Starting phenix.real_space_refine on Sat Jul 4 04:21:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h69_34497/07_2026/8h69_34497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h69_34497/07_2026/8h69_34497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8h69_34497/07_2026/8h69_34497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h69_34497/07_2026/8h69_34497.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8h69_34497/07_2026/8h69_34497.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h69_34497/07_2026/8h69_34497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h69_34497/07_2026/8h69_34497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h69_34497/07_2026/8h69_34497.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 128 5.16 5 C 11214 2.51 5 N 3150 2.21 5 O 3500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18028 Number of models: 1 Model: "" Number of chains: 5 Chain: "3" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 369 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 4, 'rna3p_pyr': 9} Link IDs: {'rna2p': 5, 'rna3p': 12} Chain: "5" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "A" Number of atoms: 5790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 716, 5790 Classifications: {'peptide': 716} Link IDs: {'PTRANS': 33, 'TRANS': 682} Chain: "B" Number of atoms: 6022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 754, 6022 Classifications: {'peptide': 754} Link IDs: {'PTRANS': 32, 'TRANS': 721} Chain: "C" Number of atoms: 5436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5436 Classifications: {'peptide': 683} Link IDs: {'PTRANS': 27, 'TRANS': 655} Time building chain proxies: 4.86, per 1000 atoms: 0.27 Number of scatterers: 18028 At special positions: 0 Unit cell: (136.24, 123.76, 116.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 128 16.00 P 36 15.00 O 3500 8.00 N 3150 7.00 C 11214 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: 1.68 Conformation dependent library (CDL) restraints added in 623.1 milliseconds 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4058 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 22 sheets defined 42.3% alpha, 11.5% beta 8 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 10 through 22 removed outlier: 3.653A pdb=" N LEU A 16 " --> pdb=" O MET A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 48 removed outlier: 3.817A pdb=" N CYS A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.600A pdb=" N TRP A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 removed outlier: 3.998A pdb=" N TYR A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LEU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 4.014A pdb=" N ALA A 159 " --> pdb=" O ALA A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 186 removed outlier: 3.864A pdb=" N GLY A 186 " --> pdb=" O MET A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 4.059A pdb=" N ASP A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.570A pdb=" N GLN A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 313 removed outlier: 3.643A pdb=" N ILE A 308 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A 309 " --> pdb=" O TYR A 305 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 345 removed outlier: 4.083A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.762A pdb=" N TRP A 368 " --> pdb=" O SER A 364 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 369' Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.629A pdb=" N SER A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 446 through 449 Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.553A pdb=" N TYR A 458 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 464 " --> pdb=" O MET A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.549A pdb=" N GLU A 533 " --> pdb=" O PRO A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 583 through 598 removed outlier: 4.040A pdb=" N GLN A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE A 592 " --> pdb=" O SER A 588 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE A 596 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 597 " --> pdb=" O GLU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 604 removed outlier: 3.730A pdb=" N LYS A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.722A pdb=" N PHE A 611 " --> pdb=" O MET A 607 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 612' Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.774A pdb=" N ARG A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 641 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 648 " --> pdb=" O SER A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 660 removed outlier: 3.882A pdb=" N GLU A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 674 removed outlier: 4.347A pdb=" N ILE A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 699 through 712 removed outlier: 3.624A pdb=" N SER A 705 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 removed outlier: 3.882A pdb=" N PHE B 9 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.516A pdb=" N THR B 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.568A pdb=" N THR B 42 " --> pdb=" O TYR B 38 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 4.209A pdb=" N GLU B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 removed outlier: 3.506A pdb=" N SER B 98 " --> pdb=" O PHE B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.678A pdb=" N ASN B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU B 109 " --> pdb=" O ASN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.718A pdb=" N LEU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 150 " --> pdb=" O THR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.705A pdb=" N VAL B 170 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 222 removed outlier: 3.671A pdb=" N ARG B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 266 removed outlier: 4.075A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY B 250 " --> pdb=" O MET B 246 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N CYS B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 265 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 removed outlier: 3.666A pdb=" N LYS B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 291 removed outlier: 3.503A pdb=" N THR B 291 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 371 through 375 removed outlier: 3.650A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.760A pdb=" N LYS B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 415 through 427 removed outlier: 3.780A pdb=" N LEU B 424 " --> pdb=" O GLY B 420 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 427 " --> pdb=" O ILE B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 471 removed outlier: 3.613A pdb=" N ASP B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG B 465 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 525 through 534 removed outlier: 3.546A pdb=" N ILE B 530 " --> pdb=" O GLY B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.647A pdb=" N LYS B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 558 " --> pdb=" O ASP B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 583 removed outlier: 3.766A pdb=" N LYS B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 579 " --> pdb=" O GLU B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.919A pdb=" N GLY B 588 " --> pdb=" O SER B 585 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 585 through 589' Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.658A pdb=" N ASP B 593 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 removed outlier: 4.307A pdb=" N GLN B 621 " --> pdb=" O ASP B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 676 removed outlier: 3.502A pdb=" N ASN B 676 " --> pdb=" O SER B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 683 removed outlier: 3.652A pdb=" N ILE B 682 " --> pdb=" O GLN B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 701 through 705 removed outlier: 4.059A pdb=" N SER B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 731 removed outlier: 3.848A pdb=" N VAL B 719 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG B 721 " --> pdb=" O ALA B 717 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG B 727 " --> pdb=" O ARG B 723 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ILE B 728 " --> pdb=" O ILE B 724 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP B 729 " --> pdb=" O ASP B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 752 removed outlier: 3.541A pdb=" N GLU B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 746 " --> pdb=" O GLU B 742 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS B 747 " --> pdb=" O ILE B 743 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 748 " --> pdb=" O MET B 744 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 749 " --> pdb=" O LYS B 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 10 removed outlier: 4.407A pdb=" N GLU C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 Processing helix chain 'C' and resid 42 through 51 removed outlier: 3.594A pdb=" N ARG C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.179A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.525A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.635A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 168 removed outlier: 3.756A pdb=" N PHE C 168 " --> pdb=" O MET C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 172 removed outlier: 3.673A pdb=" N VAL C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 172' Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.870A pdb=" N ILE C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.569A pdb=" N LEU C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 273 removed outlier: 4.049A pdb=" N ILE C 261 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 262 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 272 " --> pdb=" O ARG C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.691A pdb=" N LEU C 280 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU C 281 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 286 No H-bonds generated for 'chain 'C' and resid 284 through 286' Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 305 through 315 removed outlier: 3.894A pdb=" N MET C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 405 Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 429 through 441 removed outlier: 3.662A pdb=" N ARG C 436 " --> pdb=" O HIS C 432 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 449 Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 541 through 556 removed outlier: 3.551A pdb=" N LEU C 546 " --> pdb=" O PRO C 542 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR C 550 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE C 554 " --> pdb=" O TYR C 550 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 555 " --> pdb=" O GLN C 551 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN C 556 " --> pdb=" O TRP C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 566 removed outlier: 3.877A pdb=" N ILE C 562 " --> pdb=" O GLU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 579 through 583 removed outlier: 3.593A pdb=" N SER C 582 " --> pdb=" O SER C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 607 removed outlier: 3.598A pdb=" N THR C 598 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 607 " --> pdb=" O MET C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 619 removed outlier: 3.762A pdb=" N ILE C 616 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 619 " --> pdb=" O ILE C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 624 removed outlier: 3.883A pdb=" N ALA C 623 " --> pdb=" O PRO C 620 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA C 624 " --> pdb=" O PHE C 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 620 through 624' Processing helix chain 'C' and resid 677 through 682 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.209A pdb=" N PHE A 117 " --> pdb=" O HIS A 144 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N HIS A 146 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU A 119 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N PHE A 148 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY A 121 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.007A pdb=" N LEU A 500 " --> pdb=" O SER A 487 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER A 487 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 502 " --> pdb=" O MET A 485 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 481 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A 480 " --> pdb=" O MET A 360 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS A 358 " --> pdb=" O LEU A 482 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 293 removed outlier: 3.560A pdb=" N VAL A 557 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 559 " --> pdb=" O MET A 548 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET A 548 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 377 through 378 removed outlier: 3.588A pdb=" N ARG B 365 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU B 364 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR B 355 " --> pdb=" O ILE B 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.691A pdb=" N GLY A 627 " --> pdb=" O GLU A 623 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU A 623 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLU A 629 " --> pdb=" O ILE A 621 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.637A pdb=" N GLN B 210 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 186 through 192 removed outlier: 3.619A pdb=" N THR B 204 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 202 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 243 removed outlier: 6.930A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 437 through 442 Processing sheet with id=AB3, first strand: chain 'B' and resid 489 through 490 removed outlier: 3.621A pdb=" N PHE B 490 " --> pdb=" O TYR B 497 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 643 through 644 removed outlier: 3.683A pdb=" N ALA B 643 " --> pdb=" O MET B 655 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.339A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 129 through 134 removed outlier: 4.448A pdb=" N MET C 243 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N VAL C 133 " --> pdb=" O GLU C 241 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLU C 241 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 141 through 147 removed outlier: 3.679A pdb=" N ILE C 141 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 292 through 293 removed outlier: 3.593A pdb=" N ILE C 292 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.965A pdb=" N GLU C 362 " --> pdb=" O THR C 333 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR C 371 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL C 386 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE C 373 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU C 384 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG C 375 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ARG C 479 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU C 384 " --> pdb=" O ARG C 479 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N SER C 481 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 386 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL C 478 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE C 463 " --> pdb=" O VAL C 478 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 470 " --> pdb=" O GLY C 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 341 through 345 Processing sheet with id=AC2, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AC3, first strand: chain 'C' and resid 636 through 639 removed outlier: 3.530A pdb=" N LEU C 636 " --> pdb=" O ILE C 647 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 656 through 659 removed outlier: 3.565A pdb=" N ASN C 659 " --> pdb=" O ARG C 664 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 664 " --> pdb=" O ASN C 659 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU C 665 " --> pdb=" O ALA C 672 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1560 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4003 1.33 - 1.45: 4105 1.45 - 1.57: 10050 1.57 - 1.69: 71 1.69 - 1.81: 224 Bond restraints: 18453 Sorted by residual: bond pdb=" CA PHE A 205 " pdb=" CB PHE A 205 " ideal model delta sigma weight residual 1.525 1.472 0.053 1.47e-02 4.63e+03 1.29e+01 bond pdb=" N ASN B 314 " pdb=" CA ASN B 314 " ideal model delta sigma weight residual 1.457 1.407 0.050 1.41e-02 5.03e+03 1.26e+01 bond pdb=" N ASN C 429 " pdb=" CA ASN C 429 " ideal model delta sigma weight residual 1.453 1.493 -0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" N ARG C 427 " pdb=" CA ARG C 427 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.45e+00 bond pdb=" N ARG C 423 " pdb=" CA ARG C 423 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.82e+00 ... (remaining 18448 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 23518 2.11 - 4.23: 1297 4.23 - 6.34: 183 6.34 - 8.46: 46 8.46 - 10.57: 14 Bond angle restraints: 25058 Sorted by residual: angle pdb=" N VAL B 286 " pdb=" CA VAL B 286 " pdb=" C VAL B 286 " ideal model delta sigma weight residual 113.16 103.05 10.11 1.49e+00 4.50e-01 4.60e+01 angle pdb=" N ALA C 587 " pdb=" CA ALA C 587 " pdb=" C ALA C 587 " ideal model delta sigma weight residual 112.23 104.58 7.65 1.26e+00 6.30e-01 3.69e+01 angle pdb=" C HIS A 297 " pdb=" N GLU A 298 " pdb=" CA GLU A 298 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" N LEU B 271 " pdb=" CA LEU B 271 " pdb=" C LEU B 271 " ideal model delta sigma weight residual 113.16 120.52 -7.36 1.42e+00 4.96e-01 2.68e+01 angle pdb=" N VAL C 421 " pdb=" CA VAL C 421 " pdb=" C VAL C 421 " ideal model delta sigma weight residual 109.34 98.77 10.57 2.08e+00 2.31e-01 2.58e+01 ... (remaining 25053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 10508 17.69 - 35.37: 591 35.37 - 53.06: 113 53.06 - 70.75: 22 70.75 - 88.43: 7 Dihedral angle restraints: 11241 sinusoidal: 4974 harmonic: 6267 Sorted by residual: dihedral pdb=" CA CYS C 239 " pdb=" C CYS C 239 " pdb=" N TRP C 240 " pdb=" CA TRP C 240 " ideal model delta harmonic sigma weight residual -180.00 -150.90 -29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA GLN B 545 " pdb=" C GLN B 545 " pdb=" N MET B 546 " pdb=" CA MET B 546 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA LYS C 197 " pdb=" C LYS C 197 " pdb=" N ILE C 198 " pdb=" CA ILE C 198 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 ... (remaining 11238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1906 0.057 - 0.113: 698 0.113 - 0.170: 154 0.170 - 0.226: 24 0.226 - 0.283: 8 Chirality restraints: 2790 Sorted by residual: chirality pdb=" CA LEU B 224 " pdb=" N LEU B 224 " pdb=" C LEU B 224 " pdb=" CB LEU B 224 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE B 450 " pdb=" CA ILE B 450 " pdb=" CG1 ILE B 450 " pdb=" CG2 ILE B 450 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CG LEU B 604 " pdb=" CB LEU B 604 " pdb=" CD1 LEU B 604 " pdb=" CD2 LEU B 604 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2787 not shown) Planarity restraints: 3100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 633 " 0.035 2.00e-02 2.50e+03 2.86e-02 1.44e+01 pdb=" CG PHE C 633 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE C 633 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 633 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE C 633 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 PHE C 633 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 633 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 537 " 0.013 2.00e-02 2.50e+03 1.88e-02 8.87e+00 pdb=" CG TRP A 537 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP A 537 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 537 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 537 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 537 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 537 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 537 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 537 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 537 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 344 " 0.020 2.00e-02 2.50e+03 2.18e-02 8.35e+00 pdb=" CG PHE B 344 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 344 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 344 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 344 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 344 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 344 " 0.010 2.00e-02 2.50e+03 ... (remaining 3097 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 126 2.51 - 3.11: 12856 3.11 - 3.71: 28482 3.71 - 4.30: 41001 4.30 - 4.90: 64994 Nonbonded interactions: 147459 Sorted by model distance: nonbonded pdb=" O ASN C 425 " pdb=" O GLN C 426 " model vdw 1.917 3.040 nonbonded pdb=" OG SER C 273 " pdb=" OE1 GLU C 578 " model vdw 2.196 3.040 nonbonded pdb=" N GLN C 426 " pdb=" OE1 GLN C 426 " model vdw 2.197 3.120 nonbonded pdb=" O SER B 293 " pdb=" OG SER C 643 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR C 129 " pdb=" OG1 THR C 245 " model vdw 2.259 3.040 ... (remaining 147454 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.270 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 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 : 0.009 0.082 18453 Z= 0.426 Angle : 1.121 10.572 25058 Z= 0.630 Chirality : 0.061 0.283 2790 Planarity : 0.007 0.060 3100 Dihedral : 11.865 88.432 7183 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.36 % Rotamer: Outliers : 1.52 % Allowed : 3.98 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.14), residues: 2147 helix: -4.07 (0.09), residues: 819 sheet: -2.19 (0.33), residues: 214 loop : -2.92 (0.16), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 249 TYR 0.044 0.004 TYR B 30 PHE 0.060 0.004 PHE C 633 TRP 0.049 0.004 TRP A 537 HIS 0.008 0.002 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00917 / 0.43 (18453) covalent geometry : angle 1.12069 / 0.63 (25058) hydrogen bonds : bond 0.30222 / 18.00 ( 575) hydrogen bonds : angle 10.48436 / 6.22 ( 1596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 533 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4501 (ptp) cc_final: 0.4051 (mtm) REVERT: A 79 ILE cc_start: 0.8001 (mt) cc_final: 0.7784 (mp) REVERT: A 86 MET cc_start: 0.8795 (tpt) cc_final: 0.8517 (tpt) REVERT: A 342 LEU cc_start: 0.8745 (tp) cc_final: 0.8477 (tp) REVERT: A 540 TYR cc_start: 0.9020 (m-80) cc_final: 0.8700 (m-10) REVERT: A 674 ASP cc_start: 0.6162 (t0) cc_final: 0.5854 (t0) REVERT: B 49 TYR cc_start: 0.8897 (m-80) cc_final: 0.8662 (m-10) REVERT: B 87 CYS cc_start: 0.7974 (m) cc_final: 0.7773 (m) REVERT: B 281 LYS cc_start: 0.8027 (mttt) cc_final: 0.7423 (mtpp) REVERT: B 303 THR cc_start: 0.9213 (m) cc_final: 0.8978 (p) REVERT: B 322 ILE cc_start: 0.9280 (pp) cc_final: 0.9065 (pt) REVERT: B 518 ASN cc_start: 0.7222 (m110) cc_final: 0.7007 (m-40) REVERT: B 537 ASN cc_start: 0.8220 (m-40) cc_final: 0.7339 (t0) REVERT: B 663 THR cc_start: 0.8209 (p) cc_final: 0.7995 (m) REVERT: B 665 SER cc_start: 0.8472 (m) cc_final: 0.8150 (t) REVERT: B 720 SER cc_start: 0.8976 (m) cc_final: 0.8543 (t) REVERT: C 46 ARG cc_start: 0.7515 (mmt-90) cc_final: 0.6895 (mmt180) REVERT: C 47 MET cc_start: 0.7108 (tpp) cc_final: 0.6699 (tpp) REVERT: C 160 GLN cc_start: 0.8137 (mt0) cc_final: 0.7708 (pt0) REVERT: C 217 PHE cc_start: 0.6133 (p90) cc_final: 0.5735 (p90) REVERT: C 285 HIS cc_start: 0.6643 (m-70) cc_final: 0.6064 (m-70) REVERT: C 402 MET cc_start: -0.0513 (mtt) cc_final: -0.1115 (mtp) REVERT: C 428 LEU cc_start: 0.4241 (OUTLIER) cc_final: 0.3960 (mp) REVERT: C 526 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7409 (tptt) REVERT: C 535 MET cc_start: 0.6616 (mpm) cc_final: 0.5787 (mmm) REVERT: C 536 MET cc_start: 0.3010 (pmm) cc_final: 0.2239 (pmm) REVERT: C 543 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5742 (mm-30) REVERT: C 589 ARG cc_start: 0.4514 (OUTLIER) cc_final: 0.3984 (mtp180) outliers start: 29 outliers final: 4 residues processed: 550 average time/residue: 0.1500 time to fit residues: 119.5894 Evaluate side-chains 339 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 331 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 526 LYS Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain C residue 589 ARG Chi-restraints excluded: chain C residue 633 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS A 350 ASN A 519 ASN A 670 GLN B 58 ASN B 153 ASN B 284 ASN B 306 ASN B 310 ASN B 329 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 HIS C 110 HIS C 134 HIS C 182 GLN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 510 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.185536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.141603 restraints weight = 31987.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139271 restraints weight = 19580.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140516 restraints weight = 15954.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140916 restraints weight = 12217.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141165 restraints weight = 11371.263| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18453 Z= 0.148 Angle : 0.709 10.835 25058 Z= 0.371 Chirality : 0.045 0.297 2790 Planarity : 0.005 0.056 3100 Dihedral : 9.646 82.951 2811 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 2.72 % Allowed : 12.00 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.15), residues: 2147 helix: -2.63 (0.14), residues: 846 sheet: -2.17 (0.32), residues: 232 loop : -2.48 (0.17), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 563 TYR 0.018 0.002 TYR C 205 PHE 0.038 0.002 PHE C 595 TRP 0.030 0.002 TRP A 537 HIS 0.011 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (18453) covalent geometry : angle 0.70917 / 0.37 (25058) hydrogen bonds : bond 0.04948 / 2.95 ( 575) hydrogen bonds : angle 6.08405 / 3.66 ( 1596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 408 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4936 (ptp) cc_final: 0.4547 (mtm) REVERT: A 358 LYS cc_start: 0.8293 (tptm) cc_final: 0.8085 (tptt) REVERT: A 540 TYR cc_start: 0.9049 (m-80) cc_final: 0.8843 (m-80) REVERT: A 674 ASP cc_start: 0.6462 (t0) cc_final: 0.6008 (t0) REVERT: B 41 ASP cc_start: 0.7915 (t0) cc_final: 0.7656 (t0) REVERT: B 87 CYS cc_start: 0.7926 (m) cc_final: 0.7579 (m) REVERT: B 126 ARG cc_start: 0.7423 (mtm110) cc_final: 0.6997 (ptm160) REVERT: B 277 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7346 (mt-10) REVERT: B 284 ASN cc_start: 0.7962 (m-40) cc_final: 0.7667 (m110) REVERT: B 303 THR cc_start: 0.9132 (m) cc_final: 0.8900 (p) REVERT: B 443 SER cc_start: 0.8763 (t) cc_final: 0.8520 (p) REVERT: B 478 SER cc_start: 0.8793 (t) cc_final: 0.8336 (p) REVERT: B 537 ASN cc_start: 0.8326 (m-40) cc_final: 0.8053 (t0) REVERT: B 601 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8656 (tt) REVERT: B 604 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8352 (mp) REVERT: B 665 SER cc_start: 0.8625 (m) cc_final: 0.8219 (t) REVERT: B 694 ASN cc_start: 0.7914 (m110) cc_final: 0.7628 (t0) REVERT: B 720 SER cc_start: 0.8886 (m) cc_final: 0.8679 (p) REVERT: C 28 MET cc_start: 0.7462 (tmm) cc_final: 0.7190 (tmm) REVERT: C 47 MET cc_start: 0.7241 (tpp) cc_final: 0.6705 (tpp) REVERT: C 51 MET cc_start: 0.8102 (mmm) cc_final: 0.7697 (mmm) REVERT: C 136 ARG cc_start: 0.5565 (ppt170) cc_final: 0.5083 (mmt90) REVERT: C 160 GLN cc_start: 0.7967 (mt0) cc_final: 0.7619 (tt0) REVERT: C 171 GLU cc_start: 0.8024 (mp0) cc_final: 0.7731 (pm20) REVERT: C 217 PHE cc_start: 0.5679 (p90) cc_final: 0.5466 (p90) REVERT: C 230 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7285 (mm-30) REVERT: C 402 MET cc_start: -0.0245 (mtt) cc_final: -0.0692 (mtp) REVERT: C 405 SER cc_start: 0.4128 (p) cc_final: 0.3539 (t) REVERT: C 428 LEU cc_start: 0.3348 (OUTLIER) cc_final: 0.3113 (mp) REVERT: C 595 PHE cc_start: 0.6132 (p90) cc_final: 0.5589 (t80) outliers start: 52 outliers final: 22 residues processed: 433 average time/residue: 0.1361 time to fit residues: 87.6634 Evaluate side-chains 349 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 324 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 372 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 532 SER Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 4 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 208 optimal weight: 8.9990 chunk 171 optimal weight: 0.1980 chunk 9 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 HIS B 292 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN B 676 ASN ** C 551 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 = 0.4398 r_free = 0.4398 target = 0.185214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141192 restraints weight = 32187.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138594 restraints weight = 21405.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139701 restraints weight = 19294.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.139900 restraints weight = 15804.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140161 restraints weight = 13063.696| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18453 Z= 0.137 Angle : 0.661 10.903 25058 Z= 0.341 Chirality : 0.044 0.224 2790 Planarity : 0.004 0.040 3100 Dihedral : 8.988 80.461 2796 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.46 % Allowed : 14.20 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.16), residues: 2147 helix: -1.79 (0.16), residues: 858 sheet: -2.16 (0.32), residues: 230 loop : -2.11 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 454 TYR 0.025 0.002 TYR B 689 PHE 0.034 0.002 PHE C 595 TRP 0.020 0.001 TRP A 537 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (18453) covalent geometry : angle 0.66089 / 0.34 (25058) hydrogen bonds : bond 0.03911 / 2.34 ( 575) hydrogen bonds : angle 5.40849 / 3.28 ( 1596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 356 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4722 (ptp) cc_final: 0.4226 (mtm) REVERT: A 84 ARG cc_start: 0.7886 (mmm160) cc_final: 0.7631 (mmm160) REVERT: A 155 MET cc_start: -0.0474 (OUTLIER) cc_final: -0.0735 (ptp) REVERT: A 234 ASP cc_start: 0.7770 (p0) cc_final: 0.7549 (p0) REVERT: A 524 GLU cc_start: 0.8147 (mp0) cc_final: 0.7543 (mp0) REVERT: A 581 MET cc_start: 0.7656 (ttm) cc_final: 0.7454 (mtp) REVERT: A 595 MET cc_start: 0.7734 (mtp) cc_final: 0.7493 (mtm) REVERT: A 609 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6959 (tptt) REVERT: A 643 LYS cc_start: 0.8885 (tttp) cc_final: 0.8495 (ttpt) REVERT: A 674 ASP cc_start: 0.6578 (t0) cc_final: 0.6283 (t0) REVERT: A 682 ASP cc_start: 0.7039 (p0) cc_final: 0.6755 (p0) REVERT: B 126 ARG cc_start: 0.7408 (mtm110) cc_final: 0.7093 (ptm160) REVERT: B 176 LYS cc_start: 0.8170 (mppt) cc_final: 0.7939 (mtmt) REVERT: B 284 ASN cc_start: 0.7951 (m-40) cc_final: 0.7703 (m110) REVERT: B 303 THR cc_start: 0.9172 (m) cc_final: 0.8859 (p) REVERT: B 478 SER cc_start: 0.9050 (t) cc_final: 0.8261 (p) REVERT: B 537 ASN cc_start: 0.8632 (m-40) cc_final: 0.8042 (t0) REVERT: B 601 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8751 (tt) REVERT: B 665 SER cc_start: 0.8637 (m) cc_final: 0.8346 (t) REVERT: B 694 ASN cc_start: 0.7983 (m110) cc_final: 0.7609 (t0) REVERT: B 699 PHE cc_start: 0.6411 (t80) cc_final: 0.5654 (t80) REVERT: B 705 TYR cc_start: 0.8567 (t80) cc_final: 0.8303 (t80) REVERT: B 720 SER cc_start: 0.8861 (m) cc_final: 0.8645 (p) REVERT: C 2 GLU cc_start: 0.7327 (mt-10) cc_final: 0.6969 (tp30) REVERT: C 47 MET cc_start: 0.7293 (tpp) cc_final: 0.6636 (tpp) REVERT: C 51 MET cc_start: 0.8191 (mmm) cc_final: 0.7697 (mmm) REVERT: C 160 GLN cc_start: 0.7936 (mt0) cc_final: 0.7449 (tt0) REVERT: C 164 MET cc_start: 0.8150 (mmt) cc_final: 0.7878 (mmp) REVERT: C 171 GLU cc_start: 0.8033 (mp0) cc_final: 0.7476 (pm20) REVERT: C 187 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8386 (pptt) REVERT: C 217 PHE cc_start: 0.5862 (p90) cc_final: 0.5129 (p90) REVERT: C 230 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7258 (mm-30) REVERT: C 294 MET cc_start: 0.6525 (ppp) cc_final: 0.6258 (ppp) REVERT: C 305 GLU cc_start: 0.7060 (tm-30) cc_final: 0.4989 (mp0) REVERT: C 312 LYS cc_start: 0.7275 (mttt) cc_final: 0.6860 (mtmm) REVERT: C 331 LYS cc_start: 0.5217 (mttt) cc_final: 0.5013 (mtmt) REVERT: C 407 GLU cc_start: 0.5068 (OUTLIER) cc_final: 0.4473 (mp0) REVERT: C 428 LEU cc_start: 0.3409 (OUTLIER) cc_final: 0.3060 (mp) outliers start: 47 outliers final: 25 residues processed: 379 average time/residue: 0.1421 time to fit residues: 80.7127 Evaluate side-chains 345 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 315 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 459 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 192 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN B 115 GLN B 136 ASN B 292 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 265 ASN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.177639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134059 restraints weight = 31981.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130692 restraints weight = 21416.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131970 restraints weight = 19565.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132356 restraints weight = 14395.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.132544 restraints weight = 13326.189| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18453 Z= 0.259 Angle : 0.741 11.397 25058 Z= 0.381 Chirality : 0.047 0.304 2790 Planarity : 0.005 0.050 3100 Dihedral : 9.158 79.204 2795 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.56 % Allowed : 15.40 % Favored : 81.04 % 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: -2.79 (0.17), residues: 2147 helix: -1.59 (0.16), residues: 842 sheet: -2.07 (0.30), residues: 255 loop : -1.93 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 8 TYR 0.033 0.002 TYR B 689 PHE 0.029 0.002 PHE B 740 TRP 0.018 0.002 TRP A 537 HIS 0.005 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.26 (18453) covalent geometry : angle 0.74099 / 0.38 (25058) hydrogen bonds : bond 0.04076 / 2.44 ( 575) hydrogen bonds : angle 5.45461 / 3.31 ( 1596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 320 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4524 (ptp) cc_final: 0.3998 (mtm) REVERT: A 257 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9063 (mp) REVERT: A 537 TRP cc_start: 0.8242 (m-90) cc_final: 0.7538 (m-10) REVERT: A 564 TYR cc_start: 0.8886 (m-80) cc_final: 0.8406 (m-80) REVERT: A 609 LYS cc_start: 0.7637 (OUTLIER) cc_final: 0.7332 (tptt) REVERT: A 661 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7845 (pm20) REVERT: A 670 GLN cc_start: 0.7732 (tp-100) cc_final: 0.6129 (tp40) REVERT: B 126 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7179 (ptm160) REVERT: B 284 ASN cc_start: 0.7925 (m-40) cc_final: 0.7566 (m110) REVERT: B 303 THR cc_start: 0.9193 (m) cc_final: 0.8870 (p) REVERT: B 407 MET cc_start: 0.7450 (mmt) cc_final: 0.7216 (mmm) REVERT: B 408 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6495 (ptm) REVERT: B 497 TYR cc_start: 0.8275 (t80) cc_final: 0.8024 (t80) REVERT: B 537 ASN cc_start: 0.8658 (m-40) cc_final: 0.8003 (t0) REVERT: B 601 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8740 (tt) REVERT: B 604 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8392 (mp) REVERT: B 658 ASP cc_start: 0.8303 (m-30) cc_final: 0.7843 (m-30) REVERT: B 665 SER cc_start: 0.8707 (m) cc_final: 0.8294 (t) REVERT: B 720 SER cc_start: 0.8963 (m) cc_final: 0.8717 (p) REVERT: C 2 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7471 (tp30) REVERT: C 47 MET cc_start: 0.7473 (tpp) cc_final: 0.6962 (tpp) REVERT: C 51 MET cc_start: 0.8214 (mmm) cc_final: 0.7996 (mmm) REVERT: C 160 GLN cc_start: 0.8003 (mt0) cc_final: 0.7412 (tt0) REVERT: C 171 GLU cc_start: 0.8054 (mp0) cc_final: 0.7569 (pm20) REVERT: C 216 ARG cc_start: 0.7027 (ptp-110) cc_final: 0.6775 (ptp-110) REVERT: C 294 MET cc_start: 0.6836 (ppp) cc_final: 0.6549 (ppp) REVERT: C 312 LYS cc_start: 0.7491 (mttt) cc_final: 0.7125 (mmtt) REVERT: C 428 LEU cc_start: 0.3013 (OUTLIER) cc_final: 0.2618 (mp) REVERT: C 536 MET cc_start: 0.2850 (pmm) cc_final: 0.1885 (pmm) REVERT: C 595 PHE cc_start: 0.5851 (p90) cc_final: 0.5620 (p90) outliers start: 68 outliers final: 37 residues processed: 361 average time/residue: 0.1265 time to fit residues: 69.8147 Evaluate side-chains 330 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 476 ASN Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 190 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 170 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 136 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 213 optimal weight: 20.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.178730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.134962 restraints weight = 32131.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.132426 restraints weight = 22064.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.133649 restraints weight = 18703.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133969 restraints weight = 13977.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.134230 restraints weight = 13064.795| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18453 Z= 0.178 Angle : 0.677 11.231 25058 Z= 0.345 Chirality : 0.045 0.293 2790 Planarity : 0.004 0.056 3100 Dihedral : 8.850 80.505 2795 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.56 % Allowed : 16.29 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.17), residues: 2147 helix: -1.35 (0.17), residues: 857 sheet: -2.09 (0.30), residues: 262 loop : -1.83 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 204 TYR 0.027 0.002 TYR B 689 PHE 0.029 0.002 PHE B 740 TRP 0.016 0.001 TRP A 537 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (18453) covalent geometry : angle 0.67727 / 0.35 (25058) hydrogen bonds : bond 0.03632 / 2.16 ( 575) hydrogen bonds : angle 5.26058 / 3.23 ( 1596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 320 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4496 (ptp) cc_final: 0.4021 (mtm) REVERT: A 257 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9035 (mp) REVERT: A 523 MET cc_start: 0.8747 (mpp) cc_final: 0.8515 (mpp) REVERT: A 536 LYS cc_start: 0.9009 (tttt) cc_final: 0.8787 (ttmt) REVERT: A 564 TYR cc_start: 0.8919 (m-80) cc_final: 0.8548 (m-80) REVERT: A 595 MET cc_start: 0.8294 (mtp) cc_final: 0.7713 (mtm) REVERT: A 609 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7308 (tptt) REVERT: A 661 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: B 20 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8720 (m) REVERT: B 126 ARG cc_start: 0.7513 (mtm110) cc_final: 0.7186 (ptm160) REVERT: B 281 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8398 (mmmm) REVERT: B 284 ASN cc_start: 0.7702 (m-40) cc_final: 0.7366 (m110) REVERT: B 303 THR cc_start: 0.9168 (m) cc_final: 0.8806 (p) REVERT: B 407 MET cc_start: 0.7339 (mmt) cc_final: 0.7105 (mmm) REVERT: B 497 TYR cc_start: 0.8319 (t80) cc_final: 0.8002 (t80) REVERT: B 537 ASN cc_start: 0.8546 (m-40) cc_final: 0.7886 (t0) REVERT: B 578 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6534 (tmmt) REVERT: B 601 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8782 (tt) REVERT: B 611 LEU cc_start: 0.9418 (tp) cc_final: 0.9178 (tp) REVERT: B 646 MET cc_start: 0.5195 (mpp) cc_final: 0.4853 (tmm) REVERT: B 658 ASP cc_start: 0.8335 (m-30) cc_final: 0.8005 (m-30) REVERT: B 665 SER cc_start: 0.8743 (m) cc_final: 0.8286 (t) REVERT: C 64 MET cc_start: 0.7288 (mtm) cc_final: 0.7064 (ptp) REVERT: C 171 GLU cc_start: 0.8216 (mp0) cc_final: 0.7719 (pm20) REVERT: C 294 MET cc_start: 0.6895 (ppp) cc_final: 0.6581 (ppp) REVERT: C 312 LYS cc_start: 0.7517 (mttt) cc_final: 0.7105 (mttt) REVERT: C 428 LEU cc_start: 0.2950 (OUTLIER) cc_final: 0.2559 (mp) REVERT: C 536 MET cc_start: 0.2446 (pmm) cc_final: 0.1711 (pmm) REVERT: C 591 GLN cc_start: 0.7521 (pt0) cc_final: 0.7193 (pm20) REVERT: C 595 PHE cc_start: 0.5935 (p90) cc_final: 0.5293 (t80) outliers start: 68 outliers final: 37 residues processed: 368 average time/residue: 0.1392 time to fit residues: 76.7323 Evaluate side-chains 336 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 571 SER Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 633 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 29 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 143 optimal weight: 0.0770 chunk 51 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS A 499 ASN B 16 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN ** C 448 ASN ** 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 = 0.4353 r_free = 0.4353 target = 0.180984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137886 restraints weight = 31890.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135129 restraints weight = 21124.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136443 restraints weight = 17789.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.136788 restraints weight = 13383.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136964 restraints weight = 12412.724| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18453 Z= 0.133 Angle : 0.665 10.764 25058 Z= 0.337 Chirality : 0.043 0.223 2790 Planarity : 0.004 0.043 3100 Dihedral : 8.613 81.425 2795 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.09 % Allowed : 17.71 % Favored : 79.20 % 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: -2.35 (0.17), residues: 2147 helix: -1.10 (0.17), residues: 841 sheet: -1.96 (0.32), residues: 242 loop : -1.78 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 572 TYR 0.026 0.001 TYR B 689 PHE 0.031 0.002 PHE B 740 TRP 0.013 0.001 TRP A 537 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (18453) covalent geometry : angle 0.66476 / 0.34 (25058) hydrogen bonds : bond 0.03497 / 2.09 ( 575) hydrogen bonds : angle 5.10383 / 3.11 ( 1596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 317 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4580 (ptp) cc_final: 0.4092 (mtm) REVERT: A 410 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7929 (mt-10) REVERT: A 536 LYS cc_start: 0.9002 (tttt) cc_final: 0.8472 (ttmt) REVERT: A 566 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7476 (ttt-90) REVERT: A 583 ARG cc_start: 0.8272 (mtm110) cc_final: 0.8060 (mtm180) REVERT: A 609 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7284 (tptt) REVERT: A 661 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: A 670 GLN cc_start: 0.6936 (tp-100) cc_final: 0.6597 (tp-100) REVERT: B 126 ARG cc_start: 0.7608 (mtm110) cc_final: 0.7321 (ptm160) REVERT: B 133 LEU cc_start: 0.9019 (mm) cc_final: 0.8721 (mp) REVERT: B 284 ASN cc_start: 0.7774 (m-40) cc_final: 0.7436 (m110) REVERT: B 303 THR cc_start: 0.9115 (m) cc_final: 0.8744 (p) REVERT: B 414 MET cc_start: 0.7216 (tpt) cc_final: 0.6979 (tpt) REVERT: B 470 CYS cc_start: 0.8134 (m) cc_final: 0.7766 (m) REVERT: B 487 THR cc_start: 0.7674 (p) cc_final: 0.7467 (p) REVERT: B 497 TYR cc_start: 0.8266 (t80) cc_final: 0.7929 (t80) REVERT: B 537 ASN cc_start: 0.8604 (m-40) cc_final: 0.7855 (t0) REVERT: B 578 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6523 (tmmt) REVERT: B 611 LEU cc_start: 0.9362 (tp) cc_final: 0.9136 (tp) REVERT: B 646 MET cc_start: 0.5261 (mpp) cc_final: 0.4784 (tmm) REVERT: B 656 GLU cc_start: 0.7871 (pm20) cc_final: 0.7666 (pm20) REVERT: B 658 ASP cc_start: 0.8324 (m-30) cc_final: 0.7976 (m-30) REVERT: C 187 LYS cc_start: 0.8228 (pptt) cc_final: 0.7476 (mtmt) REVERT: C 190 LYS cc_start: 0.7349 (pptt) cc_final: 0.6777 (pptt) REVERT: C 294 MET cc_start: 0.6943 (ppp) cc_final: 0.6629 (ppp) REVERT: C 312 LYS cc_start: 0.7491 (mttt) cc_final: 0.7149 (mttt) REVERT: C 428 LEU cc_start: 0.2844 (OUTLIER) cc_final: 0.2500 (mp) REVERT: C 536 MET cc_start: 0.2428 (pmm) cc_final: 0.2112 (pmm) REVERT: C 595 PHE cc_start: 0.5840 (p90) cc_final: 0.5389 (t80) outliers start: 59 outliers final: 34 residues processed: 353 average time/residue: 0.1327 time to fit residues: 70.9052 Evaluate side-chains 339 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 300 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 688 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 633 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.2980 chunk 71 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 100 optimal weight: 0.0970 chunk 76 optimal weight: 0.7980 chunk 196 optimal weight: 0.0670 chunk 57 optimal weight: 0.7980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS A 144 HIS B 115 GLN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** 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 = 0.4366 r_free = 0.4366 target = 0.182302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.139247 restraints weight = 32357.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135984 restraints weight = 21910.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.137096 restraints weight = 20028.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.137695 restraints weight = 14050.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137918 restraints weight = 12764.000| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18453 Z= 0.120 Angle : 0.662 10.568 25058 Z= 0.334 Chirality : 0.043 0.302 2790 Planarity : 0.004 0.060 3100 Dihedral : 8.487 81.828 2795 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.67 % Allowed : 18.81 % Favored : 78.52 % 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: -2.14 (0.17), residues: 2147 helix: -0.94 (0.17), residues: 836 sheet: -1.79 (0.34), residues: 227 loop : -1.67 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 375 TYR 0.036 0.001 TYR C 360 PHE 0.030 0.001 PHE B 740 TRP 0.017 0.001 TRP A 706 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (18453) covalent geometry : angle 0.66162 / 0.33 (25058) hydrogen bonds : bond 0.03443 / 2.06 ( 575) hydrogen bonds : angle 4.97717 / 3.01 ( 1596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 319 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4564 (ptp) cc_final: 0.4098 (mtm) REVERT: A 257 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8843 (mp) REVERT: A 544 GLU cc_start: 0.7559 (tp30) cc_final: 0.7357 (tp30) REVERT: A 548 MET cc_start: 0.7338 (pmm) cc_final: 0.6939 (pmm) REVERT: A 566 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7524 (ttt-90) REVERT: A 583 ARG cc_start: 0.8165 (mtm110) cc_final: 0.7895 (mtm180) REVERT: A 609 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7351 (tptt) REVERT: A 670 GLN cc_start: 0.7094 (tp-100) cc_final: 0.6714 (tp-100) REVERT: B 133 LEU cc_start: 0.8986 (mm) cc_final: 0.8669 (mp) REVERT: B 174 MET cc_start: 0.7868 (mtt) cc_final: 0.7648 (mtp) REVERT: B 303 THR cc_start: 0.9064 (m) cc_final: 0.8685 (p) REVERT: B 358 GLU cc_start: 0.7503 (tm-30) cc_final: 0.7196 (tm-30) REVERT: B 497 TYR cc_start: 0.8277 (t80) cc_final: 0.8022 (t80) REVERT: B 537 ASN cc_start: 0.8473 (m-40) cc_final: 0.7839 (t0) REVERT: B 559 TYR cc_start: 0.7916 (m-80) cc_final: 0.7589 (m-80) REVERT: B 578 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6602 (tmmt) REVERT: B 611 LEU cc_start: 0.9325 (tp) cc_final: 0.9082 (tp) REVERT: B 658 ASP cc_start: 0.8252 (m-30) cc_final: 0.7966 (m-30) REVERT: C 187 LYS cc_start: 0.8225 (pptt) cc_final: 0.7465 (mtmt) REVERT: C 190 LYS cc_start: 0.7383 (pptt) cc_final: 0.6853 (pptt) REVERT: C 294 MET cc_start: 0.6941 (ppp) cc_final: 0.6646 (ppp) REVERT: C 312 LYS cc_start: 0.7363 (mttt) cc_final: 0.7075 (mtmm) REVERT: C 536 MET cc_start: 0.2474 (pmm) cc_final: 0.2201 (pmm) REVERT: C 595 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.5598 (p90) outliers start: 51 outliers final: 33 residues processed: 352 average time/residue: 0.1263 time to fit residues: 67.5993 Evaluate side-chains 329 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 291 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 633 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 96 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 165 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 0.0010 chunk 44 optimal weight: 2.9990 chunk 208 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 overall best weight: 1.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 591 GLN B 136 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** 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 = 0.4335 r_free = 0.4335 target = 0.179659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137825 restraints weight = 32079.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133385 restraints weight = 23802.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.134920 restraints weight = 19033.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.135329 restraints weight = 13908.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135545 restraints weight = 12864.622| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18453 Z= 0.167 Angle : 0.699 12.626 25058 Z= 0.353 Chirality : 0.045 0.301 2790 Planarity : 0.004 0.058 3100 Dihedral : 8.463 81.769 2793 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.25 % Allowed : 19.17 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.17), residues: 2147 helix: -0.99 (0.17), residues: 842 sheet: -1.72 (0.33), residues: 236 loop : -1.72 (0.18), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 563 TYR 0.028 0.002 TYR C 360 PHE 0.024 0.002 PHE B 740 TRP 0.009 0.001 TRP B 666 HIS 0.008 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (18453) covalent geometry : angle 0.69912 / 0.35 (25058) hydrogen bonds : bond 0.03560 / 2.14 ( 575) hydrogen bonds : angle 5.04568 / 3.06 ( 1596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 290 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4633 (ptp) cc_final: 0.4149 (mtm) REVERT: A 257 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8914 (mp) REVERT: A 410 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7813 (mt-10) REVERT: A 548 MET cc_start: 0.7317 (pmm) cc_final: 0.6788 (pmm) REVERT: A 566 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7342 (ttt-90) REVERT: A 583 ARG cc_start: 0.8229 (mtm110) cc_final: 0.7974 (mtm180) REVERT: A 607 MET cc_start: 0.5493 (mtm) cc_final: 0.5058 (mtm) REVERT: A 609 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7373 (tptt) REVERT: A 661 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7789 (pm20) REVERT: A 670 GLN cc_start: 0.7018 (tp-100) cc_final: 0.6620 (tp40) REVERT: B 133 LEU cc_start: 0.9084 (mm) cc_final: 0.8756 (mp) REVERT: B 288 LYS cc_start: 0.8565 (mptt) cc_final: 0.8325 (mptt) REVERT: B 303 THR cc_start: 0.9148 (m) cc_final: 0.8762 (p) REVERT: B 358 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7228 (tm-30) REVERT: B 470 CYS cc_start: 0.8112 (m) cc_final: 0.7815 (m) REVERT: B 497 TYR cc_start: 0.8295 (t80) cc_final: 0.7958 (t80) REVERT: B 537 ASN cc_start: 0.8517 (m-40) cc_final: 0.7873 (t0) REVERT: B 578 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6628 (tmmt) REVERT: B 611 LEU cc_start: 0.9382 (tp) cc_final: 0.9106 (tp) REVERT: B 658 ASP cc_start: 0.8314 (m-30) cc_final: 0.8001 (m-30) REVERT: C 187 LYS cc_start: 0.8328 (pptt) cc_final: 0.7484 (ptpp) REVERT: C 190 LYS cc_start: 0.7413 (pptt) cc_final: 0.6875 (pptt) REVERT: C 294 MET cc_start: 0.6906 (ppp) cc_final: 0.6398 (ppp) REVERT: C 312 LYS cc_start: 0.7471 (mttt) cc_final: 0.7184 (mtmm) REVERT: C 595 PHE cc_start: 0.5873 (OUTLIER) cc_final: 0.5550 (p90) outliers start: 62 outliers final: 41 residues processed: 330 average time/residue: 0.1228 time to fit residues: 61.3681 Evaluate side-chains 324 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 277 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 224 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 551 GLN Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 633 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.8980 chunk 78 optimal weight: 0.1980 chunk 123 optimal weight: 0.6980 chunk 183 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 96 optimal weight: 0.9990 chunk 125 optimal weight: 0.0770 chunk 209 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 136 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 ASN ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 634 HIS ** C 42 ASN ** 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 = 0.4361 r_free = 0.4361 target = 0.181959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.140354 restraints weight = 31941.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.136293 restraints weight = 22725.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137796 restraints weight = 18199.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.138298 restraints weight = 13311.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138454 restraints weight = 12212.531| |-----------------------------------------------------------------------------| r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 18453 Z= 0.129 Angle : 0.719 17.974 25058 Z= 0.358 Chirality : 0.044 0.321 2790 Planarity : 0.004 0.055 3100 Dihedral : 8.284 82.508 2793 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.51 % Allowed : 20.01 % Favored : 77.48 % 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: -2.08 (0.17), residues: 2147 helix: -0.88 (0.17), residues: 846 sheet: -1.64 (0.34), residues: 223 loop : -1.68 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 563 TYR 0.026 0.001 TYR C 360 PHE 0.026 0.001 PHE B 740 TRP 0.009 0.001 TRP A 706 HIS 0.008 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (18453) covalent geometry : angle 0.71915 / 0.36 (25058) hydrogen bonds : bond 0.03523 / 2.12 ( 575) hydrogen bonds : angle 5.02897 / 3.04 ( 1596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 302 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4607 (ptp) cc_final: 0.4135 (mtm) REVERT: A 257 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8773 (mp) REVERT: A 566 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7485 (ttt-90) REVERT: A 609 LYS cc_start: 0.7762 (OUTLIER) cc_final: 0.7426 (tptt) REVERT: A 661 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7768 (pm20) REVERT: A 670 GLN cc_start: 0.6968 (tp-100) cc_final: 0.6513 (tp40) REVERT: B 1 MET cc_start: 0.8166 (ppp) cc_final: 0.7954 (ppp) REVERT: B 133 LEU cc_start: 0.9041 (mm) cc_final: 0.8723 (mp) REVERT: B 303 THR cc_start: 0.9069 (m) cc_final: 0.8661 (p) REVERT: B 358 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7193 (tm-30) REVERT: B 470 CYS cc_start: 0.8108 (m) cc_final: 0.7812 (m) REVERT: B 497 TYR cc_start: 0.8236 (t80) cc_final: 0.7999 (t80) REVERT: B 537 ASN cc_start: 0.8509 (m-40) cc_final: 0.7821 (t0) REVERT: B 578 LYS cc_start: 0.7116 (OUTLIER) cc_final: 0.6556 (tmmt) REVERT: B 611 LEU cc_start: 0.9339 (tp) cc_final: 0.9062 (tp) REVERT: B 658 ASP cc_start: 0.8274 (m-30) cc_final: 0.7971 (m-30) REVERT: C 51 MET cc_start: 0.8181 (mmm) cc_final: 0.7958 (mmm) REVERT: C 187 LYS cc_start: 0.8349 (pptt) cc_final: 0.7449 (ptpp) REVERT: C 190 LYS cc_start: 0.7484 (pptt) cc_final: 0.6953 (pptt) REVERT: C 294 MET cc_start: 0.6892 (ppp) cc_final: 0.6461 (ppp) REVERT: C 312 LYS cc_start: 0.7333 (mttt) cc_final: 0.7055 (mtmm) REVERT: C 595 PHE cc_start: 0.5878 (OUTLIER) cc_final: 0.5546 (p90) outliers start: 48 outliers final: 36 residues processed: 332 average time/residue: 0.1278 time to fit residues: 64.6470 Evaluate side-chains 326 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 551 GLN Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 633 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 166 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 0.0670 chunk 84 optimal weight: 0.4980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.182472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.140101 restraints weight = 31825.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135961 restraints weight = 21597.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137655 restraints weight = 16784.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138151 restraints weight = 13053.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138301 restraints weight = 11911.232| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.6071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18453 Z= 0.129 Angle : 0.708 15.655 25058 Z= 0.352 Chirality : 0.044 0.335 2790 Planarity : 0.004 0.044 3100 Dihedral : 8.222 82.422 2793 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.62 % Allowed : 19.91 % Favored : 77.48 % 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: -2.01 (0.18), residues: 2147 helix: -0.82 (0.17), residues: 851 sheet: -1.66 (0.34), residues: 226 loop : -1.64 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 583 TYR 0.030 0.001 TYR C 205 PHE 0.028 0.001 PHE B 740 TRP 0.016 0.001 TRP C 552 HIS 0.007 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (18453) covalent geometry : angle 0.70789 / 0.35 (25058) hydrogen bonds : bond 0.03452 / 2.08 ( 575) hydrogen bonds : angle 5.04035 / 3.07 ( 1596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4294 Ramachandran restraints generated. 2147 Oldfield, 0 Emsley, 2147 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.4642 (ptp) cc_final: 0.4170 (mtm) REVERT: A 204 ARG cc_start: 0.6505 (tmt170) cc_final: 0.5985 (tmt170) REVERT: A 257 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8767 (mp) REVERT: A 544 GLU cc_start: 0.7572 (tp30) cc_final: 0.7364 (tp30) REVERT: A 566 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7314 (ttt-90) REVERT: A 609 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7358 (tptt) REVERT: A 661 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: A 670 GLN cc_start: 0.6874 (tp-100) cc_final: 0.6438 (tp40) REVERT: B 133 LEU cc_start: 0.8980 (mm) cc_final: 0.8639 (mp) REVERT: B 174 MET cc_start: 0.7744 (mtt) cc_final: 0.7460 (mtp) REVERT: B 303 THR cc_start: 0.9070 (m) cc_final: 0.8619 (p) REVERT: B 358 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7223 (tm-30) REVERT: B 470 CYS cc_start: 0.7964 (m) cc_final: 0.7705 (m) REVERT: B 497 TYR cc_start: 0.8204 (t80) cc_final: 0.7929 (t80) REVERT: B 537 ASN cc_start: 0.8487 (m-40) cc_final: 0.7892 (t0) REVERT: B 578 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6541 (tmmt) REVERT: B 611 LEU cc_start: 0.9305 (tp) cc_final: 0.9022 (tp) REVERT: B 658 ASP cc_start: 0.8243 (m-30) cc_final: 0.7944 (m-30) REVERT: C 53 MET cc_start: 0.5478 (mmt) cc_final: 0.5047 (mmt) REVERT: C 187 LYS cc_start: 0.8375 (pptt) cc_final: 0.7475 (ptpp) REVERT: C 190 LYS cc_start: 0.7492 (pptt) cc_final: 0.6984 (pptt) REVERT: C 269 ARG cc_start: 0.6841 (mmm160) cc_final: 0.6448 (ttp80) REVERT: C 294 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6419 (ppp) REVERT: C 312 LYS cc_start: 0.7302 (mttt) cc_final: 0.7044 (mtmm) REVERT: C 536 MET cc_start: 0.2816 (pmm) cc_final: 0.1846 (pmm) REVERT: C 595 PHE cc_start: 0.5909 (OUTLIER) cc_final: 0.5534 (p90) outliers start: 50 outliers final: 38 residues processed: 325 average time/residue: 0.1268 time to fit residues: 62.4390 Evaluate side-chains 326 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 394 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 551 GLN Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 633 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 88 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 0.0770 chunk 143 optimal weight: 0.0270 chunk 123 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 175 optimal weight: 10.0000 chunk 127 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN B 136 ASN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.183740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.141226 restraints weight = 31942.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138129 restraints weight = 21072.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.139688 restraints weight = 17796.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.140052 restraints weight = 12959.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140268 restraints weight = 12065.425| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18453 Z= 0.124 Angle : 0.709 15.016 25058 Z= 0.351 Chirality : 0.044 0.308 2790 Planarity : 0.004 0.055 3100 Dihedral : 8.141 82.356 2793 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.62 % Allowed : 20.22 % Favored : 77.16 % 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: -1.88 (0.18), residues: 2147 helix: -0.66 (0.17), residues: 838 sheet: -1.60 (0.35), residues: 210 loop : -1.61 (0.18), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 583 TYR 0.038 0.001 TYR A 48 PHE 0.026 0.001 PHE B 740 TRP 0.010 0.001 TRP A 706 HIS 0.007 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (18453) covalent geometry : angle 0.70888 / 0.35 (25058) hydrogen bonds : bond 0.03415 / 2.07 ( 575) hydrogen bonds : angle 5.00174 / 3.04 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2848.49 seconds wall clock time: 50 minutes 19.83 seconds (3019.83 seconds total)