Starting phenix.real_space_refine on Fri Mar 6 07:32:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ni0_12348/03_2026/7ni0_12348.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ni0_12348/03_2026/7ni0_12348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ni0_12348/03_2026/7ni0_12348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ni0_12348/03_2026/7ni0_12348.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ni0_12348/03_2026/7ni0_12348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ni0_12348/03_2026/7ni0_12348.map" } resolution = 3.32 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= 0.002 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 S 109 5.16 5 C 9239 2.51 5 N 2605 2.21 5 O 2858 1.98 5 H 14500 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29334 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 8270 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 489} Chain: "B" Number of atoms: 11747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 738, 11747 Classifications: {'peptide': 738} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 32, 'TRANS': 705} Chain breaks: 1 Chain: "C" Number of atoms: 8571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 8571 Classifications: {'peptide': 539} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 519} Chain: "E" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 255 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "D" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 491 Classifications: {'RNA': 15} Modifications used: {'3*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna2p': 3, 'rna3p': 11} Time building chain proxies: 4.35, per 1000 atoms: 0.15 Number of scatterers: 29334 At special positions: 0 Unit cell: (114.675, 106.425, 121.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 109 16.00 P 23 15.00 O 2858 8.00 N 2605 7.00 C 9239 6.00 H 14500 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 830.1 milliseconds 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3380 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 21 sheets defined 48.4% alpha, 13.4% beta 4 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 209 through 217 Processing helix chain 'A' and resid 225 through 236 Processing helix chain 'A' and resid 241 through 249 Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.529A pdb=" N THR A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.922A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.721A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 452 removed outlier: 4.402A pdb=" N HIS A 452 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 476 Processing helix chain 'A' and resid 533 through 538 removed outlier: 4.035A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 579 Processing helix chain 'A' and resid 582 through 601 removed outlier: 3.536A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 removed outlier: 3.534A pdb=" N LYS A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 3.706A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 697 through 714 Processing helix chain 'B' and resid 4 through 11 removed outlier: 3.512A pdb=" N LEU B 7 " --> pdb=" O ASN B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 124 removed outlier: 3.778A pdb=" N LYS B 121 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 154 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.927A pdb=" N GLU B 159 " --> pdb=" O THR B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.560A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.627A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 291 Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.503A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 346 removed outlier: 4.486A pdb=" N ALA B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 375 removed outlier: 3.828A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.317A pdb=" N TYR B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 455 through 472 Processing helix chain 'B' and resid 508 through 512 Processing helix chain 'B' and resid 518 through 536 Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 573 through 583 Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.801A pdb=" N GLY B 588 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 589' Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.582A pdb=" N GLY B 594 " --> pdb=" O VAL B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.615A pdb=" N LEU B 604 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 636 through 640 removed outlier: 3.552A pdb=" N VAL B 640 " --> pdb=" O ILE B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 680 removed outlier: 3.847A pdb=" N LEU B 675 " --> pdb=" O ARG B 672 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER B 678 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN B 679 " --> pdb=" O ASN B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 700 Processing helix chain 'B' and resid 701 through 704 removed outlier: 4.226A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 701 through 704' Processing helix chain 'B' and resid 713 through 732 removed outlier: 3.562A pdb=" N ALA B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 756 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 13 through 23 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 42 through 50 removed outlier: 3.560A pdb=" N MET C 50 " --> pdb=" O ARG C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 53 No H-bonds generated for 'chain 'C' and resid 51 through 53' Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.512A pdb=" N THR C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 115 removed outlier: 4.162A pdb=" N LYS C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.701A pdb=" N ASP C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.633A pdb=" N GLU C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 212 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.723A pdb=" N GLN C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 273 removed outlier: 4.030A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 286 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 390 through 406 removed outlier: 3.649A pdb=" N GLN C 406 " --> pdb=" O MET C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 429 through 438 Processing helix chain 'C' and resid 442 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.649A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 324 removed outlier: 5.896A pdb=" N VAL A 322 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU A 544 " --> pdb=" O VAL A 322 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N MET A 561 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP A 547 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ARG A 559 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE A 505 " --> pdb=" O GLN A 481 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLN A 481 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 490 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 379 removed outlier: 5.865A pdb=" N GLU A 377 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N GLN B 367 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL A 379 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 619 through 623 removed outlier: 3.509A pdb=" N ILE A 621 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA7, first strand: chain 'B' and resid 127 through 130 Processing sheet with id=AA8, first strand: chain 'B' and resid 178 through 184 Processing sheet with id=AA9, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.841A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 437 through 443 Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB3, first strand: chain 'B' and resid 642 through 645 Processing sheet with id=AB4, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.587A pdb=" N THR C 81 " --> pdb=" O MET C 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 129 through 135 removed outlier: 6.199A pdb=" N PHE C 130 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR C 245 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET C 243 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 141 through 146 Processing sheet with id=AB7, first strand: chain 'C' and resid 292 through 293 Processing sheet with id=AB8, first strand: chain 'C' and resid 324 through 325 Processing sheet with id=AB9, first strand: chain 'C' and resid 331 through 334 removed outlier: 6.147A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ARG C 479 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 384 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 342 through 345 Processing sheet with id=AC2, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AC3, first strand: chain 'C' and resid 496 through 498 removed outlier: 6.481A pdb=" N VAL C 504 " --> pdb=" O LEU C 512 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1899 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 10 hydrogen bonds 20 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 6.57 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14474 1.03 - 1.23: 43 1.23 - 1.42: 6284 1.42 - 1.62: 8672 1.62 - 1.82: 192 Bond restraints: 29665 Sorted by residual: bond pdb=" CG1 ILE C 373 " pdb=" CD1 ILE C 373 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.37e+00 bond pdb=" CG GLU B 159 " pdb=" CD GLU B 159 " ideal model delta sigma weight residual 1.516 1.470 0.046 2.50e-02 1.60e+03 3.32e+00 bond pdb=" CG GLU C 192 " pdb=" CD GLU C 192 " ideal model delta sigma weight residual 1.516 1.477 0.039 2.50e-02 1.60e+03 2.44e+00 bond pdb=" CB GLU B 358 " pdb=" CG GLU B 358 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.65e+00 bond pdb=" CE LYS B 363 " pdb=" NZ LYS B 363 " ideal model delta sigma weight residual 1.489 1.452 0.037 3.00e-02 1.11e+03 1.54e+00 ... (remaining 29660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 52922 1.99 - 3.98: 591 3.98 - 5.98: 39 5.98 - 7.97: 12 7.97 - 9.96: 2 Bond angle restraints: 53566 Sorted by residual: angle pdb=" CA PRO C 93 " pdb=" N PRO C 93 " pdb=" CD PRO C 93 " ideal model delta sigma weight residual 112.00 104.70 7.30 1.40e+00 5.10e-01 2.72e+01 angle pdb=" CA LYS B 363 " pdb=" CB LYS B 363 " pdb=" CG LYS B 363 " ideal model delta sigma weight residual 114.10 124.06 -9.96 2.00e+00 2.50e-01 2.48e+01 angle pdb=" CA ARG C 8 " pdb=" CB ARG C 8 " pdb=" CG ARG C 8 " ideal model delta sigma weight residual 114.10 121.70 -7.60 2.00e+00 2.50e-01 1.44e+01 angle pdb=" N LYS B 363 " pdb=" CA LYS B 363 " pdb=" CB LYS B 363 " ideal model delta sigma weight residual 111.65 105.93 5.72 1.58e+00 4.01e-01 1.31e+01 angle pdb=" C GLU C 487 " pdb=" CA GLU C 487 " pdb=" CB GLU C 487 " ideal model delta sigma weight residual 110.42 103.83 6.59 1.99e+00 2.53e-01 1.10e+01 ... (remaining 53561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 12445 17.90 - 35.79: 1111 35.79 - 53.69: 275 53.69 - 71.58: 95 71.58 - 89.48: 23 Dihedral angle restraints: 13949 sinusoidal: 7938 harmonic: 6011 Sorted by residual: dihedral pdb=" CA TYR A 540 " pdb=" C TYR A 540 " pdb=" N CYS A 541 " pdb=" CA CYS A 541 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA MET B 409 " pdb=" C MET B 409 " pdb=" N GLY B 410 " pdb=" CA GLY B 410 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA LEU C 464 " pdb=" C LEU C 464 " pdb=" N PRO C 465 " pdb=" CA PRO C 465 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 13946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1789 0.044 - 0.088: 383 0.088 - 0.131: 97 0.131 - 0.175: 15 0.175 - 0.219: 2 Chirality restraints: 2286 Sorted by residual: chirality pdb=" CA PRO C 93 " pdb=" N PRO C 93 " pdb=" C PRO C 93 " pdb=" CB PRO C 93 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA LYS C 22 " pdb=" N LYS C 22 " pdb=" C LYS C 22 " pdb=" CB LYS C 22 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA ILE B 568 " pdb=" N ILE B 568 " pdb=" C ILE B 568 " pdb=" CB ILE B 568 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.05e-01 ... (remaining 2283 not shown) Planarity restraints: 4301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 92 " -0.073 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO C 93 " 0.184 5.00e-02 4.00e+02 pdb=" CA PRO C 93 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 93 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 407 " -0.021 2.00e-02 2.50e+03 4.15e-02 1.72e+01 pdb=" C ILE A 407 " 0.072 2.00e-02 2.50e+03 pdb=" O ILE A 407 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN A 408 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 28 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.33e+00 pdb=" C MET C 28 " 0.053 2.00e-02 2.50e+03 pdb=" O MET C 28 " -0.020 2.00e-02 2.50e+03 pdb=" N ALA C 29 " -0.018 2.00e-02 2.50e+03 ... (remaining 4298 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 791 2.11 - 2.73: 52557 2.73 - 3.36: 85885 3.36 - 3.98: 109522 3.98 - 4.60: 172601 Nonbonded interactions: 421356 Sorted by model distance: nonbonded pdb=" OD1 ASN A 647 " pdb=" HE1 TRP A 699 " model vdw 1.488 2.450 nonbonded pdb=" OD2 ASP A 389 " pdb=" H SER B 361 " model vdw 1.511 2.450 nonbonded pdb=" HZ2 LYS A 328 " pdb=" O3' A D 1 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP B 76 " pdb=" H ASN B 77 " model vdw 1.587 2.450 nonbonded pdb=" HZ2 LYS C 140 " pdb=" OE1 GLN C 236 " model vdw 1.595 2.450 ... (remaining 421351 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.790 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 : 0.003 0.082 15165 Z= 0.148 Angle : 0.656 9.961 20563 Z= 0.364 Chirality : 0.040 0.219 2286 Planarity : 0.006 0.106 2571 Dihedral : 15.093 89.478 5959 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.14 % Favored : 95.80 % Rotamer: Outliers : 0.06 % Allowed : 0.19 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.17), residues: 1786 helix: -0.58 (0.16), residues: 793 sheet: -2.47 (0.32), residues: 195 loop : -2.20 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 571 TYR 0.037 0.002 TYR A 393 PHE 0.028 0.001 PHE C 330 TRP 0.029 0.001 TRP B 437 HIS 0.003 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00327 (15165) covalent geometry : angle 0.65631 (20563) hydrogen bonds : bond 0.13293 ( 693) hydrogen bonds : angle 6.19662 ( 1919) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Evaluate side-chains 313 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 312 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 713 HIS cc_start: 0.8852 (OUTLIER) cc_final: 0.8485 (m90) REVERT: B 522 ASP cc_start: 0.7496 (m-30) cc_final: 0.7048 (m-30) REVERT: B 523 MET cc_start: 0.8132 (tpp) cc_final: 0.7597 (tpt) REVERT: B 696 PHE cc_start: 0.7336 (t80) cc_final: 0.6960 (t80) REVERT: C 182 GLN cc_start: 0.8076 (mt0) cc_final: 0.7233 (mm-40) outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 0.3112 time to fit residues: 138.1791 Evaluate side-chains 188 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 713 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 GLN B 276 ASN B 425 ASN B 533 ASN ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.106550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.084185 restraints weight = 119065.303| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.64 r_work: 0.3411 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15165 Z= 0.227 Angle : 0.621 6.196 20563 Z= 0.336 Chirality : 0.040 0.153 2286 Planarity : 0.005 0.066 2571 Dihedral : 10.442 77.831 2311 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.42 % Rotamer: Outliers : 1.45 % Allowed : 7.36 % Favored : 91.19 % 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: -1.18 (0.18), residues: 1786 helix: 0.69 (0.18), residues: 798 sheet: -2.08 (0.32), residues: 193 loop : -2.00 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 754 TYR 0.030 0.002 TYR A 305 PHE 0.017 0.002 PHE A 520 TRP 0.015 0.002 TRP B 437 HIS 0.005 0.001 HIS C 151 Details of bonding type rmsd covalent geometry : bond 0.00498 (15165) covalent geometry : angle 0.62080 (20563) hydrogen bonds : bond 0.04725 ( 693) hydrogen bonds : angle 4.91940 ( 1919) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Evaluate side-chains 217 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.8714 (ttp) cc_final: 0.8385 (tpp) REVERT: A 609 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7600 (mptt) REVERT: A 656 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: B 289 MET cc_start: 0.7689 (mmp) cc_final: 0.7397 (mmp) REVERT: B 522 ASP cc_start: 0.7580 (m-30) cc_final: 0.7278 (m-30) REVERT: B 523 MET cc_start: 0.8209 (tpp) cc_final: 0.7775 (tpt) REVERT: B 696 PHE cc_start: 0.7845 (t80) cc_final: 0.7271 (t80) REVERT: C 87 ASP cc_start: 0.8288 (t0) cc_final: 0.8049 (t0) REVERT: C 180 GLU cc_start: 0.8284 (tp30) cc_final: 0.7734 (mp0) REVERT: C 294 MET cc_start: 0.7081 (ptm) cc_final: 0.6430 (ptm) outliers start: 23 outliers final: 15 residues processed: 211 average time/residue: 0.2602 time to fit residues: 82.9504 Evaluate side-chains 180 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 268 GLN Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 26 ASP Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 164 MET Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 491 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 160 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 HIS ** C 432 HIS ** 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 = 0.3926 r_free = 0.3926 target = 0.103790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.080691 restraints weight = 122740.481| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.72 r_work: 0.3349 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 15165 Z= 0.240 Angle : 0.600 5.515 20563 Z= 0.325 Chirality : 0.040 0.158 2286 Planarity : 0.005 0.048 2571 Dihedral : 10.319 79.486 2309 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.25 % Rotamer: Outliers : 1.64 % Allowed : 8.62 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.19), residues: 1786 helix: 0.87 (0.18), residues: 805 sheet: -1.80 (0.30), residues: 223 loop : -1.74 (0.20), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 572 TYR 0.018 0.002 TYR A 305 PHE 0.018 0.002 PHE B 696 TRP 0.015 0.001 TRP A 368 HIS 0.005 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00527 (15165) covalent geometry : angle 0.60016 (20563) hydrogen bonds : bond 0.04629 ( 693) hydrogen bonds : angle 4.81173 ( 1919) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 441 MET cc_start: 0.8770 (ttp) cc_final: 0.8543 (tpp) REVERT: A 571 SER cc_start: 0.8714 (m) cc_final: 0.8503 (m) REVERT: A 607 MET cc_start: 0.8785 (mmp) cc_final: 0.8567 (mmm) REVERT: A 609 LYS cc_start: 0.8011 (OUTLIER) cc_final: 0.7709 (mmtt) REVERT: A 656 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: B 522 ASP cc_start: 0.7518 (m-30) cc_final: 0.7161 (m-30) REVERT: B 523 MET cc_start: 0.8308 (tpp) cc_final: 0.7883 (tpt) REVERT: B 700 PHE cc_start: 0.8111 (m-80) cc_final: 0.7800 (m-80) REVERT: C 47 MET cc_start: 0.8670 (tpp) cc_final: 0.8460 (tpp) REVERT: C 87 ASP cc_start: 0.8291 (t0) cc_final: 0.8052 (t0) REVERT: C 180 GLU cc_start: 0.8389 (tp30) cc_final: 0.7953 (mp0) REVERT: C 402 MET cc_start: 0.4259 (OUTLIER) cc_final: 0.4034 (mtt) REVERT: C 463 ILE cc_start: 0.1724 (OUTLIER) cc_final: 0.1181 (mt) REVERT: C 525 GLU cc_start: 0.8833 (pm20) cc_final: 0.8355 (mp0) outliers start: 26 outliers final: 14 residues processed: 184 average time/residue: 0.2480 time to fit residues: 70.9964 Evaluate side-chains 178 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 402 MET Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 527 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 170 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 160 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.105061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.082215 restraints weight = 121437.457| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 3.70 r_work: 0.3383 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15165 Z= 0.132 Angle : 0.532 5.833 20563 Z= 0.282 Chirality : 0.038 0.153 2286 Planarity : 0.004 0.044 2571 Dihedral : 10.165 79.804 2309 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.53 % Favored : 96.36 % Rotamer: Outliers : 1.19 % Allowed : 9.81 % Favored : 88.99 % 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: -0.43 (0.19), residues: 1786 helix: 1.18 (0.18), residues: 817 sheet: -1.67 (0.30), residues: 232 loop : -1.48 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.017 0.001 TYR A 305 PHE 0.010 0.001 PHE C 119 TRP 0.015 0.001 TRP A 368 HIS 0.003 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00294 (15165) covalent geometry : angle 0.53151 (20563) hydrogen bonds : bond 0.03876 ( 693) hydrogen bonds : angle 4.41147 ( 1919) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.9314 (tpt) cc_final: 0.9083 (tpt) REVERT: A 441 MET cc_start: 0.8762 (ttp) cc_final: 0.8359 (tpp) REVERT: A 656 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: B 522 ASP cc_start: 0.7548 (m-30) cc_final: 0.7193 (m-30) REVERT: B 700 PHE cc_start: 0.8251 (m-80) cc_final: 0.7955 (m-80) REVERT: C 47 MET cc_start: 0.8661 (tpp) cc_final: 0.8414 (tpp) REVERT: C 87 ASP cc_start: 0.8358 (t0) cc_final: 0.8112 (t0) REVERT: C 180 GLU cc_start: 0.8388 (tp30) cc_final: 0.8010 (mp0) REVERT: C 525 GLU cc_start: 0.8800 (pm20) cc_final: 0.8317 (mp0) outliers start: 19 outliers final: 13 residues processed: 182 average time/residue: 0.2470 time to fit residues: 69.9181 Evaluate side-chains 175 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 527 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 91 optimal weight: 5.9990 chunk 172 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN B 134 ASN B 184 HIS ** C 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.100540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.077898 restraints weight = 125101.274| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.64 r_work: 0.3290 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 15165 Z= 0.284 Angle : 0.623 6.242 20563 Z= 0.339 Chirality : 0.041 0.152 2286 Planarity : 0.005 0.049 2571 Dihedral : 10.407 81.738 2309 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 1.89 % Allowed : 10.69 % Favored : 87.42 % 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: -0.72 (0.19), residues: 1786 helix: 0.86 (0.18), residues: 814 sheet: -1.59 (0.32), residues: 217 loop : -1.62 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 572 TYR 0.017 0.002 TYR A 305 PHE 0.022 0.002 PHE C 420 TRP 0.013 0.002 TRP B 580 HIS 0.007 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00624 (15165) covalent geometry : angle 0.62335 (20563) hydrogen bonds : bond 0.04706 ( 693) hydrogen bonds : angle 4.79589 ( 1919) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 609 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7932 (mmtt) REVERT: B 311 GLU cc_start: 0.8370 (mp0) cc_final: 0.7997 (mp0) REVERT: B 522 ASP cc_start: 0.7471 (m-30) cc_final: 0.7063 (m-30) REVERT: B 523 MET cc_start: 0.8375 (tpp) cc_final: 0.7838 (tpt) REVERT: B 534 MET cc_start: 0.9048 (ttt) cc_final: 0.8779 (ttt) REVERT: C 72 GLU cc_start: 0.8717 (mp0) cc_final: 0.8513 (mp0) REVERT: C 180 GLU cc_start: 0.8462 (tp30) cc_final: 0.8126 (mp0) REVERT: C 206 MET cc_start: 0.8554 (mmm) cc_final: 0.8309 (mmm) REVERT: C 463 ILE cc_start: 0.1825 (OUTLIER) cc_final: 0.1403 (mt) REVERT: C 525 GLU cc_start: 0.8813 (pm20) cc_final: 0.8285 (mp0) outliers start: 30 outliers final: 24 residues processed: 180 average time/residue: 0.2391 time to fit residues: 67.7217 Evaluate side-chains 179 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 527 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 28 optimal weight: 3.9990 chunk 137 optimal weight: 0.0170 chunk 162 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 86 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 1.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.102600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.080075 restraints weight = 122170.308| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.61 r_work: 0.3341 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15165 Z= 0.126 Angle : 0.531 6.403 20563 Z= 0.280 Chirality : 0.037 0.150 2286 Planarity : 0.004 0.046 2571 Dihedral : 10.190 81.322 2309 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.81 % Favored : 96.08 % Rotamer: Outliers : 1.26 % Allowed : 12.08 % Favored : 86.67 % 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: -0.31 (0.19), residues: 1786 helix: 1.25 (0.18), residues: 811 sheet: -1.37 (0.33), residues: 216 loop : -1.46 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 287 TYR 0.016 0.002 TYR A 305 PHE 0.011 0.001 PHE C 119 TRP 0.016 0.001 TRP A 368 HIS 0.004 0.001 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00279 (15165) covalent geometry : angle 0.53088 (20563) hydrogen bonds : bond 0.03880 ( 693) hydrogen bonds : angle 4.34782 ( 1919) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 MET cc_start: 0.7653 (mmm) cc_final: 0.7373 (mmm) REVERT: A 656 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: B 522 ASP cc_start: 0.7566 (m-30) cc_final: 0.7135 (m-30) REVERT: B 523 MET cc_start: 0.8291 (tpp) cc_final: 0.7814 (tpt) REVERT: C 87 ASP cc_start: 0.8332 (t0) cc_final: 0.8087 (t0) REVERT: C 180 GLU cc_start: 0.8430 (tp30) cc_final: 0.8110 (mp0) REVERT: C 206 MET cc_start: 0.8470 (mmm) cc_final: 0.8220 (mmm) REVERT: C 525 GLU cc_start: 0.8738 (pm20) cc_final: 0.8119 (mp0) outliers start: 20 outliers final: 17 residues processed: 174 average time/residue: 0.2341 time to fit residues: 64.9048 Evaluate side-chains 171 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 527 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 36 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 69 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 157 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.100482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.077900 restraints weight = 124297.142| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 3.63 r_work: 0.3295 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15165 Z= 0.226 Angle : 0.576 6.598 20563 Z= 0.309 Chirality : 0.039 0.142 2286 Planarity : 0.004 0.048 2571 Dihedral : 10.289 81.844 2309 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.38 % Favored : 94.51 % Rotamer: Outliers : 1.64 % Allowed : 12.45 % Favored : 85.91 % 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: -0.44 (0.20), residues: 1786 helix: 1.12 (0.18), residues: 811 sheet: -1.36 (0.33), residues: 219 loop : -1.52 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 287 TYR 0.012 0.002 TYR A 445 PHE 0.016 0.001 PHE A 520 TRP 0.013 0.001 TRP A 368 HIS 0.005 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00498 (15165) covalent geometry : angle 0.57618 (20563) hydrogen bonds : bond 0.04234 ( 693) hydrogen bonds : angle 4.54660 ( 1919) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 169 ASP cc_start: 0.8567 (m-30) cc_final: 0.8257 (m-30) REVERT: B 522 ASP cc_start: 0.7587 (m-30) cc_final: 0.7150 (m-30) REVERT: B 523 MET cc_start: 0.8353 (tpp) cc_final: 0.7851 (tpt) REVERT: C 180 GLU cc_start: 0.8435 (tp30) cc_final: 0.8131 (mp0) REVERT: C 206 MET cc_start: 0.8532 (mmm) cc_final: 0.8203 (mmm) REVERT: C 463 ILE cc_start: 0.2082 (OUTLIER) cc_final: 0.1600 (mt) REVERT: C 525 GLU cc_start: 0.8782 (pm20) cc_final: 0.8121 (mp0) outliers start: 26 outliers final: 22 residues processed: 172 average time/residue: 0.2239 time to fit residues: 61.3208 Evaluate side-chains 176 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 527 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 158 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 159 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.102903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.080305 restraints weight = 122458.462| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 3.68 r_work: 0.3347 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15165 Z= 0.106 Angle : 0.525 6.996 20563 Z= 0.274 Chirality : 0.037 0.151 2286 Planarity : 0.004 0.046 2571 Dihedral : 10.082 81.412 2309 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.75 % Favored : 96.14 % Rotamer: Outliers : 1.38 % Allowed : 12.52 % Favored : 86.10 % 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: -0.03 (0.20), residues: 1786 helix: 1.48 (0.19), residues: 811 sheet: -1.15 (0.32), residues: 226 loop : -1.34 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.012 0.001 TYR A 305 PHE 0.012 0.001 PHE C 119 TRP 0.017 0.001 TRP A 368 HIS 0.002 0.001 HIS B 664 Details of bonding type rmsd covalent geometry : bond 0.00236 (15165) covalent geometry : angle 0.52464 (20563) hydrogen bonds : bond 0.03592 ( 693) hydrogen bonds : angle 4.15595 ( 1919) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 MET cc_start: 0.7700 (mmm) cc_final: 0.7471 (mmm) REVERT: A 656 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: B 169 ASP cc_start: 0.8530 (m-30) cc_final: 0.8203 (m-30) REVERT: B 372 MET cc_start: 0.8262 (ttm) cc_final: 0.8020 (ttm) REVERT: B 522 ASP cc_start: 0.7685 (m-30) cc_final: 0.7286 (m-30) REVERT: B 523 MET cc_start: 0.8223 (tpp) cc_final: 0.7765 (tpt) REVERT: B 696 PHE cc_start: 0.8326 (t80) cc_final: 0.8005 (t80) REVERT: C 87 ASP cc_start: 0.8369 (t0) cc_final: 0.8084 (t0) REVERT: C 180 GLU cc_start: 0.8420 (tp30) cc_final: 0.8104 (mp0) REVERT: C 525 GLU cc_start: 0.8712 (pm20) cc_final: 0.8013 (mp0) outliers start: 22 outliers final: 19 residues processed: 172 average time/residue: 0.2164 time to fit residues: 59.9081 Evaluate side-chains 177 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 527 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 165 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.100580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.078125 restraints weight = 124089.341| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 3.65 r_work: 0.3299 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 15165 Z= 0.216 Angle : 0.567 7.489 20563 Z= 0.302 Chirality : 0.039 0.139 2286 Planarity : 0.004 0.047 2571 Dihedral : 10.180 81.918 2309 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.43 % Favored : 94.46 % Rotamer: Outliers : 1.32 % Allowed : 12.89 % Favored : 85.79 % 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: -0.22 (0.20), residues: 1786 helix: 1.30 (0.19), residues: 811 sheet: -1.22 (0.33), residues: 221 loop : -1.41 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 663 TYR 0.011 0.002 TYR A 445 PHE 0.016 0.001 PHE A 520 TRP 0.011 0.001 TRP A 368 HIS 0.004 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00478 (15165) covalent geometry : angle 0.56740 (20563) hydrogen bonds : bond 0.04070 ( 693) hydrogen bonds : angle 4.42374 ( 1919) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 548 MET cc_start: 0.7668 (mmm) cc_final: 0.7465 (mmm) REVERT: B 169 ASP cc_start: 0.8537 (m-30) cc_final: 0.8190 (m-30) REVERT: B 372 MET cc_start: 0.8539 (ttm) cc_final: 0.8287 (ttm) REVERT: B 522 ASP cc_start: 0.7670 (m-30) cc_final: 0.7232 (m-30) REVERT: B 523 MET cc_start: 0.8338 (tpp) cc_final: 0.7847 (tpt) REVERT: C 87 ASP cc_start: 0.8333 (t0) cc_final: 0.8097 (t0) REVERT: C 180 GLU cc_start: 0.8444 (tp30) cc_final: 0.8113 (mp0) REVERT: C 525 GLU cc_start: 0.8728 (pm20) cc_final: 0.8177 (mp0) outliers start: 21 outliers final: 21 residues processed: 171 average time/residue: 0.2189 time to fit residues: 60.5700 Evaluate side-chains 174 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 527 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 147 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 152 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.102520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.080021 restraints weight = 122179.418| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.66 r_work: 0.3343 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15165 Z= 0.115 Angle : 0.530 8.543 20563 Z= 0.276 Chirality : 0.037 0.150 2286 Planarity : 0.004 0.046 2571 Dihedral : 10.043 81.454 2309 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.92 % Favored : 95.97 % Rotamer: Outliers : 1.26 % Allowed : 12.96 % Favored : 85.79 % 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: 0.06 (0.20), residues: 1786 helix: 1.55 (0.19), residues: 811 sheet: -1.08 (0.33), residues: 228 loop : -1.29 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 287 TYR 0.012 0.001 TYR A 305 PHE 0.011 0.001 PHE C 119 TRP 0.016 0.001 TRP A 368 HIS 0.002 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00258 (15165) covalent geometry : angle 0.52972 (20563) hydrogen bonds : bond 0.03578 ( 693) hydrogen bonds : angle 4.12520 ( 1919) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3572 Ramachandran restraints generated. 1786 Oldfield, 0 Emsley, 1786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 404 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue THR 271 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue VAL 338 is missing expected H atoms. Skipping. Residue VAL 344 is missing expected H atoms. Skipping. Residue ILE 382 is missing expected H atoms. Skipping. Residue ILE 394 is missing expected H atoms. Skipping. Residue ILE 463 is missing expected H atoms. Skipping. Residue VAL 478 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 656 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: B 169 ASP cc_start: 0.8526 (m-30) cc_final: 0.8179 (m-30) REVERT: B 372 MET cc_start: 0.8495 (ttm) cc_final: 0.8251 (ttm) REVERT: B 522 ASP cc_start: 0.7696 (m-30) cc_final: 0.7269 (m-30) REVERT: B 523 MET cc_start: 0.8211 (tpp) cc_final: 0.7751 (tpt) REVERT: C 87 ASP cc_start: 0.8302 (t0) cc_final: 0.8014 (t0) REVERT: C 180 GLU cc_start: 0.8433 (tp30) cc_final: 0.8123 (mp0) REVERT: C 243 MET cc_start: 0.8200 (tpp) cc_final: 0.7811 (mmt) REVERT: C 525 GLU cc_start: 0.8716 (pm20) cc_final: 0.8127 (mp0) outliers start: 20 outliers final: 18 residues processed: 171 average time/residue: 0.2117 time to fit residues: 58.7604 Evaluate side-chains 176 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 649 LEU Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 400 THR Chi-restraints excluded: chain B residue 425 ASN Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 649 HIS Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 120 GLU Chi-restraints excluded: chain C residue 284 CYS Chi-restraints excluded: chain C residue 487 GLU Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 527 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 169 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 166 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.101139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.078716 restraints weight = 123700.935| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.66 r_work: 0.3312 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15165 Z= 0.171 Angle : 0.551 8.704 20563 Z= 0.290 Chirality : 0.038 0.141 2286 Planarity : 0.004 0.047 2571 Dihedral : 10.079 81.602 2309 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.10 % Favored : 94.79 % Rotamer: Outliers : 1.38 % Allowed : 12.89 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.20), residues: 1786 helix: 1.48 (0.19), residues: 811 sheet: -1.10 (0.33), residues: 228 loop : -1.30 (0.22), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 663 TYR 0.011 0.001 TYR A 445 PHE 0.013 0.001 PHE A 520 TRP 0.012 0.001 TRP A 368 HIS 0.003 0.001 HIS B 634 Details of bonding type rmsd covalent geometry : bond 0.00380 (15165) covalent geometry : angle 0.55109 (20563) hydrogen bonds : bond 0.03815 ( 693) hydrogen bonds : angle 4.25120 ( 1919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6225.40 seconds wall clock time: 106 minutes 36.83 seconds (6396.83 seconds total)