Starting phenix.real_space_refine on Sat Jul 4 00:54:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptz_17926/07_2026/8ptz_17926.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptz_17926/07_2026/8ptz_17926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ptz_17926/07_2026/8ptz_17926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptz_17926/07_2026/8ptz_17926.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ptz_17926/07_2026/8ptz_17926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptz_17926/07_2026/8ptz_17926.map" } resolution = 3.35 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= 0.001 sd= 0.018 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 78 5.49 5 Mg 2 5.21 5 S 101 5.16 5 C 10603 2.51 5 N 2985 2.21 5 O 3421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17194 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5357 Classifications: {'peptide': 685} Link IDs: {'PTRANS': 35, 'TRANS': 649} Chain breaks: 1 Chain: "B" Number of atoms: 5861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5861 Classifications: {'peptide': 741} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 710} Chain breaks: 2 Chain: "C" Number of atoms: 4296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4296 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 29, 'TRANS': 508} Chain: "X" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1593 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna2p': 16, 'rna3p': 58} Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Unusual residues: {'5AD': 1, 'A2U': 1, 'SF4': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11902 SG CYS C 99 47.793 90.167 84.419 1.00144.88 S ATOM 11977 SG CYS C 109 46.158 88.468 78.360 1.00155.95 S ATOM 12002 SG CYS C 112 45.327 84.906 83.753 1.00144.21 S Time building chain proxies: 3.02, per 1000 atoms: 0.18 Number of scatterers: 17194 At special positions: 0 Unit cell: (111.35, 152.15, 158.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 S 101 16.00 P 78 15.00 Mg 2 11.99 O 3421 8.00 N 2985 7.00 C 10603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 620.3 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 601 " pdb="FE4 SF4 C 601 " - pdb=" SG CYS C 112 " pdb="FE1 SF4 C 601 " - pdb=" SG CYS C 99 " pdb="FE3 SF4 C 601 " - pdb=" SG CYS C 109 " Number of angles added : 9 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 33 sheets defined 13.5% alpha, 27.1% beta 18 base pairs and 38 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 669 through 677 Processing helix chain 'B' and resid 467 through 479 removed outlier: 3.712A pdb=" N VAL B 471 " --> pdb=" O PRO B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 486 Processing helix chain 'B' and resid 547 through 553 removed outlier: 3.555A pdb=" N LEU B 551 " --> pdb=" O THR B 547 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 33 removed outlier: 3.570A pdb=" N LEU C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS C 24 " --> pdb=" O GLY C 20 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU C 28 " --> pdb=" O LYS C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 45 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.639A pdb=" N ALA C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 Processing helix chain 'C' and resid 131 through 139 removed outlier: 3.755A pdb=" N ARG C 139 " --> pdb=" O MET C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 158 Processing helix chain 'C' and resid 178 through 195 Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.876A pdb=" N ARG C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 227 Processing helix chain 'C' and resid 228 through 239 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 263 through 278 removed outlier: 3.532A pdb=" N VAL C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 307 Processing helix chain 'C' and resid 326 through 335 removed outlier: 4.030A pdb=" N GLU C 330 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 331 " --> pdb=" O GLY C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 356 Processing helix chain 'C' and resid 382 through 395 Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.601A pdb=" N ILE C 411 " --> pdb=" O GLY C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.334A pdb=" N LEU C 500 " --> pdb=" O GLY C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 532 removed outlier: 3.569A pdb=" N TYR C 530 " --> pdb=" O THR C 526 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C 532 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 13 removed outlier: 7.028A pdb=" N ASP A 372 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR A 9 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA A 370 " --> pdb=" O THR A 9 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU A 11 " --> pdb=" O TYR A 368 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR A 368 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N HIS A 367 " --> pdb=" O CYS A 363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 27 removed outlier: 3.511A pdb=" N THR A 32 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN A 53 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP A 45 " --> pdb=" O VAL A 51 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N VAL A 51 " --> pdb=" O ASP A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 117 removed outlier: 4.187A pdb=" N VAL A 114 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N THR A 137 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 197 through 200 removed outlier: 3.634A pdb=" N GLN A 197 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 218 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASN A 225 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU A 230 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 245 through 246 removed outlier: 4.214A pdb=" N GLY A 276 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLU A 269 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 274 " --> pdb=" O GLU A 269 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 287 through 293 removed outlier: 7.256A pdb=" N TRP A 304 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N LEU A 292 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA A 302 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 301 " --> pdb=" O TRP A 323 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS A 317 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 318 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 378 through 379 removed outlier: 4.577A pdb=" N ASP A 378 " --> pdb=" O ALA A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 424 through 429 removed outlier: 3.554A pdb=" N GLN A 426 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASP A 443 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ILE A 448 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG A 485 " --> pdb=" O ILE A 448 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL A 450 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU A 545 " --> pdb=" O ARG A 485 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 487 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL A 547 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL A 547 " --> pdb=" O THR A 532 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR A 532 " --> pdb=" O VAL A 547 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 549 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA A 516 " --> pdb=" O HIS A 529 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N VAL A 517 " --> pdb=" O LEU A 505 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LEU A 505 " --> pdb=" O VAL A 517 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 557 through 562 removed outlier: 6.846A pdb=" N GLN A 572 " --> pdb=" O ILE A 558 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A 560 " --> pdb=" O VAL A 570 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A 570 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 569 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 609 through 615 removed outlier: 3.715A pdb=" N GLN A 609 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 641 through 647 removed outlier: 6.904A pdb=" N THR A 654 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE A 644 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 652 " --> pdb=" O PHE A 644 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 646 " --> pdb=" O PHE A 650 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N PHE A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 696 through 701 removed outlier: 7.095A pdb=" N VAL A 708 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL A 700 " --> pdb=" O LYS A 706 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 706 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 716 " --> pdb=" O ASP C 426 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 424 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR C 435 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG C 452 " --> pdb=" O THR C 435 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 437 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N LEU C 450 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N TYR C 439 " --> pdb=" O ILE C 448 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 446 " --> pdb=" O ASP C 441 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS C 476 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU C 474 " --> pdb=" O ARG C 452 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 6 through 10 removed outlier: 6.391A pdb=" N ILE B 818 " --> pdb=" O SER B 9 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 32 through 36 removed outlier: 3.608A pdb=" N VAL B 40 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASP B 44 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL B 50 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.438A pdb=" N GLU B 93 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LEU B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 110 through 115 removed outlier: 6.564A pdb=" N ALA B 133 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL B 113 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 131 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ALA B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 167 through 169 removed outlier: 4.128A pdb=" N ARG B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN B 193 " --> pdb=" O GLN B 196 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 167 through 169 removed outlier: 4.128A pdb=" N ARG B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE B 187 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 189 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 201 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 214 through 218 removed outlier: 3.589A pdb=" N LEU B 224 " --> pdb=" O TRP B 236 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 286 through 290 removed outlier: 6.740A pdb=" N ALA B 310 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N VAL B 289 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 308 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 309 " --> pdb=" O ILE B 317 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 317 " --> pdb=" O SER B 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 295 through 297 removed outlier: 3.549A pdb=" N VAL B 300 " --> pdb=" O LYS B 297 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 344 through 348 removed outlier: 3.906A pdb=" N ASP B 346 " --> pdb=" O HIS B 359 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 396 removed outlier: 3.774A pdb=" N GLY B 407 " --> pdb=" O THR B 411 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR B 412 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG B 433 " --> pdb=" O THR B 412 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU B 414 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR B 427 " --> pdb=" O TRP B 418 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 455 removed outlier: 3.783A pdb=" N ARG B 462 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 570 through 575 removed outlier: 6.908A pdb=" N ALA B 585 " --> pdb=" O PHE B 571 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL B 573 " --> pdb=" O ALA B 583 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA B 583 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N CYS B 575 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU B 581 " --> pdb=" O CYS B 575 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N CYS B 586 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ALA B 595 " --> pdb=" O CYS B 586 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASN B 600 " --> pdb=" O GLN B 606 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN B 606 " --> pdb=" O ASN B 600 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 621 through 622 removed outlier: 4.071A pdb=" N ALA B 621 " --> pdb=" O LEU B 630 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 630 " --> pdb=" O ALA B 621 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 641 through 643 Processing sheet with id=AD2, first strand: chain 'B' and resid 672 through 677 removed outlier: 3.587A pdb=" N ASP B 676 " --> pdb=" O PHE B 685 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 688 " --> pdb=" O LYS B 692 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS B 692 " --> pdb=" O SER B 688 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 726 through 728 removed outlier: 3.567A pdb=" N SER B 727 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU B 751 " --> pdb=" O CYS B 769 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 782 through 784 Processing sheet with id=AD5, first strand: chain 'C' and resid 88 through 93 removed outlier: 6.295A pdb=" N VAL C 165 " --> pdb=" O CYS C 215 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLY C 217 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU C 221 " --> pdb=" O VAL C 169 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 469 through 472 451 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 38 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.41: 7272 1.41 - 1.63: 10339 1.63 - 1.85: 139 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 17762 Sorted by residual: bond pdb=" C30 A2U C 603 " pdb=" C45 A2U C 603 " ideal model delta sigma weight residual 1.539 1.322 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C32 A2U C 603 " pdb=" C43 A2U C 603 " ideal model delta sigma weight residual 1.560 1.374 0.186 2.00e-02 2.50e+03 8.69e+01 bond pdb=" C36 A2U C 603 " pdb=" C42 A2U C 603 " ideal model delta sigma weight residual 1.544 1.373 0.171 2.00e-02 2.50e+03 7.32e+01 bond pdb=" C37 A2U C 603 " pdb=" N38 A2U C 603 " ideal model delta sigma weight residual 1.304 1.473 -0.169 2.00e-02 2.50e+03 7.14e+01 bond pdb=" O50 A2U C 603 " pdb=" P47 A2U C 603 " ideal model delta sigma weight residual 1.671 1.504 0.167 2.00e-02 2.50e+03 6.95e+01 ... (remaining 17757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.00: 24497 11.00 - 22.01: 7 22.01 - 33.01: 1 33.01 - 44.01: 0 44.01 - 55.01: 1 Bond angle restraints: 24506 Sorted by residual: angle pdb=" O49 A2U C 603 " pdb=" P47 A2U C 603 " pdb=" O50 A2U C 603 " ideal model delta sigma weight residual 54.49 109.50 -55.01 3.00e+00 1.11e-01 3.36e+02 angle pdb=" N33 A2U C 603 " pdb=" C32 A2U C 603 " pdb=" O31 A2U C 603 " ideal model delta sigma weight residual 105.69 129.22 -23.53 3.00e+00 1.11e-01 6.15e+01 angle pdb=" O48 A2U C 603 " pdb=" P47 A2U C 603 " pdb=" O49 A2U C 603 " ideal model delta sigma weight residual 130.45 109.56 20.89 3.00e+00 1.11e-01 4.85e+01 angle pdb=" O48 A2U C 603 " pdb=" P47 A2U C 603 " pdb=" O50 A2U C 603 " ideal model delta sigma weight residual 128.85 109.42 19.43 3.00e+00 1.11e-01 4.20e+01 angle pdb=" O24 A2U C 603 " pdb=" P25 A2U C 603 " pdb=" O28 A2U C 603 " ideal model delta sigma weight residual 95.67 111.32 -15.65 3.00e+00 1.11e-01 2.72e+01 ... (remaining 24501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.78: 10072 29.78 - 59.57: 519 59.57 - 89.35: 114 89.35 - 119.13: 2 119.13 - 148.91: 1 Dihedral angle restraints: 10708 sinusoidal: 5028 harmonic: 5680 Sorted by residual: dihedral pdb=" O4' U X 20 " pdb=" C1' U X 20 " pdb=" N1 U X 20 " pdb=" C2 U X 20 " ideal model delta sinusoidal sigma weight residual -128.00 20.91 -148.91 1 1.70e+01 3.46e-03 6.17e+01 dihedral pdb=" CA ASN C 291 " pdb=" C ASN C 291 " pdb=" N VAL C 292 " pdb=" CA VAL C 292 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ARG B 17 " pdb=" C ARG B 17 " pdb=" N VAL B 18 " pdb=" CA VAL B 18 " ideal model delta harmonic sigma weight residual -180.00 -154.27 -25.73 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 10705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2687 0.112 - 0.224: 89 0.224 - 0.335: 0 0.335 - 0.447: 7 0.447 - 0.559: 13 Chirality restraints: 2796 Sorted by residual: chirality pdb=" C45 A2U C 603 " pdb=" C30 A2U C 603 " pdb=" C43 A2U C 603 " pdb=" O46 A2U C 603 " both_signs ideal model delta sigma weight residual False 2.95 2.39 0.56 2.00e-01 2.50e+01 7.82e+00 chirality pdb=" P C X 70 " pdb=" OP1 C X 70 " pdb=" OP2 C X 70 " pdb=" O5' C X 70 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.51 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" P G X 2 " pdb=" OP1 G X 2 " pdb=" OP2 G X 2 " pdb=" O5' G X 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.44e+00 ... (remaining 2793 not shown) Planarity restraints: 2856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 65 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.07e+00 pdb=" N PRO C 66 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 66 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 66 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 677 " 0.014 2.00e-02 2.50e+03 1.34e-02 4.50e+00 pdb=" CG TRP B 677 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 677 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 677 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 677 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 677 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 677 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 677 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 677 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 677 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 733 " -0.028 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B 734 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 734 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 734 " -0.024 5.00e-02 4.00e+02 ... (remaining 2853 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 104 2.51 - 3.11: 12119 3.11 - 3.70: 26530 3.70 - 4.30: 36686 4.30 - 4.90: 60065 Nonbonded interactions: 135504 Sorted by model distance: nonbonded pdb=" O2' G X 12 " pdb=" OP1 U X 13 " model vdw 1.910 3.040 nonbonded pdb=" OP2 G X 12 " pdb="MG MG X 102 " model vdw 2.039 2.170 nonbonded pdb=" OP1 A X 37 " pdb="MG MG X 101 " model vdw 2.087 2.170 nonbonded pdb=" OG SER C 341 " pdb=" OD2 ASP C 344 " model vdw 2.202 3.040 nonbonded pdb=" OD2 ASP A 387 " pdb=" OG SER A 436 " model vdw 2.207 3.040 ... (remaining 135499 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: 8.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 17.190 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 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 : 0.006 0.217 17765 Z= 0.297 Angle : 0.878 55.013 24515 Z= 0.461 Chirality : 0.061 0.559 2796 Planarity : 0.005 0.075 2856 Dihedral : 17.448 148.915 7036 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 0.23 % Allowed : 0.64 % Favored : 99.13 % 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: -2.31 (0.19), residues: 1952 helix: -0.03 (0.34), residues: 238 sheet: -1.32 (0.22), residues: 564 loop : -2.04 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 602 TYR 0.016 0.001 TYR B 345 PHE 0.015 0.001 PHE C 145 TRP 0.033 0.002 TRP B 677 HIS 0.008 0.001 HIS B 814 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.30 (17762) covalent geometry : angle 0.86689 / 0.46 (24506) hydrogen bonds : bond 0.19176 / 12.80 ( 489) hydrogen bonds : angle 7.92043 / 5.41 ( 1341) metal coordination : bond 0.00912 / 0.46 ( 3) metal coordination : angle 7.26202 / 3.04 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 368 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 ASP cc_start: 0.7591 (t0) cc_final: 0.7293 (t0) REVERT: A 74 VAL cc_start: 0.7305 (t) cc_final: 0.6853 (p) REVERT: A 120 ASP cc_start: 0.6754 (p0) cc_final: 0.6530 (p0) REVERT: A 136 MET cc_start: 0.6424 (mmm) cc_final: 0.6103 (mmm) REVERT: A 147 GLN cc_start: 0.7818 (mt0) cc_final: 0.7537 (mt0) REVERT: A 271 ASN cc_start: 0.7847 (t0) cc_final: 0.7564 (t0) REVERT: A 346 ILE cc_start: 0.6456 (mm) cc_final: 0.6043 (mm) REVERT: A 358 ARG cc_start: 0.7561 (ttm-80) cc_final: 0.7107 (ttt90) REVERT: A 361 VAL cc_start: 0.7029 (t) cc_final: 0.6801 (t) REVERT: A 367 HIS cc_start: 0.5893 (t-170) cc_final: 0.5334 (t-170) REVERT: A 389 SER cc_start: 0.8366 (m) cc_final: 0.7801 (p) REVERT: A 429 PHE cc_start: 0.8128 (m-80) cc_final: 0.7797 (m-80) REVERT: A 554 ASP cc_start: 0.6918 (t0) cc_final: 0.6511 (t0) REVERT: A 570 VAL cc_start: 0.7761 (t) cc_final: 0.7483 (m) REVERT: A 601 VAL cc_start: 0.7441 (t) cc_final: 0.7134 (m) REVERT: A 611 GLU cc_start: 0.6573 (mp0) cc_final: 0.6324 (mp0) REVERT: A 635 ILE cc_start: 0.8123 (tt) cc_final: 0.7688 (pt) REVERT: A 695 SER cc_start: 0.8375 (m) cc_final: 0.8023 (p) REVERT: B 1 MET cc_start: 0.6754 (mtt) cc_final: 0.6551 (mtt) REVERT: B 31 LEU cc_start: 0.7753 (mt) cc_final: 0.7511 (mt) REVERT: B 91 GLU cc_start: 0.7336 (tp30) cc_final: 0.6187 (mt-10) REVERT: B 139 VAL cc_start: 0.7812 (t) cc_final: 0.7441 (p) REVERT: B 378 TRP cc_start: 0.6060 (m100) cc_final: 0.5627 (m100) REVERT: B 387 HIS cc_start: 0.6758 (m-70) cc_final: 0.5884 (m-70) REVERT: B 401 GLU cc_start: 0.5895 (mp0) cc_final: 0.5439 (mp0) REVERT: B 555 THR cc_start: 0.6672 (m) cc_final: 0.6355 (p) REVERT: B 597 ILE cc_start: 0.7243 (mt) cc_final: 0.7021 (mt) REVERT: B 716 VAL cc_start: 0.7221 (m) cc_final: 0.6956 (p) REVERT: B 727 SER cc_start: 0.7686 (t) cc_final: 0.7378 (m) REVERT: B 784 LYS cc_start: 0.7711 (tttp) cc_final: 0.7495 (mtpt) REVERT: B 788 LYS cc_start: 0.6450 (tttt) cc_final: 0.5986 (tttm) REVERT: B 804 TRP cc_start: 0.6836 (m100) cc_final: 0.6473 (m100) REVERT: B 824 CYS cc_start: 0.6936 (t) cc_final: 0.6631 (t) REVERT: C 42 LYS cc_start: 0.4973 (mtmt) cc_final: 0.4346 (mtmt) REVERT: C 107 ASN cc_start: 0.6416 (t0) cc_final: 0.6192 (t0) REVERT: C 236 LEU cc_start: 0.6123 (mt) cc_final: 0.5811 (mt) REVERT: C 259 ASN cc_start: 0.7575 (t0) cc_final: 0.7172 (t0) REVERT: C 280 LYS cc_start: 0.6962 (mtmm) cc_final: 0.6625 (mtmm) REVERT: C 288 ASP cc_start: 0.7026 (t0) cc_final: 0.6625 (t70) REVERT: C 321 LEU cc_start: 0.7210 (mt) cc_final: 0.6937 (mt) REVERT: C 337 TYR cc_start: 0.7663 (t80) cc_final: 0.7144 (t80) REVERT: C 361 ARG cc_start: 0.7863 (ttt90) cc_final: 0.7545 (ttt90) REVERT: C 373 LEU cc_start: 0.7685 (mt) cc_final: 0.7371 (mp) REVERT: C 406 VAL cc_start: 0.7531 (t) cc_final: 0.7329 (t) REVERT: C 411 ILE cc_start: 0.7369 (pt) cc_final: 0.7145 (mp) REVERT: C 427 TYR cc_start: 0.6403 (m-80) cc_final: 0.5817 (m-80) REVERT: C 480 SER cc_start: 0.7672 (m) cc_final: 0.7071 (t) outliers start: 4 outliers final: 1 residues processed: 370 average time/residue: 0.1262 time to fit residues: 69.2556 Evaluate side-chains 316 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 315 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 376 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.0050 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.0050 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 489 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 550 HIS ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.163295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.136192 restraints weight = 25822.639| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.22 r_work: 0.3682 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3528 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17765 Z= 0.165 Angle : 0.653 12.817 24515 Z= 0.346 Chirality : 0.047 0.230 2796 Planarity : 0.006 0.064 2856 Dihedral : 16.952 150.599 3367 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 1.22 % Allowed : 9.34 % Favored : 89.44 % 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: -2.26 (0.19), residues: 1952 helix: -0.03 (0.32), residues: 250 sheet: -1.20 (0.21), residues: 633 loop : -2.08 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 226 TYR 0.016 0.002 TYR C 127 PHE 0.031 0.002 PHE C 304 TRP 0.022 0.002 TRP C 433 HIS 0.010 0.001 HIS B 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (17762) covalent geometry : angle 0.64160 / 0.35 (24506) hydrogen bonds : bond 0.05748 / 3.73 ( 489) hydrogen bonds : angle 5.93019 / 4.03 ( 1341) metal coordination : bond 0.02997 / 1.50 ( 3) metal coordination : angle 6.38608 / 2.80 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 314 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6715 (mm-30) REVERT: A 120 ASP cc_start: 0.6979 (p0) cc_final: 0.6763 (p0) REVERT: A 231 GLN cc_start: 0.7854 (mm110) cc_final: 0.7581 (mm-40) REVERT: A 271 ASN cc_start: 0.7987 (t0) cc_final: 0.7748 (t0) REVERT: A 346 ILE cc_start: 0.6979 (mm) cc_final: 0.6486 (mm) REVERT: A 348 SER cc_start: 0.7833 (t) cc_final: 0.7480 (m) REVERT: A 358 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7609 (ttt90) REVERT: A 389 SER cc_start: 0.8295 (m) cc_final: 0.8044 (p) REVERT: A 554 ASP cc_start: 0.7463 (t0) cc_final: 0.7101 (t0) REVERT: A 635 ILE cc_start: 0.8775 (tt) cc_final: 0.8480 (pt) REVERT: B 18 VAL cc_start: 0.8427 (p) cc_final: 0.8188 (m) REVERT: B 91 GLU cc_start: 0.7920 (tp30) cc_final: 0.7369 (mt-10) REVERT: B 139 VAL cc_start: 0.8646 (t) cc_final: 0.8364 (p) REVERT: B 387 HIS cc_start: 0.7361 (m-70) cc_final: 0.6814 (m-70) REVERT: B 401 GLU cc_start: 0.6748 (mp0) cc_final: 0.6467 (mp0) REVERT: B 406 VAL cc_start: 0.8182 (t) cc_final: 0.7936 (p) REVERT: B 547 THR cc_start: 0.4200 (OUTLIER) cc_final: 0.3233 (p) REVERT: B 716 VAL cc_start: 0.7779 (m) cc_final: 0.7556 (p) REVERT: B 727 SER cc_start: 0.8495 (t) cc_final: 0.8013 (m) REVERT: B 804 TRP cc_start: 0.7676 (m100) cc_final: 0.7023 (m100) REVERT: B 824 CYS cc_start: 0.7211 (t) cc_final: 0.6889 (t) REVERT: C 16 MET cc_start: 0.6515 (ppp) cc_final: 0.6302 (ppp) REVERT: C 42 LYS cc_start: 0.7142 (mtmt) cc_final: 0.6415 (mtpt) REVERT: C 107 ASN cc_start: 0.7472 (t0) cc_final: 0.7233 (t0) REVERT: C 135 MET cc_start: 0.7516 (mpp) cc_final: 0.7223 (mtm) REVERT: C 236 LEU cc_start: 0.6988 (mt) cc_final: 0.6695 (mt) REVERT: C 259 ASN cc_start: 0.8116 (t0) cc_final: 0.7901 (t0) REVERT: C 288 ASP cc_start: 0.7614 (t0) cc_final: 0.7257 (t70) REVERT: C 321 LEU cc_start: 0.7933 (mt) cc_final: 0.7632 (mt) REVERT: C 337 TYR cc_start: 0.8314 (t80) cc_final: 0.7772 (t80) REVERT: C 361 ARG cc_start: 0.8024 (ttt90) cc_final: 0.7821 (ttt90) REVERT: C 388 LEU cc_start: 0.7757 (mm) cc_final: 0.7552 (mm) REVERT: C 411 ILE cc_start: 0.7973 (pt) cc_final: 0.7504 (mp) REVERT: C 480 SER cc_start: 0.8023 (m) cc_final: 0.7738 (t) outliers start: 21 outliers final: 15 residues processed: 324 average time/residue: 0.1230 time to fit residues: 60.3492 Evaluate side-chains 317 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 301 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain C residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 87 optimal weight: 0.0020 chunk 20 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 178 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 192 optimal weight: 0.0870 chunk 97 optimal weight: 0.0370 chunk 73 optimal weight: 0.0670 chunk 107 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 0.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 HIS A 489 GLN A 661 GLN B 16 ASN B 156 ASN B 284 ASN B 302 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.166381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.138859 restraints weight = 25972.115| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.32 r_work: 0.3724 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 17765 Z= 0.111 Angle : 0.583 13.205 24515 Z= 0.306 Chirality : 0.044 0.210 2796 Planarity : 0.005 0.055 2856 Dihedral : 16.880 148.919 3367 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.03 % Allowed : 11.95 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.18), residues: 1952 helix: 0.08 (0.32), residues: 258 sheet: -1.06 (0.21), residues: 610 loop : -2.13 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 195 TYR 0.011 0.001 TYR C 529 PHE 0.032 0.001 PHE C 304 TRP 0.018 0.001 TRP A 224 HIS 0.007 0.001 HIS A 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (17762) covalent geometry : angle 0.56675 / 0.31 (24506) hydrogen bonds : bond 0.04659 / 3.01 ( 489) hydrogen bonds : angle 5.44790 / 3.67 ( 1341) metal coordination : bond 0.01212 / 0.61 ( 3) metal coordination : angle 7.17673 / 3.31 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 333 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 120 ASP cc_start: 0.6977 (p0) cc_final: 0.6728 (p0) REVERT: A 271 ASN cc_start: 0.7967 (t0) cc_final: 0.7734 (t0) REVERT: A 346 ILE cc_start: 0.6657 (mm) cc_final: 0.6206 (mm) REVERT: A 348 SER cc_start: 0.7747 (t) cc_final: 0.7435 (p) REVERT: A 358 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7652 (ttt90) REVERT: A 389 SER cc_start: 0.8323 (m) cc_final: 0.8017 (p) REVERT: A 554 ASP cc_start: 0.7498 (t0) cc_final: 0.7148 (t0) REVERT: A 635 ILE cc_start: 0.8710 (tt) cc_final: 0.8407 (pt) REVERT: A 695 SER cc_start: 0.8688 (m) cc_final: 0.8363 (p) REVERT: B 18 VAL cc_start: 0.8416 (p) cc_final: 0.8176 (m) REVERT: B 91 GLU cc_start: 0.7844 (tp30) cc_final: 0.7251 (mt-10) REVERT: B 139 VAL cc_start: 0.8635 (t) cc_final: 0.8316 (p) REVERT: B 385 SER cc_start: 0.8456 (p) cc_final: 0.8015 (m) REVERT: B 387 HIS cc_start: 0.7327 (m-70) cc_final: 0.6756 (m-70) REVERT: B 406 VAL cc_start: 0.8079 (t) cc_final: 0.7864 (p) REVERT: B 716 VAL cc_start: 0.7772 (m) cc_final: 0.7571 (p) REVERT: B 727 SER cc_start: 0.8409 (t) cc_final: 0.7952 (m) REVERT: B 804 TRP cc_start: 0.7588 (m100) cc_final: 0.6892 (m100) REVERT: B 824 CYS cc_start: 0.7116 (t) cc_final: 0.6882 (t) REVERT: C 16 MET cc_start: 0.6501 (ppp) cc_final: 0.6175 (ppp) REVERT: C 42 LYS cc_start: 0.7139 (mtmt) cc_final: 0.6508 (mtpt) REVERT: C 107 ASN cc_start: 0.7431 (t0) cc_final: 0.7186 (t0) REVERT: C 236 LEU cc_start: 0.6838 (mt) cc_final: 0.6529 (mt) REVERT: C 259 ASN cc_start: 0.8053 (t0) cc_final: 0.7832 (t0) REVERT: C 288 ASP cc_start: 0.7460 (t0) cc_final: 0.7023 (t70) REVERT: C 321 LEU cc_start: 0.7861 (mt) cc_final: 0.7516 (mt) REVERT: C 411 ILE cc_start: 0.7905 (pt) cc_final: 0.7474 (mp) REVERT: C 440 GLU cc_start: 0.7590 (pt0) cc_final: 0.7144 (pt0) REVERT: C 480 SER cc_start: 0.7860 (m) cc_final: 0.7614 (t) outliers start: 35 outliers final: 23 residues processed: 345 average time/residue: 0.1196 time to fit residues: 62.7812 Evaluate side-chains 340 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 317 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 528 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 124 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 194 optimal weight: 0.9990 chunk 114 optimal weight: 0.4980 chunk 174 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.161199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133733 restraints weight = 25827.971| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.23 r_work: 0.3653 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 17765 Z= 0.247 Angle : 0.694 14.905 24515 Z= 0.366 Chirality : 0.048 0.207 2796 Planarity : 0.006 0.058 2856 Dihedral : 16.912 148.988 3367 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.30 % Favored : 89.65 % Rotamer: Outliers : 2.96 % Allowed : 14.27 % Favored : 82.77 % 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: -2.34 (0.18), residues: 1952 helix: -0.31 (0.31), residues: 251 sheet: -1.13 (0.21), residues: 634 loop : -2.17 (0.18), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 449 TYR 0.020 0.002 TYR A 416 PHE 0.038 0.003 PHE A 24 TRP 0.033 0.003 TRP B 378 HIS 0.009 0.002 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.25 (17762) covalent geometry : angle 0.68037 / 0.37 (24506) hydrogen bonds : bond 0.05940 / 3.98 ( 489) hydrogen bonds : angle 5.39532 / 3.65 ( 1341) metal coordination : bond 0.01376 / 0.68 ( 3) metal coordination : angle 7.25202 / 3.83 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 337 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7840 (m) REVERT: A 120 ASP cc_start: 0.7082 (p0) cc_final: 0.6822 (p0) REVERT: A 210 SER cc_start: 0.8006 (t) cc_final: 0.7560 (p) REVERT: A 346 ILE cc_start: 0.7101 (mm) cc_final: 0.6735 (mm) REVERT: A 358 ARG cc_start: 0.7897 (ttm-80) cc_final: 0.7581 (ttt90) REVERT: A 379 ARG cc_start: 0.7613 (ptm-80) cc_final: 0.7303 (ptm-80) REVERT: A 385 SER cc_start: 0.8463 (p) cc_final: 0.8262 (m) REVERT: A 389 SER cc_start: 0.8310 (m) cc_final: 0.8044 (p) REVERT: A 484 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7678 (mmmt) REVERT: A 554 ASP cc_start: 0.7519 (t0) cc_final: 0.7140 (t0) REVERT: A 601 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.7194 (m) REVERT: A 635 ILE cc_start: 0.8758 (tt) cc_final: 0.8476 (pt) REVERT: B 23 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7714 (m-40) REVERT: B 91 GLU cc_start: 0.7942 (tp30) cc_final: 0.7507 (mt-10) REVERT: B 139 VAL cc_start: 0.8615 (t) cc_final: 0.8316 (p) REVERT: B 387 HIS cc_start: 0.7417 (m-70) cc_final: 0.6652 (m-70) REVERT: B 406 VAL cc_start: 0.8401 (t) cc_final: 0.8150 (p) REVERT: B 408 THR cc_start: 0.8133 (m) cc_final: 0.7850 (t) REVERT: B 442 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7646 (mttt) REVERT: B 716 VAL cc_start: 0.7837 (m) cc_final: 0.7601 (p) REVERT: B 727 SER cc_start: 0.8484 (t) cc_final: 0.8064 (m) REVERT: B 804 TRP cc_start: 0.7707 (m100) cc_final: 0.7051 (m100) REVERT: C 16 MET cc_start: 0.6646 (ppp) cc_final: 0.6383 (ppp) REVERT: C 42 LYS cc_start: 0.7248 (mtmt) cc_final: 0.6439 (mtpt) REVERT: C 107 ASN cc_start: 0.7451 (t0) cc_final: 0.7203 (t0) REVERT: C 236 LEU cc_start: 0.7088 (mt) cc_final: 0.6855 (mt) REVERT: C 256 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8063 (ttp80) REVERT: C 259 ASN cc_start: 0.8103 (t0) cc_final: 0.7885 (t0) REVERT: C 361 ARG cc_start: 0.8100 (ttt90) cc_final: 0.7891 (ttt90) REVERT: C 411 ILE cc_start: 0.7994 (pt) cc_final: 0.7666 (mt) REVERT: C 427 TYR cc_start: 0.6203 (m-80) cc_final: 0.5899 (m-80) REVERT: C 480 SER cc_start: 0.8173 (m) cc_final: 0.7862 (t) outliers start: 51 outliers final: 39 residues processed: 364 average time/residue: 0.1177 time to fit residues: 65.3926 Evaluate side-chains 361 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 319 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 785 LEU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 526 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 49 optimal weight: 1.9990 chunk 170 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 146 optimal weight: 0.9990 chunk 153 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 103 optimal weight: 0.0770 chunk 139 optimal weight: 0.7980 chunk 102 optimal weight: 0.1980 chunk 144 optimal weight: 5.9990 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 65 GLN B 89 HIS B 114 HIS B 188 HIS B 370 GLN B 561 GLN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.163853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136229 restraints weight = 25478.775| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.31 r_work: 0.3685 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17765 Z= 0.126 Angle : 0.609 15.610 24515 Z= 0.318 Chirality : 0.044 0.195 2796 Planarity : 0.005 0.063 2856 Dihedral : 16.867 149.111 3367 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 2.67 % Allowed : 16.07 % Favored : 81.26 % 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: -2.21 (0.18), residues: 1952 helix: -0.13 (0.31), residues: 253 sheet: -1.00 (0.21), residues: 637 loop : -2.15 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 256 TYR 0.015 0.001 TYR A 416 PHE 0.023 0.002 PHE C 304 TRP 0.054 0.002 TRP B 378 HIS 0.005 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (17762) covalent geometry : angle 0.59135 / 0.32 (24506) hydrogen bonds : bond 0.04747 / 3.14 ( 489) hydrogen bonds : angle 5.20595 / 3.53 ( 1341) metal coordination : bond 0.01101 / 0.56 ( 3) metal coordination : angle 7.68409 / 3.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 331 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7640 (m-30) cc_final: 0.7322 (p0) REVERT: A 33 VAL cc_start: 0.8038 (OUTLIER) cc_final: 0.7730 (m) REVERT: A 120 ASP cc_start: 0.7135 (p0) cc_final: 0.6834 (p0) REVERT: A 210 SER cc_start: 0.8043 (t) cc_final: 0.7587 (p) REVERT: A 343 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.6525 (tptt) REVERT: A 346 ILE cc_start: 0.6798 (mm) cc_final: 0.6386 (mm) REVERT: A 358 ARG cc_start: 0.7941 (ttm-80) cc_final: 0.7653 (ttm170) REVERT: A 367 HIS cc_start: 0.6076 (t-170) cc_final: 0.5853 (t-170) REVERT: A 379 ARG cc_start: 0.7568 (ptm-80) cc_final: 0.7242 (ptm-80) REVERT: A 389 SER cc_start: 0.8280 (m) cc_final: 0.7950 (p) REVERT: A 484 LYS cc_start: 0.8015 (mmmt) cc_final: 0.7639 (mmmt) REVERT: A 554 ASP cc_start: 0.7484 (t0) cc_final: 0.7107 (t0) REVERT: A 635 ILE cc_start: 0.8705 (tt) cc_final: 0.8416 (pt) REVERT: B 23 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7715 (m-40) REVERT: B 32 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7475 (tp) REVERT: B 67 ILE cc_start: 0.8236 (mt) cc_final: 0.8033 (mt) REVERT: B 91 GLU cc_start: 0.7903 (tp30) cc_final: 0.7436 (mt-10) REVERT: B 139 VAL cc_start: 0.8570 (t) cc_final: 0.8272 (p) REVERT: B 387 HIS cc_start: 0.7345 (m-70) cc_final: 0.6705 (m-70) REVERT: B 401 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: B 406 VAL cc_start: 0.8276 (t) cc_final: 0.8014 (p) REVERT: B 408 THR cc_start: 0.8102 (m) cc_final: 0.7814 (t) REVERT: B 442 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7686 (mttt) REVERT: B 716 VAL cc_start: 0.7879 (m) cc_final: 0.7642 (p) REVERT: B 727 SER cc_start: 0.8486 (t) cc_final: 0.8023 (m) REVERT: B 804 TRP cc_start: 0.7677 (m100) cc_final: 0.7021 (m100) REVERT: C 16 MET cc_start: 0.6634 (ppp) cc_final: 0.6365 (ppp) REVERT: C 41 VAL cc_start: 0.7709 (m) cc_final: 0.7369 (p) REVERT: C 107 ASN cc_start: 0.7472 (t0) cc_final: 0.7207 (t0) REVERT: C 236 LEU cc_start: 0.6918 (mt) cc_final: 0.6675 (mt) REVERT: C 256 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8116 (ttp80) REVERT: C 259 ASN cc_start: 0.8055 (t0) cc_final: 0.7810 (t0) REVERT: C 288 ASP cc_start: 0.7411 (t70) cc_final: 0.7142 (t70) REVERT: C 321 LEU cc_start: 0.7856 (mp) cc_final: 0.7477 (mt) REVERT: C 337 TYR cc_start: 0.8170 (t80) cc_final: 0.7849 (t80) REVERT: C 411 ILE cc_start: 0.7936 (pt) cc_final: 0.7527 (mp) REVERT: C 427 TYR cc_start: 0.6104 (m-80) cc_final: 0.5781 (m-80) REVERT: C 440 GLU cc_start: 0.7764 (pt0) cc_final: 0.7219 (pt0) REVERT: C 480 SER cc_start: 0.7994 (m) cc_final: 0.7715 (t) outliers start: 46 outliers final: 35 residues processed: 352 average time/residue: 0.1275 time to fit residues: 68.2068 Evaluate side-chains 360 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 320 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 526 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 0.0870 chunk 128 optimal weight: 0.3980 chunk 193 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 102 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.162615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.135157 restraints weight = 25449.128| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.26 r_work: 0.3664 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17765 Z= 0.174 Angle : 0.635 18.416 24515 Z= 0.331 Chirality : 0.045 0.205 2796 Planarity : 0.005 0.070 2856 Dihedral : 16.812 149.333 3367 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.84 % Favored : 90.11 % Rotamer: Outliers : 3.13 % Allowed : 17.05 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.18), residues: 1952 helix: -0.18 (0.31), residues: 252 sheet: -0.99 (0.21), residues: 640 loop : -2.16 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 256 TYR 0.017 0.001 TYR A 416 PHE 0.026 0.002 PHE A 24 TRP 0.029 0.002 TRP B 378 HIS 0.010 0.001 HIS B 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (17762) covalent geometry : angle 0.61460 / 0.33 (24506) hydrogen bonds : bond 0.05071 / 3.38 ( 489) hydrogen bonds : angle 5.20646 / 3.54 ( 1341) metal coordination : bond 0.01334 / 0.67 ( 3) metal coordination : angle 8.39678 / 4.50 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 337 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7773 (m) REVERT: A 120 ASP cc_start: 0.7144 (p0) cc_final: 0.6844 (p0) REVERT: A 210 SER cc_start: 0.8026 (t) cc_final: 0.7595 (p) REVERT: A 343 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6441 (tptt) REVERT: A 346 ILE cc_start: 0.6850 (mm) cc_final: 0.6486 (mm) REVERT: A 358 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7629 (ttt90) REVERT: A 379 ARG cc_start: 0.7600 (ptm-80) cc_final: 0.7264 (ptm-80) REVERT: A 389 SER cc_start: 0.8274 (m) cc_final: 0.7963 (p) REVERT: A 484 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7689 (mmmt) REVERT: A 554 ASP cc_start: 0.7464 (t0) cc_final: 0.7074 (t0) REVERT: A 635 ILE cc_start: 0.8723 (tt) cc_final: 0.8425 (pt) REVERT: B 32 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7524 (tp) REVERT: B 67 ILE cc_start: 0.8273 (mt) cc_final: 0.8068 (mt) REVERT: B 91 GLU cc_start: 0.7949 (tp30) cc_final: 0.7512 (mt-10) REVERT: B 132 SER cc_start: 0.8435 (m) cc_final: 0.7802 (p) REVERT: B 139 VAL cc_start: 0.8573 (t) cc_final: 0.8278 (p) REVERT: B 387 HIS cc_start: 0.7372 (m-70) cc_final: 0.6710 (m-70) REVERT: B 401 GLU cc_start: 0.7385 (mp0) cc_final: 0.6618 (mp0) REVERT: B 406 VAL cc_start: 0.8319 (t) cc_final: 0.8064 (p) REVERT: B 408 THR cc_start: 0.8120 (m) cc_final: 0.7863 (t) REVERT: B 442 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7674 (mttt) REVERT: B 716 VAL cc_start: 0.7953 (m) cc_final: 0.7700 (p) REVERT: B 727 SER cc_start: 0.8525 (t) cc_final: 0.8072 (m) REVERT: B 804 TRP cc_start: 0.7689 (m100) cc_final: 0.7026 (m100) REVERT: B 812 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6748 (tm-30) REVERT: C 16 MET cc_start: 0.6696 (ppp) cc_final: 0.6430 (ppp) REVERT: C 41 VAL cc_start: 0.7648 (m) cc_final: 0.7315 (p) REVERT: C 107 ASN cc_start: 0.7426 (t0) cc_final: 0.7159 (t0) REVERT: C 236 LEU cc_start: 0.7008 (mt) cc_final: 0.6778 (mt) REVERT: C 256 ARG cc_start: 0.8527 (ttp80) cc_final: 0.8131 (ttp80) REVERT: C 257 ASP cc_start: 0.7361 (m-30) cc_final: 0.7072 (m-30) REVERT: C 259 ASN cc_start: 0.8070 (t0) cc_final: 0.7839 (t0) REVERT: C 275 LYS cc_start: 0.7664 (mtpp) cc_final: 0.7430 (mtpt) REVERT: C 288 ASP cc_start: 0.7597 (t70) cc_final: 0.7320 (t70) REVERT: C 337 TYR cc_start: 0.8223 (t80) cc_final: 0.7892 (t80) REVERT: C 411 ILE cc_start: 0.7971 (pt) cc_final: 0.7571 (mp) REVERT: C 427 TYR cc_start: 0.6150 (m-80) cc_final: 0.5853 (m-80) REVERT: C 440 GLU cc_start: 0.7806 (pt0) cc_final: 0.7479 (pt0) REVERT: C 480 SER cc_start: 0.8097 (m) cc_final: 0.7800 (t) REVERT: C 536 ARG cc_start: 0.7297 (mtm110) cc_final: 0.7015 (ttm110) outliers start: 54 outliers final: 43 residues processed: 365 average time/residue: 0.1222 time to fit residues: 67.3691 Evaluate side-chains 368 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 322 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 376 ARG Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 623 SER Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 526 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 152 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 89 optimal weight: 0.0870 chunk 198 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN B 89 HIS B 284 ASN B 370 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.159833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.132883 restraints weight = 25493.257| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.15 r_work: 0.3634 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 17765 Z= 0.270 Angle : 0.750 20.834 24515 Z= 0.388 Chirality : 0.050 0.255 2796 Planarity : 0.006 0.076 2856 Dihedral : 16.858 150.060 3367 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.96 % Favored : 88.83 % Rotamer: Outliers : 3.02 % Allowed : 18.33 % Favored : 78.65 % 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: -2.50 (0.18), residues: 1952 helix: -0.65 (0.30), residues: 250 sheet: -1.14 (0.21), residues: 645 loop : -2.30 (0.17), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 223 TYR 0.024 0.003 TYR A 416 PHE 0.035 0.003 PHE A 24 TRP 0.034 0.003 TRP B 378 HIS 0.009 0.002 HIS C 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.27 (17762) covalent geometry : angle 0.73090 / 0.39 (24506) hydrogen bonds : bond 0.06266 / 4.21 ( 489) hydrogen bonds : angle 5.41000 / 3.67 ( 1341) metal coordination : bond 0.01909 / 0.95 ( 3) metal coordination : angle 8.87087 / 4.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 339 time to evaluate : 0.607 Fit side-chains revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7979 (m) REVERT: A 120 ASP cc_start: 0.7240 (p0) cc_final: 0.6906 (p0) REVERT: A 210 SER cc_start: 0.7944 (t) cc_final: 0.7553 (p) REVERT: A 343 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6315 (tppt) REVERT: A 346 ILE cc_start: 0.7082 (mm) cc_final: 0.6869 (mm) REVERT: A 358 ARG cc_start: 0.7858 (ttm-80) cc_final: 0.7532 (ttt90) REVERT: A 379 ARG cc_start: 0.7674 (ptm-80) cc_final: 0.7342 (ptm-80) REVERT: A 389 SER cc_start: 0.8287 (m) cc_final: 0.7999 (p) REVERT: A 484 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7729 (mmmt) REVERT: A 554 ASP cc_start: 0.7494 (t0) cc_final: 0.7120 (t0) REVERT: A 643 SER cc_start: 0.8199 (p) cc_final: 0.7829 (m) REVERT: B 32 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7517 (tp) REVERT: B 91 GLU cc_start: 0.7975 (tp30) cc_final: 0.7631 (mt-10) REVERT: B 132 SER cc_start: 0.8481 (m) cc_final: 0.7880 (p) REVERT: B 139 VAL cc_start: 0.8617 (t) cc_final: 0.8320 (p) REVERT: B 277 THR cc_start: 0.6730 (OUTLIER) cc_final: 0.6098 (m) REVERT: B 387 HIS cc_start: 0.7391 (m-70) cc_final: 0.6659 (m-70) REVERT: B 406 VAL cc_start: 0.8356 (t) cc_final: 0.8114 (p) REVERT: B 408 THR cc_start: 0.8199 (m) cc_final: 0.7922 (t) REVERT: B 422 ASP cc_start: 0.7746 (m-30) cc_final: 0.7513 (m-30) REVERT: B 691 LYS cc_start: 0.8052 (mtmm) cc_final: 0.7783 (mtmm) REVERT: B 716 VAL cc_start: 0.7965 (m) cc_final: 0.7693 (p) REVERT: B 727 SER cc_start: 0.8599 (t) cc_final: 0.8138 (m) REVERT: B 804 TRP cc_start: 0.7833 (m100) cc_final: 0.7163 (m100) REVERT: C 16 MET cc_start: 0.6764 (ppp) cc_final: 0.6497 (ppp) REVERT: C 107 ASN cc_start: 0.7416 (t0) cc_final: 0.7142 (t0) REVERT: C 236 LEU cc_start: 0.7207 (mt) cc_final: 0.6987 (mt) REVERT: C 256 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8109 (ttp80) REVERT: C 259 ASN cc_start: 0.8013 (t0) cc_final: 0.7797 (t0) REVERT: C 275 LYS cc_start: 0.7792 (mtpp) cc_final: 0.7547 (mtpt) REVERT: C 410 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6895 (mm-30) REVERT: C 411 ILE cc_start: 0.8058 (pt) cc_final: 0.7771 (mt) REVERT: C 414 LYS cc_start: 0.7383 (tptp) cc_final: 0.7121 (tptp) REVERT: C 480 SER cc_start: 0.8182 (m) cc_final: 0.7935 (t) REVERT: C 536 ARG cc_start: 0.7198 (mtm110) cc_final: 0.6930 (ttm110) outliers start: 52 outliers final: 40 residues processed: 365 average time/residue: 0.1236 time to fit residues: 68.1440 Evaluate side-chains 372 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 328 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 383 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 526 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 167 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN B 284 ASN C 32 GLN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.161059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.133588 restraints weight = 25445.146| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.25 r_work: 0.3644 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17765 Z= 0.213 Angle : 0.700 23.447 24515 Z= 0.360 Chirality : 0.048 0.231 2796 Planarity : 0.006 0.075 2856 Dihedral : 16.733 150.479 3363 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.09 % Favored : 89.81 % Rotamer: Outliers : 3.42 % Allowed : 18.39 % Favored : 78.19 % 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: -2.50 (0.18), residues: 1952 helix: -0.58 (0.30), residues: 251 sheet: -1.14 (0.21), residues: 618 loop : -2.30 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 223 TYR 0.020 0.002 TYR A 416 PHE 0.027 0.002 PHE A 24 TRP 0.028 0.002 TRP B 378 HIS 0.005 0.001 HIS C 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (17762) covalent geometry : angle 0.67443 / 0.36 (24506) hydrogen bonds : bond 0.05592 / 3.74 ( 489) hydrogen bonds : angle 5.30858 / 3.59 ( 1341) metal coordination : bond 0.01202 / 0.60 ( 3) metal coordination : angle 9.85756 / 5.45 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 339 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.8000 (m) REVERT: A 120 ASP cc_start: 0.7299 (p0) cc_final: 0.6933 (p0) REVERT: A 210 SER cc_start: 0.7956 (t) cc_final: 0.7550 (p) REVERT: A 343 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6382 (tppt) REVERT: A 379 ARG cc_start: 0.7654 (ptm-80) cc_final: 0.7333 (ptm-80) REVERT: A 389 SER cc_start: 0.8303 (m) cc_final: 0.7962 (p) REVERT: A 484 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7744 (mmmt) REVERT: A 554 ASP cc_start: 0.7521 (t0) cc_final: 0.7135 (t0) REVERT: A 609 GLN cc_start: 0.7672 (tt0) cc_final: 0.6815 (tm-30) REVERT: A 611 GLU cc_start: 0.7107 (mp0) cc_final: 0.6639 (mp0) REVERT: A 643 SER cc_start: 0.8219 (p) cc_final: 0.7790 (m) REVERT: B 17 ARG cc_start: 0.7507 (mtm180) cc_final: 0.7259 (mtm180) REVERT: B 32 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7499 (tp) REVERT: B 91 GLU cc_start: 0.7981 (tp30) cc_final: 0.7591 (mt-10) REVERT: B 132 SER cc_start: 0.8436 (m) cc_final: 0.7822 (p) REVERT: B 139 VAL cc_start: 0.8612 (t) cc_final: 0.8311 (p) REVERT: B 387 HIS cc_start: 0.7273 (m-70) cc_final: 0.6513 (m-70) REVERT: B 406 VAL cc_start: 0.8348 (t) cc_final: 0.8080 (p) REVERT: B 408 THR cc_start: 0.8194 (m) cc_final: 0.7889 (t) REVERT: B 422 ASP cc_start: 0.7756 (m-30) cc_final: 0.7507 (m-30) REVERT: B 691 LYS cc_start: 0.7995 (mtmm) cc_final: 0.7755 (mtmm) REVERT: B 727 SER cc_start: 0.8552 (t) cc_final: 0.8082 (m) REVERT: B 804 TRP cc_start: 0.7839 (m100) cc_final: 0.7202 (m100) REVERT: C 16 MET cc_start: 0.6756 (ppp) cc_final: 0.6469 (ppp) REVERT: C 107 ASN cc_start: 0.7404 (t0) cc_final: 0.7121 (m-40) REVERT: C 236 LEU cc_start: 0.7102 (mt) cc_final: 0.6847 (mt) REVERT: C 256 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8105 (ttp80) REVERT: C 259 ASN cc_start: 0.8008 (t0) cc_final: 0.7771 (t0) REVERT: C 275 LYS cc_start: 0.7721 (mtpp) cc_final: 0.7448 (mtpt) REVERT: C 410 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6879 (mm-30) REVERT: C 411 ILE cc_start: 0.8007 (pt) cc_final: 0.7728 (mt) REVERT: C 414 LYS cc_start: 0.7434 (tptp) cc_final: 0.7174 (tptp) REVERT: C 480 SER cc_start: 0.8200 (m) cc_final: 0.7907 (t) REVERT: C 536 ARG cc_start: 0.7226 (mtm110) cc_final: 0.6963 (ttm110) outliers start: 59 outliers final: 44 residues processed: 367 average time/residue: 0.1239 time to fit residues: 68.5241 Evaluate side-chains 381 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 334 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 235 MET Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 526 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 24 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 165 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN B 89 HIS C 32 GLN ** C 366 GLN ** 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 = 0.4129 r_free = 0.4129 target = 0.161977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134676 restraints weight = 25385.359| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.22 r_work: 0.3650 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17765 Z= 0.177 Angle : 0.688 24.024 24515 Z= 0.352 Chirality : 0.047 0.218 2796 Planarity : 0.006 0.081 2856 Dihedral : 16.648 150.534 3363 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.19 % Favored : 89.65 % Rotamer: Outliers : 3.19 % Allowed : 18.97 % Favored : 77.84 % 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: -2.44 (0.18), residues: 1952 helix: -0.56 (0.31), residues: 251 sheet: -1.09 (0.21), residues: 618 loop : -2.26 (0.17), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 223 TYR 0.018 0.002 TYR A 416 PHE 0.024 0.002 PHE B 452 TRP 0.028 0.002 TRP B 378 HIS 0.007 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (17762) covalent geometry : angle 0.66100 / 0.35 (24506) hydrogen bonds : bond 0.05348 / 3.54 ( 489) hydrogen bonds : angle 5.27828 / 3.57 ( 1341) metal coordination : bond 0.01142 / 0.58 ( 3) metal coordination : angle 10.02743 / 5.56 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 333 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8265 (OUTLIER) cc_final: 0.7977 (m) REVERT: A 114 VAL cc_start: 0.8245 (m) cc_final: 0.8014 (p) REVERT: A 120 ASP cc_start: 0.7286 (p0) cc_final: 0.6894 (p0) REVERT: A 210 SER cc_start: 0.7964 (t) cc_final: 0.7548 (p) REVERT: A 343 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6385 (tppt) REVERT: A 379 ARG cc_start: 0.7599 (ptm-80) cc_final: 0.7295 (ptm-80) REVERT: A 389 SER cc_start: 0.8290 (m) cc_final: 0.7932 (p) REVERT: A 438 ASP cc_start: 0.7652 (m-30) cc_final: 0.7202 (m-30) REVERT: A 484 LYS cc_start: 0.8113 (mmmt) cc_final: 0.7756 (mmmt) REVERT: A 554 ASP cc_start: 0.7533 (t0) cc_final: 0.7143 (t0) REVERT: A 609 GLN cc_start: 0.7690 (tt0) cc_final: 0.6830 (tm-30) REVERT: A 611 GLU cc_start: 0.7144 (mp0) cc_final: 0.6603 (mp0) REVERT: B 32 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7424 (tp) REVERT: B 91 GLU cc_start: 0.7981 (tp30) cc_final: 0.7617 (mt-10) REVERT: B 132 SER cc_start: 0.8431 (m) cc_final: 0.7835 (p) REVERT: B 139 VAL cc_start: 0.8599 (t) cc_final: 0.8298 (p) REVERT: B 277 THR cc_start: 0.6598 (OUTLIER) cc_final: 0.5983 (m) REVERT: B 387 HIS cc_start: 0.7261 (m-70) cc_final: 0.6545 (m-70) REVERT: B 406 VAL cc_start: 0.8334 (t) cc_final: 0.8046 (p) REVERT: B 408 THR cc_start: 0.8172 (m) cc_final: 0.7891 (t) REVERT: B 422 ASP cc_start: 0.7778 (m-30) cc_final: 0.7528 (m-30) REVERT: B 691 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7744 (mtmm) REVERT: B 727 SER cc_start: 0.8544 (t) cc_final: 0.8075 (m) REVERT: B 804 TRP cc_start: 0.7825 (m100) cc_final: 0.7228 (m100) REVERT: C 16 MET cc_start: 0.6733 (ppp) cc_final: 0.6329 (ppp) REVERT: C 107 ASN cc_start: 0.7404 (t0) cc_final: 0.7122 (m-40) REVERT: C 236 LEU cc_start: 0.7055 (mt) cc_final: 0.6808 (mt) REVERT: C 259 ASN cc_start: 0.8002 (t0) cc_final: 0.7763 (t0) REVERT: C 280 LYS cc_start: 0.7479 (mtmm) cc_final: 0.7028 (mtmm) REVERT: C 321 LEU cc_start: 0.8049 (mp) cc_final: 0.7775 (mt) REVERT: C 410 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6792 (mm-30) REVERT: C 411 ILE cc_start: 0.7989 (pt) cc_final: 0.7703 (mt) REVERT: C 414 LYS cc_start: 0.7433 (tptp) cc_final: 0.7152 (tptp) REVERT: C 480 SER cc_start: 0.8168 (m) cc_final: 0.7889 (t) REVERT: C 536 ARG cc_start: 0.7269 (mtm110) cc_final: 0.7002 (ttm110) outliers start: 55 outliers final: 44 residues processed: 360 average time/residue: 0.1268 time to fit residues: 68.9094 Evaluate side-chains 371 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 323 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 526 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 95 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 184 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS B 593 HIS C 32 GLN ** C 366 GLN ** 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 = 0.4126 r_free = 0.4126 target = 0.161798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.134773 restraints weight = 25297.589| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.19 r_work: 0.3662 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 17765 Z= 0.183 Angle : 0.711 26.042 24515 Z= 0.361 Chirality : 0.047 0.223 2796 Planarity : 0.006 0.085 2856 Dihedral : 16.603 150.605 3363 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.30 % Favored : 89.60 % Rotamer: Outliers : 2.84 % Allowed : 19.55 % Favored : 77.61 % 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: -2.43 (0.18), residues: 1952 helix: -0.59 (0.31), residues: 251 sheet: -1.07 (0.21), residues: 616 loop : -2.26 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 223 TYR 0.019 0.002 TYR A 416 PHE 0.025 0.002 PHE B 452 TRP 0.027 0.002 TRP B 378 HIS 0.007 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (17762) covalent geometry : angle 0.68092 / 0.36 (24506) hydrogen bonds : bond 0.05369 / 3.56 ( 489) hydrogen bonds : angle 5.25675 / 3.55 ( 1341) metal coordination : bond 0.01303 / 0.65 ( 3) metal coordination : angle 10.76568 / 5.98 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 329 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6964 (mtm110) cc_final: 0.6760 (mtm110) REVERT: A 14 ASP cc_start: 0.7758 (m-30) cc_final: 0.7512 (p0) REVERT: A 33 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7974 (m) REVERT: A 114 VAL cc_start: 0.8255 (m) cc_final: 0.8025 (p) REVERT: A 120 ASP cc_start: 0.7298 (p0) cc_final: 0.6898 (p0) REVERT: A 210 SER cc_start: 0.7971 (t) cc_final: 0.7558 (p) REVERT: A 343 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6382 (tppt) REVERT: A 379 ARG cc_start: 0.7569 (ptm-80) cc_final: 0.7264 (ptm-80) REVERT: A 389 SER cc_start: 0.8277 (m) cc_final: 0.7922 (p) REVERT: A 438 ASP cc_start: 0.7439 (m-30) cc_final: 0.7038 (m-30) REVERT: A 484 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7776 (mmmt) REVERT: A 554 ASP cc_start: 0.7522 (t0) cc_final: 0.7139 (t0) REVERT: A 609 GLN cc_start: 0.7642 (tt0) cc_final: 0.6777 (tm-30) REVERT: A 611 GLU cc_start: 0.7099 (mp0) cc_final: 0.6560 (mp0) REVERT: B 32 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7432 (tp) REVERT: B 91 GLU cc_start: 0.7974 (tp30) cc_final: 0.7619 (mt-10) REVERT: B 132 SER cc_start: 0.8452 (m) cc_final: 0.7855 (p) REVERT: B 139 VAL cc_start: 0.8591 (t) cc_final: 0.8293 (p) REVERT: B 277 THR cc_start: 0.6615 (OUTLIER) cc_final: 0.5983 (m) REVERT: B 387 HIS cc_start: 0.7272 (m-70) cc_final: 0.6520 (m-70) REVERT: B 406 VAL cc_start: 0.8260 (t) cc_final: 0.7980 (p) REVERT: B 408 THR cc_start: 0.8142 (m) cc_final: 0.7875 (t) REVERT: B 422 ASP cc_start: 0.7740 (m-30) cc_final: 0.7483 (m-30) REVERT: B 691 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7722 (mtmm) REVERT: B 727 SER cc_start: 0.8540 (t) cc_final: 0.8069 (m) REVERT: B 804 TRP cc_start: 0.7837 (m100) cc_final: 0.7292 (m100) REVERT: C 16 MET cc_start: 0.6667 (ppp) cc_final: 0.6414 (ppp) REVERT: C 107 ASN cc_start: 0.7422 (t0) cc_final: 0.7142 (m-40) REVERT: C 127 TYR cc_start: 0.7281 (m-80) cc_final: 0.6823 (m-80) REVERT: C 236 LEU cc_start: 0.7060 (mt) cc_final: 0.6782 (mt) REVERT: C 259 ASN cc_start: 0.7980 (t0) cc_final: 0.7745 (t0) REVERT: C 280 LYS cc_start: 0.7388 (mtmm) cc_final: 0.7070 (mtmm) REVERT: C 321 LEU cc_start: 0.8055 (mp) cc_final: 0.7775 (mt) REVERT: C 410 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6811 (mm-30) REVERT: C 411 ILE cc_start: 0.7986 (pt) cc_final: 0.7718 (mt) REVERT: C 414 LYS cc_start: 0.7448 (tptp) cc_final: 0.7170 (tptp) REVERT: C 480 SER cc_start: 0.8192 (m) cc_final: 0.7917 (t) REVERT: C 536 ARG cc_start: 0.7195 (mtm110) cc_final: 0.6949 (ttm110) outliers start: 49 outliers final: 41 residues processed: 355 average time/residue: 0.1363 time to fit residues: 72.9979 Evaluate side-chains 371 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 326 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 656 HIS Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 429 HIS Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 32 GLN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 213 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 300 GLN Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 427 TYR Chi-restraints excluded: chain C residue 526 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 190 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 193 optimal weight: 0.0870 chunk 2 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 126 optimal weight: 0.0670 chunk 120 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN B 89 HIS B 768 HIS C 32 GLN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.163020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.135671 restraints weight = 25290.398| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.25 r_work: 0.3666 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17765 Z= 0.146 Angle : 0.688 26.161 24515 Z= 0.348 Chirality : 0.046 0.222 2796 Planarity : 0.006 0.084 2856 Dihedral : 16.537 150.611 3363 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.63 % Favored : 90.27 % Rotamer: Outliers : 2.84 % Allowed : 19.84 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.18), residues: 1952 helix: -0.51 (0.31), residues: 252 sheet: -1.03 (0.21), residues: 616 loop : -2.23 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 364 TYR 0.016 0.001 TYR A 368 PHE 0.022 0.002 PHE B 452 TRP 0.026 0.002 TRP A 224 HIS 0.007 0.001 HIS B 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (17762) covalent geometry : angle 0.65574 / 0.35 (24506) hydrogen bonds : bond 0.04993 / 3.28 ( 489) hydrogen bonds : angle 5.16178 / 3.48 ( 1341) metal coordination : bond 0.01082 / 0.55 ( 3) metal coordination : angle 10.81356 / 6.00 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4571.49 seconds wall clock time: 79 minutes 1.91 seconds (4741.91 seconds total)