.4614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 ASN ** B 269 ASN ** 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 = 0.4027 r_free = 0.4027 target = 0.175178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146350 restraints weight = 12788.118| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.09 r_work: 0.3583 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10836 Z= 0.100 Angle : 0.590 8.553 14718 Z= 0.300 Chirality : 0.043 0.159 1726 Planarity : 0.004 0.072 1786 Dihedral : 6.756 108.740 1484 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.19 % Favored : 90.65 % Rotamer: Outliers : 3.63 % Allowed : 33.04 % Favored : 63.32 % 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: 1316 helix: -1.90 (0.18), residues: 750 sheet: -0.24 (0.54), residues: 106 loop : -2.06 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 324 TYR 0.019 0.001 TYR B 421 PHE 0.022 0.001 PHE A 502 TRP 0.008 0.001 TRP A 258 HIS 0.002 0.000 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (10836) covalent geometry : angle 0.59009 / 0.30 (14718) hydrogen bonds : bond 0.02887 / 1.83 ( 283) hydrogen bonds : angle 4.47264 / 3.03 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2492.11 seconds wall clock time: 43 minutes 24.36 seconds (2604.36 seconds total)