Starting phenix.real_space_refine on Mon May 4 01:32:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ptz_17926/05_2026/8ptz_17926.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ptz_17926/05_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_17926/05_2026/8ptz_17926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ptz_17926/05_2026/8ptz_17926.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ptz_17926/05_2026/8ptz_17926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ptz_17926/05_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/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: 3.89, per 1000 atoms: 0.23 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: 1.34 Conformation dependent library (CDL) restraints added in 604.1 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: 2.01 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: 3.48 Time building geometry restraints manager: 1.75 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: 8.750 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 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= 0.290 Angle : 0.878 55.013 24515 Z= 0.429 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 covalent geometry : bond 0.00557 (17762) covalent geometry : angle 0.86686 (24506) hydrogen bonds : bond 0.19176 ( 489) hydrogen bonds : angle 7.92043 ( 1341) metal coordination : bond 0.00912 ( 3) metal coordination : angle 7.26202 ( 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 : 0.531 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: 0.1459 time to fit residues: 79.1992 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 : 0.579 ------------------------------------------------------------------------------- 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: 8.9990 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... Flipped N/Q/H residues before XYZ refinement: A 329 HIS A 489 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 ASN B 284 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 412 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.163164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.135788 restraints weight = 25735.124| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 2.28 r_work: 0.3678 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17765 Z= 0.161 Angle : 0.663 10.707 24515 Z= 0.339 Chirality : 0.046 0.228 2796 Planarity : 0.005 0.056 2856 Dihedral : 16.944 144.673 3367 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.89 % Favored : 90.06 % Rotamer: Outliers : 1.39 % Allowed : 9.63 % Favored : 88.98 % 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: -2.28 (0.18), residues: 1952 helix: -0.06 (0.32), residues: 252 sheet: -1.21 (0.21), residues: 638 loop : -2.11 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 454 TYR 0.015 0.001 TYR A 416 PHE 0.027 0.002 PHE C 304 TRP 0.021 0.002 TRP C 433 HIS 0.006 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00366 (17762) covalent geometry : angle 0.65167 (24506) hydrogen bonds : bond 0.05299 ( 489) hydrogen bonds : angle 5.67839 ( 1341) metal coordination : bond 0.01846 ( 3) metal coordination : angle 6.48455 ( 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 353 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 329 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7285 (ttm-80) cc_final: 0.6633 (mtm110) REVERT: A 14 ASP cc_start: 0.7599 (m-30) cc_final: 0.7281 (p0) REVERT: A 120 ASP cc_start: 0.7005 (p0) cc_final: 0.6772 (p0) REVERT: A 210 SER cc_start: 0.7828 (t) cc_final: 0.7336 (p) REVERT: A 231 GLN cc_start: 0.7933 (mm110) cc_final: 0.7702 (mm-40) REVERT: A 271 ASN cc_start: 0.7990 (t0) cc_final: 0.7726 (t0) REVERT: A 346 ILE cc_start: 0.7013 (mm) cc_final: 0.6554 (mm) REVERT: A 348 SER cc_start: 0.7884 (t) cc_final: 0.7544 (p) REVERT: A 389 SER cc_start: 0.8306 (m) cc_final: 0.8033 (p) REVERT: A 554 ASP cc_start: 0.7500 (t0) cc_final: 0.7108 (t0) REVERT: A 635 ILE cc_start: 0.8766 (tt) cc_final: 0.8453 (pt) REVERT: B 23 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7753 (m-40) REVERT: B 91 GLU cc_start: 0.7906 (tp30) cc_final: 0.7389 (mt-10) REVERT: B 139 VAL cc_start: 0.8564 (t) cc_final: 0.8230 (p) REVERT: B 387 HIS cc_start: 0.7420 (m-70) cc_final: 0.6711 (m-70) REVERT: B 401 GLU cc_start: 0.6783 (mp0) cc_final: 0.6494 (mp0) REVERT: B 406 VAL cc_start: 0.8217 (t) cc_final: 0.7968 (p) REVERT: B 408 THR cc_start: 0.8169 (m) cc_final: 0.7838 (t) REVERT: B 547 THR cc_start: 0.4252 (OUTLIER) cc_final: 0.3271 (p) REVERT: B 716 VAL cc_start: 0.7779 (m) cc_final: 0.7564 (p) REVERT: B 727 SER cc_start: 0.8501 (t) cc_final: 0.8027 (m) REVERT: B 750 CYS cc_start: 0.8083 (t) cc_final: 0.7424 (p) REVERT: B 804 TRP cc_start: 0.7677 (m100) cc_final: 0.7033 (m100) REVERT: B 824 CYS cc_start: 0.7219 (t) cc_final: 0.6963 (t) REVERT: C 16 MET cc_start: 0.6583 (ppp) cc_final: 0.6274 (ppp) REVERT: C 42 LYS cc_start: 0.7162 (mtmt) cc_final: 0.6558 (ttpt) REVERT: C 107 ASN cc_start: 0.7507 (t0) cc_final: 0.7254 (t0) REVERT: C 236 LEU cc_start: 0.7000 (mt) cc_final: 0.6683 (mt) REVERT: C 256 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8065 (ttp80) REVERT: C 259 ASN cc_start: 0.8099 (t0) cc_final: 0.7879 (t0) REVERT: C 288 ASP cc_start: 0.7634 (t0) cc_final: 0.7160 (t70) REVERT: C 388 LEU cc_start: 0.7833 (mm) cc_final: 0.7607 (mm) REVERT: C 411 ILE cc_start: 0.7946 (pt) cc_final: 0.7525 (mp) REVERT: C 427 TYR cc_start: 0.6210 (m-80) cc_final: 0.5926 (m-80) REVERT: C 480 SER cc_start: 0.8065 (m) cc_final: 0.7778 (t) outliers start: 24 outliers final: 18 residues processed: 338 average time/residue: 0.1305 time to fit residues: 66.2869 Evaluate side-chains 324 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 304 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 256 THR Chi-restraints excluded: chain A residue 409 VAL 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 23 ASN Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 200 VAL 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 574 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: 0.7980 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 178 optimal weight: 0.0020 chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 192 optimal weight: 0.9980 chunk 97 optimal weight: 0.0060 chunk 73 optimal weight: 0.0870 chunk 107 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 overall best weight: 0.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 23 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 HIS ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS B 302 GLN B 371 ASN B 668 HIS ** 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 = 0.4165 r_free = 0.4165 target = 0.164475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136764 restraints weight = 25827.810| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.33 r_work: 0.3691 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17765 Z= 0.122 Angle : 0.611 14.141 24515 Z= 0.310 Chirality : 0.044 0.207 2796 Planarity : 0.005 0.055 2856 Dihedral : 16.795 141.726 3367 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 2.03 % Allowed : 13.05 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.18), residues: 1952 helix: 0.08 (0.32), residues: 253 sheet: -1.03 (0.21), residues: 623 loop : -2.11 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 195 TYR 0.012 0.001 TYR A 416 PHE 0.026 0.001 PHE C 304 TRP 0.019 0.001 TRP A 224 HIS 0.005 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00276 (17762) covalent geometry : angle 0.59326 (24506) hydrogen bonds : bond 0.04431 ( 489) hydrogen bonds : angle 5.28844 ( 1341) metal coordination : bond 0.00986 ( 3) metal coordination : angle 7.69279 ( 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 369 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 334 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.7066 (mtm110) REVERT: A 14 ASP cc_start: 0.7623 (m-30) cc_final: 0.7323 (p0) REVERT: A 120 ASP cc_start: 0.7071 (p0) cc_final: 0.6787 (p0) REVERT: A 210 SER cc_start: 0.8091 (t) cc_final: 0.7638 (p) REVERT: A 346 ILE cc_start: 0.6848 (mm) cc_final: 0.6421 (mm) REVERT: A 358 ARG cc_start: 0.7817 (ttm170) cc_final: 0.7598 (ttt90) REVERT: A 379 ARG cc_start: 0.7587 (ptm-80) cc_final: 0.7275 (ptm-80) REVERT: A 389 SER cc_start: 0.8329 (m) cc_final: 0.8003 (p) REVERT: A 554 ASP cc_start: 0.7508 (t0) cc_final: 0.7131 (t0) REVERT: A 629 ARG cc_start: 0.8116 (mtp85) cc_final: 0.7907 (mtt180) REVERT: A 635 ILE cc_start: 0.8720 (tt) cc_final: 0.8422 (pt) REVERT: B 23 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7642 (m-40) REVERT: B 91 GLU cc_start: 0.7894 (tp30) cc_final: 0.7375 (mt-10) REVERT: B 139 VAL cc_start: 0.8578 (t) cc_final: 0.8216 (p) REVERT: B 387 HIS cc_start: 0.7364 (m-70) cc_final: 0.6824 (m-70) REVERT: B 406 VAL cc_start: 0.8215 (t) cc_final: 0.7998 (p) REVERT: B 408 THR cc_start: 0.8099 (m) cc_final: 0.7819 (t) REVERT: B 442 LYS cc_start: 0.7927 (mmtt) cc_final: 0.7670 (mttt) REVERT: B 464 PHE cc_start: 0.8126 (m-80) cc_final: 0.7835 (m-80) REVERT: B 586 CYS cc_start: 0.8232 (p) cc_final: 0.7903 (t) REVERT: B 716 VAL cc_start: 0.7808 (m) cc_final: 0.7590 (p) REVERT: B 727 SER cc_start: 0.8461 (t) cc_final: 0.8003 (m) REVERT: B 804 TRP cc_start: 0.7637 (m100) cc_final: 0.6992 (m100) REVERT: C 16 MET cc_start: 0.6574 (ppp) cc_final: 0.6318 (ppp) REVERT: C 107 ASN cc_start: 0.7482 (t0) cc_final: 0.7227 (t0) REVERT: C 173 THR cc_start: 0.7523 (p) cc_final: 0.7295 (t) REVERT: C 236 LEU cc_start: 0.6836 (mt) cc_final: 0.6563 (mt) REVERT: C 256 ARG cc_start: 0.8500 (ttp80) cc_final: 0.8101 (ttp80) REVERT: C 259 ASN cc_start: 0.8069 (t0) cc_final: 0.7835 (t0) REVERT: C 288 ASP cc_start: 0.7605 (t0) cc_final: 0.7116 (t70) REVERT: C 411 ILE cc_start: 0.7966 (pt) cc_final: 0.7544 (mp) REVERT: C 427 TYR cc_start: 0.6195 (m-80) cc_final: 0.5834 (m-80) REVERT: C 440 GLU cc_start: 0.7697 (pt0) cc_final: 0.7162 (pt0) REVERT: C 480 SER cc_start: 0.8026 (m) cc_final: 0.7748 (t) REVERT: C 533 ILE cc_start: 0.8114 (mm) cc_final: 0.7797 (mt) outliers start: 35 outliers final: 26 residues processed: 349 average time/residue: 0.1242 time to fit residues: 65.9313 Evaluate side-chains 343 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 316 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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 621 VAL Chi-restraints excluded: chain A residue 646 VAL 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 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 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 277 SER Chi-restraints excluded: chain C residue 341 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 124 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 55 optimal weight: 0.2980 chunk 76 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 194 optimal weight: 0.0970 chunk 114 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 136 optimal weight: 0.0980 chunk 59 optimal weight: 0.5980 chunk 132 optimal weight: 3.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 489 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 768 HIS ** 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 = 0.4165 r_free = 0.4165 target = 0.164756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.136863 restraints weight = 25766.850| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.31 r_work: 0.3689 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17765 Z= 0.121 Angle : 0.603 16.967 24515 Z= 0.303 Chirality : 0.043 0.191 2796 Planarity : 0.005 0.058 2856 Dihedral : 16.680 140.599 3367 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.36 % Allowed : 14.04 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.18), residues: 1952 helix: 0.12 (0.32), residues: 259 sheet: -0.93 (0.21), residues: 634 loop : -2.09 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 13 TYR 0.013 0.001 TYR A 416 PHE 0.025 0.002 PHE C 304 TRP 0.018 0.001 TRP A 224 HIS 0.007 0.001 HIS A 367 Details of bonding type rmsd covalent geometry : bond 0.00282 (17762) covalent geometry : angle 0.58071 (24506) hydrogen bonds : bond 0.04225 ( 489) hydrogen bonds : angle 5.04102 ( 1341) metal coordination : bond 0.01171 ( 3) metal coordination : angle 8.44841 ( 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 383 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 325 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.7851 (OUTLIER) cc_final: 0.7539 (m) REVERT: A 120 ASP cc_start: 0.6922 (p0) cc_final: 0.6613 (p0) REVERT: A 210 SER cc_start: 0.8024 (t) cc_final: 0.7607 (p) REVERT: A 346 ILE cc_start: 0.6725 (mm) cc_final: 0.6317 (mm) REVERT: A 358 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7495 (ttt90) REVERT: A 379 ARG cc_start: 0.7259 (ptm-80) cc_final: 0.6971 (ptm-80) REVERT: A 389 SER cc_start: 0.8171 (m) cc_final: 0.7797 (p) REVERT: A 554 ASP cc_start: 0.7252 (t0) cc_final: 0.6878 (t0) REVERT: A 629 ARG cc_start: 0.7827 (mtp85) cc_final: 0.7592 (mtt180) REVERT: A 635 ILE cc_start: 0.8659 (tt) cc_final: 0.8390 (pt) REVERT: B 91 GLU cc_start: 0.7698 (tp30) cc_final: 0.7389 (mt-10) REVERT: B 139 VAL cc_start: 0.8510 (t) cc_final: 0.8216 (p) REVERT: B 302 GLN cc_start: 0.6815 (mp10) cc_final: 0.6597 (mp10) REVERT: B 387 HIS cc_start: 0.7198 (m-70) cc_final: 0.6604 (m-70) REVERT: B 401 GLU cc_start: 0.6968 (mp0) cc_final: 0.6546 (mp0) REVERT: B 406 VAL cc_start: 0.8144 (t) cc_final: 0.7934 (p) REVERT: B 408 THR cc_start: 0.7997 (m) cc_final: 0.7744 (t) REVERT: B 442 LYS cc_start: 0.7769 (mmtt) cc_final: 0.7507 (mttt) REVERT: B 586 CYS cc_start: 0.7952 (p) cc_final: 0.7747 (t) REVERT: B 727 SER cc_start: 0.8403 (t) cc_final: 0.7932 (m) REVERT: B 804 TRP cc_start: 0.7550 (m100) cc_final: 0.6896 (m100) REVERT: C 16 MET cc_start: 0.6425 (ppp) cc_final: 0.6173 (ppp) REVERT: C 107 ASN cc_start: 0.7339 (t0) cc_final: 0.7098 (t0) REVERT: C 236 LEU cc_start: 0.6788 (mt) cc_final: 0.6577 (mt) REVERT: C 256 ARG cc_start: 0.8326 (ttp80) cc_final: 0.7919 (ttp80) REVERT: C 259 ASN cc_start: 0.7829 (t0) cc_final: 0.7612 (t0) REVERT: C 288 ASP cc_start: 0.7458 (t0) cc_final: 0.6963 (t70) REVERT: C 411 ILE cc_start: 0.7903 (pt) cc_final: 0.7529 (mp) REVERT: C 427 TYR cc_start: 0.5810 (m-80) cc_final: 0.5486 (m-80) REVERT: C 440 GLU cc_start: 0.7585 (pt0) cc_final: 0.7155 (pt0) REVERT: C 480 SER cc_start: 0.7799 (m) cc_final: 0.7575 (t) REVERT: C 533 ILE cc_start: 0.7996 (mm) cc_final: 0.7687 (mt) outliers start: 58 outliers final: 37 residues processed: 352 average time/residue: 0.1277 time to fit residues: 67.7466 Evaluate side-chains 356 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 318 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 509 ILE 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 376 ARG Chi-restraints excluded: chain B residue 394 LEU 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 193 LEU 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 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: 0.9990 chunk 99 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 146 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 417 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 561 GLN C 32 GLN ** C 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.162555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134885 restraints weight = 25405.679| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.28 r_work: 0.3652 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 17765 Z= 0.206 Angle : 0.683 21.303 24515 Z= 0.347 Chirality : 0.046 0.212 2796 Planarity : 0.005 0.064 2856 Dihedral : 16.667 139.791 3367 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.45 % Favored : 89.50 % 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: -2.26 (0.18), residues: 1952 helix: -0.25 (0.31), residues: 250 sheet: -0.97 (0.21), residues: 636 loop : -2.20 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 449 TYR 0.021 0.002 TYR A 416 PHE 0.027 0.002 PHE A 24 TRP 0.021 0.002 TRP C 433 HIS 0.007 0.001 HIS C 101 Details of bonding type rmsd covalent geometry : bond 0.00485 (17762) covalent geometry : angle 0.66140 (24506) hydrogen bonds : bond 0.05351 ( 489) hydrogen bonds : angle 5.20869 ( 1341) metal coordination : bond 0.01557 ( 3) metal coordination : angle 8.98535 ( 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 384 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 338 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8120 (OUTLIER) cc_final: 0.7843 (m) REVERT: A 120 ASP cc_start: 0.7157 (p0) cc_final: 0.6815 (p0) REVERT: A 210 SER cc_start: 0.8039 (t) cc_final: 0.7633 (p) REVERT: A 343 LYS cc_start: 0.6759 (tptt) cc_final: 0.6465 (tptt) REVERT: A 346 ILE cc_start: 0.7014 (mm) cc_final: 0.6740 (mm) REVERT: A 358 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7413 (ttt90) REVERT: A 379 ARG cc_start: 0.7622 (ptm-80) cc_final: 0.7297 (ptm-80) REVERT: A 389 SER cc_start: 0.8309 (m) cc_final: 0.7981 (p) REVERT: A 554 ASP cc_start: 0.7498 (t0) cc_final: 0.7127 (t0) REVERT: A 635 ILE cc_start: 0.8717 (tt) cc_final: 0.8421 (pt) REVERT: A 643 SER cc_start: 0.8214 (p) cc_final: 0.7801 (m) REVERT: B 32 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7459 (tp) REVERT: B 91 GLU cc_start: 0.7963 (tp30) cc_final: 0.7560 (mt-10) REVERT: B 132 SER cc_start: 0.8416 (m) cc_final: 0.7772 (p) REVERT: B 139 VAL cc_start: 0.8569 (t) cc_final: 0.8264 (p) REVERT: B 333 ARG cc_start: 0.5595 (tpp-160) cc_final: 0.5108 (tpp-160) REVERT: B 368 TRP cc_start: 0.8192 (m-90) cc_final: 0.7801 (m-90) REVERT: B 387 HIS cc_start: 0.7404 (m-70) cc_final: 0.6675 (m-70) REVERT: B 406 VAL cc_start: 0.8390 (t) cc_final: 0.8185 (p) REVERT: B 408 THR cc_start: 0.8117 (m) cc_final: 0.7852 (t) REVERT: B 422 ASP cc_start: 0.7749 (m-30) cc_final: 0.7518 (m-30) REVERT: B 727 SER cc_start: 0.8568 (t) cc_final: 0.8138 (m) REVERT: B 804 TRP cc_start: 0.7710 (m100) cc_final: 0.7040 (m100) REVERT: C 16 MET cc_start: 0.6656 (ppp) cc_final: 0.6374 (ppp) REVERT: C 107 ASN cc_start: 0.7405 (t0) cc_final: 0.7126 (t0) REVERT: C 236 LEU cc_start: 0.7100 (mt) cc_final: 0.6864 (mt) REVERT: C 259 ASN cc_start: 0.8050 (t0) cc_final: 0.7828 (t0) REVERT: C 275 LYS cc_start: 0.7690 (mtpp) cc_final: 0.7454 (mtpt) REVERT: C 288 ASP cc_start: 0.7792 (t0) cc_final: 0.7541 (t70) REVERT: C 411 ILE cc_start: 0.7999 (pt) cc_final: 0.7699 (mt) REVERT: C 427 TYR cc_start: 0.6183 (m-80) cc_final: 0.5951 (m-80) REVERT: C 480 SER cc_start: 0.8174 (m) cc_final: 0.7881 (t) REVERT: C 536 ARG cc_start: 0.7274 (mtm110) cc_final: 0.6989 (ttm110) outliers start: 46 outliers final: 38 residues processed: 360 average time/residue: 0.1317 time to fit residues: 71.2904 Evaluate side-chains 361 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 321 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 136 MET 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 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 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 32 GLN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 286 MET 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 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: 0.0970 chunk 128 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 139 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN B 23 ASN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4137 r_free = 0.4137 target = 0.162657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135144 restraints weight = 25441.718| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.24 r_work: 0.3661 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17765 Z= 0.172 Angle : 0.660 22.400 24515 Z= 0.331 Chirality : 0.046 0.237 2796 Planarity : 0.005 0.070 2856 Dihedral : 16.511 138.887 3363 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.63 % Favored : 90.37 % Rotamer: Outliers : 3.19 % Allowed : 16.65 % Favored : 80.16 % 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 (0.18), residues: 1952 helix: -0.25 (0.31), residues: 250 sheet: -0.99 (0.21), residues: 613 loop : -2.17 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 141 TYR 0.017 0.002 TYR A 416 PHE 0.023 0.002 PHE C 304 TRP 0.022 0.002 TRP A 224 HIS 0.005 0.001 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00405 (17762) covalent geometry : angle 0.63476 (24506) hydrogen bonds : bond 0.04861 ( 489) hydrogen bonds : angle 5.07696 ( 1341) metal coordination : bond 0.01140 ( 3) metal coordination : angle 9.54633 ( 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 389 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 334 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8124 (OUTLIER) cc_final: 0.7854 (m) REVERT: A 120 ASP cc_start: 0.7255 (p0) cc_final: 0.6897 (p0) REVERT: A 210 SER cc_start: 0.8004 (t) cc_final: 0.7596 (p) REVERT: A 343 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.6377 (tppt) REVERT: A 379 ARG cc_start: 0.7640 (ptm-80) cc_final: 0.7333 (ptm-80) REVERT: A 389 SER cc_start: 0.8262 (m) cc_final: 0.7923 (p) REVERT: A 554 ASP cc_start: 0.7489 (t0) cc_final: 0.7107 (t0) REVERT: A 611 GLU cc_start: 0.7193 (mp0) cc_final: 0.6873 (mp0) REVERT: A 643 SER cc_start: 0.8172 (p) cc_final: 0.7815 (m) REVERT: B 23 ASN cc_start: 0.7715 (OUTLIER) cc_final: 0.7491 (m-40) REVERT: B 32 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7430 (tp) REVERT: B 91 GLU cc_start: 0.7920 (tp30) cc_final: 0.7566 (mt-10) REVERT: B 132 SER cc_start: 0.8415 (m) cc_final: 0.7782 (p) REVERT: B 139 VAL cc_start: 0.8555 (t) cc_final: 0.8258 (p) REVERT: B 333 ARG cc_start: 0.5591 (tpp-160) cc_final: 0.5111 (tpp-160) REVERT: B 387 HIS cc_start: 0.7248 (m-70) cc_final: 0.6544 (m-70) REVERT: B 408 THR cc_start: 0.8122 (m) cc_final: 0.7864 (t) REVERT: B 422 ASP cc_start: 0.7766 (m-30) cc_final: 0.7518 (m-30) REVERT: B 727 SER cc_start: 0.8551 (t) cc_final: 0.8117 (m) REVERT: B 804 TRP cc_start: 0.7744 (m100) cc_final: 0.7045 (m100) REVERT: C 16 MET cc_start: 0.6663 (ppp) cc_final: 0.6352 (ppp) REVERT: C 39 ASN cc_start: 0.8675 (m110) cc_final: 0.8332 (m110) REVERT: C 107 ASN cc_start: 0.7400 (t0) cc_final: 0.7116 (t0) REVERT: C 236 LEU cc_start: 0.7099 (mt) cc_final: 0.6848 (mt) REVERT: C 259 ASN cc_start: 0.8016 (t0) cc_final: 0.7795 (t0) REVERT: C 275 LYS cc_start: 0.7670 (mtpp) cc_final: 0.7429 (mtpt) REVERT: C 288 ASP cc_start: 0.7747 (t0) cc_final: 0.7513 (t70) REVERT: C 411 ILE cc_start: 0.7945 (pt) cc_final: 0.7631 (mt) REVERT: C 480 SER cc_start: 0.8134 (m) cc_final: 0.7838 (t) REVERT: C 536 ARG cc_start: 0.7210 (mtm110) cc_final: 0.6967 (ttm110) outliers start: 55 outliers final: 41 residues processed: 357 average time/residue: 0.1256 time to fit residues: 67.9646 Evaluate side-chains 368 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 323 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain A residue 136 MET 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 570 VAL Chi-restraints excluded: chain A residue 614 MET 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 A residue 659 THR 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 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 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 B residue 785 LEU 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 193 LEU 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 286 MET 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 526 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 152 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 91 optimal weight: 0.2980 chunk 43 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 89 optimal weight: 0.0980 chunk 198 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 65 GLN B 114 HIS B 435 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.163564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.135913 restraints weight = 25419.763| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.29 r_work: 0.3665 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17765 Z= 0.167 Angle : 0.667 23.449 24515 Z= 0.333 Chirality : 0.045 0.226 2796 Planarity : 0.005 0.075 2856 Dihedral : 16.455 137.967 3363 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.94 % Favored : 90.01 % Rotamer: Outliers : 3.13 % Allowed : 18.04 % Favored : 78.83 % 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: -2.27 (0.18), residues: 1952 helix: -0.25 (0.31), residues: 250 sheet: -1.00 (0.21), residues: 616 loop : -2.18 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 141 TYR 0.019 0.001 TYR A 368 PHE 0.023 0.002 PHE B 452 TRP 0.023 0.002 TRP A 224 HIS 0.005 0.001 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00393 (17762) covalent geometry : angle 0.63960 (24506) hydrogen bonds : bond 0.04808 ( 489) hydrogen bonds : angle 5.06083 ( 1341) metal coordination : bond 0.01257 ( 3) metal coordination : angle 9.95529 ( 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 378 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 324 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7889 (m) REVERT: A 114 VAL cc_start: 0.8255 (m) cc_final: 0.8029 (p) REVERT: A 120 ASP cc_start: 0.7274 (p0) cc_final: 0.6921 (p0) REVERT: A 210 SER cc_start: 0.8025 (t) cc_final: 0.7615 (p) REVERT: A 343 LYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6368 (tppt) REVERT: A 358 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7609 (ttt90) REVERT: A 379 ARG cc_start: 0.7651 (ptm-80) cc_final: 0.7362 (ptm-80) REVERT: A 389 SER cc_start: 0.8266 (m) cc_final: 0.7904 (p) REVERT: A 554 ASP cc_start: 0.7495 (t0) cc_final: 0.7111 (t0) REVERT: A 611 GLU cc_start: 0.7200 (mp0) cc_final: 0.6861 (mp0) REVERT: A 643 SER cc_start: 0.8202 (p) cc_final: 0.7819 (m) REVERT: B 32 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7411 (tp) REVERT: B 91 GLU cc_start: 0.7933 (tp30) cc_final: 0.7551 (mt-10) REVERT: B 132 SER cc_start: 0.8412 (m) cc_final: 0.7772 (p) REVERT: B 139 VAL cc_start: 0.8576 (t) cc_final: 0.8255 (p) REVERT: B 333 ARG cc_start: 0.5601 (tpp-160) cc_final: 0.5098 (tpp-160) REVERT: B 387 HIS cc_start: 0.7226 (m-70) cc_final: 0.6465 (m-70) REVERT: B 408 THR cc_start: 0.8104 (m) cc_final: 0.7845 (t) REVERT: B 422 ASP cc_start: 0.7793 (m-30) cc_final: 0.7546 (m-30) REVERT: B 727 SER cc_start: 0.8557 (t) cc_final: 0.8111 (m) REVERT: B 804 TRP cc_start: 0.7761 (m100) cc_final: 0.7068 (m100) REVERT: C 15 MET cc_start: 0.6119 (tmm) cc_final: 0.5832 (tmm) REVERT: C 16 MET cc_start: 0.6702 (ppp) cc_final: 0.6218 (ppp) REVERT: C 39 ASN cc_start: 0.8662 (m110) cc_final: 0.8314 (m110) REVERT: C 107 ASN cc_start: 0.7354 (t0) cc_final: 0.7075 (t0) REVERT: C 236 LEU cc_start: 0.7049 (mt) cc_final: 0.6801 (mt) REVERT: C 259 ASN cc_start: 0.8021 (t0) cc_final: 0.7795 (t0) REVERT: C 275 LYS cc_start: 0.7662 (mtpp) cc_final: 0.7430 (mtpt) REVERT: C 288 ASP cc_start: 0.7759 (t0) cc_final: 0.7520 (t70) REVERT: C 411 ILE cc_start: 0.7941 (pt) cc_final: 0.7635 (mt) REVERT: C 440 GLU cc_start: 0.7717 (pt0) cc_final: 0.7503 (pt0) REVERT: C 480 SER cc_start: 0.8159 (m) cc_final: 0.7832 (t) REVERT: C 533 ILE cc_start: 0.8116 (mm) cc_final: 0.7798 (mt) REVERT: C 536 ARG cc_start: 0.7281 (mtm110) cc_final: 0.7030 (ttm110) outliers start: 54 outliers final: 42 residues processed: 352 average time/residue: 0.1278 time to fit residues: 67.8202 Evaluate side-chains 364 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 319 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 136 MET 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 614 MET 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 A residue 659 THR Chi-restraints excluded: chain A residue 697 ILE 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 200 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 279 LEU 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 32 GLN 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 213 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 286 MET 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 453 LEU 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: 1.9990 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 194 optimal weight: 0.0770 chunk 111 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 GLN B 23 ASN B 102 HIS C 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.164045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.136368 restraints weight = 25437.036| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.28 r_work: 0.3671 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17765 Z= 0.158 Angle : 0.669 25.767 24515 Z= 0.331 Chirality : 0.045 0.212 2796 Planarity : 0.005 0.081 2856 Dihedral : 16.384 136.245 3363 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.73 % Favored : 90.22 % Rotamer: Outliers : 3.36 % Allowed : 17.92 % Favored : 78.71 % 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: -2.23 (0.18), residues: 1952 helix: -0.24 (0.31), residues: 250 sheet: -0.95 (0.21), residues: 605 loop : -2.15 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 449 TYR 0.018 0.001 TYR A 368 PHE 0.023 0.002 PHE B 452 TRP 0.021 0.002 TRP A 224 HIS 0.007 0.001 HIS B 102 Details of bonding type rmsd covalent geometry : bond 0.00372 (17762) covalent geometry : angle 0.63692 (24506) hydrogen bonds : bond 0.04719 ( 489) hydrogen bonds : angle 5.02444 ( 1341) metal coordination : bond 0.01363 ( 3) metal coordination : angle 10.76773 ( 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 385 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 327 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8150 (OUTLIER) cc_final: 0.7795 (m) REVERT: A 114 VAL cc_start: 0.8275 (OUTLIER) cc_final: 0.8051 (p) REVERT: A 120 ASP cc_start: 0.7306 (p0) cc_final: 0.6917 (p0) REVERT: A 210 SER cc_start: 0.8019 (t) cc_final: 0.7613 (p) REVERT: A 343 LYS cc_start: 0.6732 (OUTLIER) cc_final: 0.6342 (tppt) REVERT: A 379 ARG cc_start: 0.7592 (ptm-80) cc_final: 0.7283 (ptm-80) REVERT: A 554 ASP cc_start: 0.7501 (t0) cc_final: 0.7120 (t0) REVERT: A 609 GLN cc_start: 0.7663 (tt0) cc_final: 0.6829 (tm-30) REVERT: A 611 GLU cc_start: 0.7195 (mp0) cc_final: 0.6728 (mp0) REVERT: A 643 SER cc_start: 0.8202 (p) cc_final: 0.7766 (m) REVERT: B 91 GLU cc_start: 0.7971 (tp30) cc_final: 0.7620 (mt-10) REVERT: B 132 SER cc_start: 0.8428 (m) cc_final: 0.7800 (p) REVERT: B 139 VAL cc_start: 0.8566 (t) cc_final: 0.8233 (p) REVERT: B 387 HIS cc_start: 0.7183 (m-70) cc_final: 0.6502 (m-70) REVERT: B 408 THR cc_start: 0.8072 (m) cc_final: 0.7864 (t) REVERT: B 422 ASP cc_start: 0.7760 (m-30) cc_final: 0.7497 (m-30) REVERT: B 727 SER cc_start: 0.8569 (t) cc_final: 0.8124 (m) REVERT: B 804 TRP cc_start: 0.7766 (m100) cc_final: 0.7196 (m100) REVERT: C 16 MET cc_start: 0.6712 (ppp) cc_final: 0.6410 (ppp) REVERT: C 107 ASN cc_start: 0.7392 (t0) cc_final: 0.7113 (t0) REVERT: C 236 LEU cc_start: 0.7087 (mt) cc_final: 0.6813 (mt) REVERT: C 259 ASN cc_start: 0.8011 (t0) cc_final: 0.7787 (t0) REVERT: C 275 LYS cc_start: 0.7687 (mtpp) cc_final: 0.7432 (mtpt) REVERT: C 288 ASP cc_start: 0.7724 (t0) cc_final: 0.7506 (t70) REVERT: C 411 ILE cc_start: 0.7953 (pt) cc_final: 0.7679 (mt) REVERT: C 440 GLU cc_start: 0.7686 (pt0) cc_final: 0.7378 (pt0) REVERT: C 480 SER cc_start: 0.8155 (m) cc_final: 0.7844 (t) REVERT: C 533 ILE cc_start: 0.8093 (mm) cc_final: 0.7791 (mt) REVERT: C 536 ARG cc_start: 0.7237 (mtm110) cc_final: 0.7005 (ttm110) outliers start: 58 outliers final: 46 residues processed: 358 average time/residue: 0.1226 time to fit residues: 66.4569 Evaluate side-chains 365 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 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 114 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 136 MET 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 614 MET 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 A residue 659 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 104 GLN Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 220 ARG 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 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 177 LEU Chi-restraints excluded: chain C residue 193 LEU 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 286 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 24 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 HIS ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 ASN B 593 HIS ** 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 = 0.4128 r_free = 0.4128 target = 0.161968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.134505 restraints weight = 25432.230| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.24 r_work: 0.3653 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 17765 Z= 0.206 Angle : 0.713 28.015 24515 Z= 0.354 Chirality : 0.047 0.233 2796 Planarity : 0.006 0.086 2856 Dihedral : 16.419 134.472 3363 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.86 % Favored : 89.09 % Rotamer: Outliers : 3.36 % Allowed : 18.50 % Favored : 78.13 % 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 (0.18), residues: 1952 helix: -0.47 (0.30), residues: 251 sheet: -0.96 (0.21), residues: 614 loop : -2.20 (0.17), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 449 TYR 0.021 0.002 TYR A 416 PHE 0.028 0.002 PHE C 436 TRP 0.023 0.002 TRP A 224 HIS 0.006 0.001 HIS B 366 Details of bonding type rmsd covalent geometry : bond 0.00491 (17762) covalent geometry : angle 0.67904 (24506) hydrogen bonds : bond 0.05242 ( 489) hydrogen bonds : angle 5.15797 ( 1341) metal coordination : bond 0.01392 ( 3) metal coordination : angle 11.39648 ( 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 387 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 329 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7150 (mtm110) cc_final: 0.6905 (mtm110) REVERT: A 33 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7799 (m) REVERT: A 46 PRO cc_start: 0.8007 (Cg_endo) cc_final: 0.7659 (Cg_exo) REVERT: A 120 ASP cc_start: 0.7299 (p0) cc_final: 0.6818 (p0) REVERT: A 210 SER cc_start: 0.7984 (t) cc_final: 0.7560 (p) REVERT: A 343 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6344 (tppt) REVERT: A 379 ARG cc_start: 0.7633 (ptm-80) cc_final: 0.7332 (ptm-80) REVERT: A 554 ASP cc_start: 0.7495 (t0) cc_final: 0.7122 (t0) REVERT: A 609 GLN cc_start: 0.7677 (tt0) cc_final: 0.6791 (tm-30) REVERT: A 611 GLU cc_start: 0.7174 (mp0) cc_final: 0.6674 (mp0) REVERT: A 643 SER cc_start: 0.8195 (p) cc_final: 0.7770 (m) REVERT: B 91 GLU cc_start: 0.7973 (tp30) cc_final: 0.7658 (mt-10) REVERT: B 132 SER cc_start: 0.8451 (m) cc_final: 0.7839 (p) REVERT: B 139 VAL cc_start: 0.8576 (t) cc_final: 0.8245 (p) REVERT: B 277 THR cc_start: 0.6579 (OUTLIER) cc_final: 0.5957 (m) REVERT: B 378 TRP cc_start: 0.6525 (m100) cc_final: 0.6013 (m100) REVERT: B 387 HIS cc_start: 0.7187 (m-70) cc_final: 0.6500 (m-70) REVERT: B 408 THR cc_start: 0.8097 (m) cc_final: 0.7861 (t) REVERT: B 422 ASP cc_start: 0.7763 (m-30) cc_final: 0.7519 (m-30) REVERT: B 727 SER cc_start: 0.8579 (t) cc_final: 0.8128 (m) REVERT: B 804 TRP cc_start: 0.7812 (m100) cc_final: 0.7295 (m100) REVERT: C 16 MET cc_start: 0.6759 (ppp) cc_final: 0.6337 (ppp) REVERT: C 107 ASN cc_start: 0.7417 (t0) cc_final: 0.7159 (m-40) REVERT: C 236 LEU cc_start: 0.7139 (mt) cc_final: 0.6899 (mt) REVERT: C 259 ASN cc_start: 0.8036 (t0) cc_final: 0.7801 (t0) REVERT: C 275 LYS cc_start: 0.7734 (mtpp) cc_final: 0.7466 (mtpt) REVERT: C 280 LYS cc_start: 0.7568 (mtmm) cc_final: 0.7075 (mtmm) REVERT: C 288 ASP cc_start: 0.7808 (t0) cc_final: 0.7577 (t70) REVERT: C 411 ILE cc_start: 0.7965 (pt) cc_final: 0.7710 (mt) REVERT: C 480 SER cc_start: 0.8247 (m) cc_final: 0.7940 (t) REVERT: C 536 ARG cc_start: 0.7312 (mtm110) cc_final: 0.7068 (ttm110) outliers start: 58 outliers final: 47 residues processed: 359 average time/residue: 0.1280 time to fit residues: 68.9856 Evaluate side-chains 372 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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 136 MET 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 614 MET 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 A residue 659 THR Chi-restraints excluded: chain A residue 697 ILE 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 206 HIS 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 593 HIS 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 92 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 177 LEU 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 286 MET 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 95 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.0030 chunk 184 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 11 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS A 489 GLN A 661 GLN B 593 HIS C 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.163337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135760 restraints weight = 25236.004| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.24 r_work: 0.3670 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 17765 Z= 0.149 Angle : 0.694 29.076 24515 Z= 0.338 Chirality : 0.045 0.226 2796 Planarity : 0.005 0.083 2856 Dihedral : 16.345 132.707 3363 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.38 % Favored : 90.57 % Rotamer: Outliers : 3.13 % Allowed : 19.03 % 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: -2.24 (0.18), residues: 1952 helix: -0.31 (0.31), residues: 251 sheet: -0.94 (0.22), residues: 606 loop : -2.16 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 689 TYR 0.018 0.001 TYR A 368 PHE 0.022 0.002 PHE C 304 TRP 0.025 0.002 TRP A 224 HIS 0.007 0.001 HIS B 593 Details of bonding type rmsd covalent geometry : bond 0.00352 (17762) covalent geometry : angle 0.65009 (24506) hydrogen bonds : bond 0.04669 ( 489) hydrogen bonds : angle 5.04654 ( 1341) metal coordination : bond 0.01336 ( 3) metal coordination : angle 12.67503 ( 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 376 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 322 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7736 (m) REVERT: A 120 ASP cc_start: 0.7399 (p0) cc_final: 0.6977 (p0) REVERT: A 210 SER cc_start: 0.8015 (t) cc_final: 0.7604 (p) REVERT: A 343 LYS cc_start: 0.6685 (OUTLIER) cc_final: 0.6304 (tppt) REVERT: A 379 ARG cc_start: 0.7580 (ptm-80) cc_final: 0.7289 (ptm-80) REVERT: A 554 ASP cc_start: 0.7487 (t0) cc_final: 0.7112 (t0) REVERT: A 609 GLN cc_start: 0.7663 (tt0) cc_final: 0.6796 (tm-30) REVERT: A 611 GLU cc_start: 0.7208 (mp0) cc_final: 0.6702 (mp0) REVERT: A 643 SER cc_start: 0.8202 (p) cc_final: 0.7757 (m) REVERT: B 91 GLU cc_start: 0.7963 (tp30) cc_final: 0.7641 (mt-10) REVERT: B 132 SER cc_start: 0.8445 (m) cc_final: 0.7816 (p) REVERT: B 139 VAL cc_start: 0.8546 (t) cc_final: 0.8212 (p) REVERT: B 231 CYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8582 (m) REVERT: B 277 THR cc_start: 0.6563 (OUTLIER) cc_final: 0.5963 (m) REVERT: B 368 TRP cc_start: 0.8159 (m-90) cc_final: 0.7529 (m-10) REVERT: B 387 HIS cc_start: 0.7210 (m-70) cc_final: 0.6497 (m-70) REVERT: B 388 PHE cc_start: 0.6808 (p90) cc_final: 0.6538 (p90) REVERT: B 408 THR cc_start: 0.8078 (m) cc_final: 0.7874 (t) REVERT: B 422 ASP cc_start: 0.7755 (m-30) cc_final: 0.7496 (m-30) REVERT: B 717 LEU cc_start: 0.7336 (tp) cc_final: 0.7083 (tt) REVERT: B 727 SER cc_start: 0.8546 (t) cc_final: 0.8086 (m) REVERT: B 804 TRP cc_start: 0.7799 (m100) cc_final: 0.7379 (m100) REVERT: C 16 MET cc_start: 0.6706 (ppp) cc_final: 0.6438 (ppp) REVERT: C 107 ASN cc_start: 0.7465 (t0) cc_final: 0.7210 (t0) REVERT: C 236 LEU cc_start: 0.6994 (mt) cc_final: 0.6763 (mt) REVERT: C 259 ASN cc_start: 0.8041 (t0) cc_final: 0.7813 (t0) REVERT: C 275 LYS cc_start: 0.7660 (mtpp) cc_final: 0.7437 (mtpt) REVERT: C 288 ASP cc_start: 0.7742 (t0) cc_final: 0.7525 (t70) REVERT: C 321 LEU cc_start: 0.8037 (mp) cc_final: 0.7757 (mt) REVERT: C 411 ILE cc_start: 0.7947 (pt) cc_final: 0.7675 (mt) REVERT: C 440 GLU cc_start: 0.7687 (pt0) cc_final: 0.7406 (pt0) REVERT: C 480 SER cc_start: 0.8155 (m) cc_final: 0.7837 (t) REVERT: C 536 ARG cc_start: 0.7259 (mtm110) cc_final: 0.7026 (ttm110) outliers start: 54 outliers final: 43 residues processed: 352 average time/residue: 0.1310 time to fit residues: 70.2269 Evaluate side-chains 367 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 320 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 136 MET 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 422 HIS 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 A residue 659 THR Chi-restraints excluded: chain A residue 697 ILE Chi-restraints excluded: chain B residue 24 TRP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 206 HIS Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 231 CYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 279 LEU 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 593 HIS 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 32 GLN Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 177 LEU 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 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: 0.9990 chunk 147 optimal weight: 0.6980 chunk 69 optimal weight: 0.0970 chunk 193 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 120 optimal weight: 0.0470 chunk 56 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.164407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.136420 restraints weight = 25293.600| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 2.33 r_work: 0.3674 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 17765 Z= 0.144 Angle : 0.690 29.199 24515 Z= 0.335 Chirality : 0.045 0.227 2796 Planarity : 0.005 0.083 2856 Dihedral : 16.310 131.228 3363 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.63 % Favored : 90.32 % Rotamer: Outliers : 3.19 % Allowed : 19.14 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.18), residues: 1952 helix: -0.28 (0.31), residues: 251 sheet: -0.91 (0.21), residues: 620 loop : -2.17 (0.17), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 689 TYR 0.018 0.001 TYR A 368 PHE 0.023 0.002 PHE C 304 TRP 0.025 0.001 TRP A 224 HIS 0.005 0.001 HIS C 380 Details of bonding type rmsd covalent geometry : bond 0.00342 (17762) covalent geometry : angle 0.64351 (24506) hydrogen bonds : bond 0.04571 ( 489) hydrogen bonds : angle 5.02313 ( 1341) metal coordination : bond 0.01221 ( 3) metal coordination : angle 12.98234 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4858.82 seconds wall clock time: 83 minutes 51.48 seconds (5031.48 seconds total)