Starting phenix.real_space_refine on Fri Aug 7 00:35:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h69_34497/08_2026/8h69_34497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h69_34497/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8h69_34497/08_2026/8h69_34497.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h69_34497/08_2026/8h69_34497.cif" model { file = "/net/cci-nas-00/data/ceres_data/8h69_34497/08_2026/8h69_34497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h69_34497/08_2026/8h69_34497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h69_34497/08_2026/8h69_34497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h69_34497/08_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: {'RNAv2': 18} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 4, 'rna3p_pyr': 9} Link IDs: {'rna2p': 5, 'rna3p': 12} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 411 Classifications: {'RNAv2': 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: 3.62, per 1000 atoms: 0.20 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: 1.51 Conformation dependent library (CDL) restraints added in 567.6 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: 2.15 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: 2.94 Time building geometry restraints manager: 2.00 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: 23414 2.11 - 4.23: 1380 4.23 - 6.34: 203 6.34 - 8.46: 47 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 - 15.98: 10295 15.98 - 31.95: 682 31.95 - 47.93: 187 47.93 - 63.90: 64 63.90 - 79.88: 13 Dihedral angle restraints: 11241 sinusoidal: 4974 harmonic: 6267 Sorted by residual: dihedral pdb=" C4' A 5 7 " pdb=" C3' A 5 7 " pdb=" C2' A 5 7 " pdb=" C1' A 5 7 " ideal model delta sinusoidal sigma weight residual 36.34 -39.17 75.51 1 3.10e+00 1.04e-01 7.49e+02 dihedral pdb=" C4' U 3 14 " pdb=" C3' U 3 14 " pdb=" C2' U 3 14 " pdb=" C1' U 3 14 " ideal model delta sinusoidal sigma weight residual 36.35 -37.54 73.89 1 3.10e+00 1.04e-01 7.22e+02 dihedral pdb=" C4' U 3 12 " pdb=" C3' U 3 12 " pdb=" C2' U 3 12 " pdb=" C1' U 3 12 " ideal model delta sinusoidal sigma weight residual 36.34 -35.28 71.63 1 3.10e+00 1.04e-01 6.84e+02 ... (remaining 11238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2079 0.068 - 0.136: 570 0.136 - 0.203: 85 0.203 - 0.271: 42 0.271 - 0.339: 14 Chirality restraints: 2790 Sorted by residual: chirality pdb=" C3' A 5 7 " pdb=" C4' A 5 7 " pdb=" O3' A 5 7 " pdb=" C2' A 5 7 " both_signs ideal model delta sigma weight residual False -2.50 -2.84 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C2' A 5 7 " pdb=" C3' A 5 7 " pdb=" O2' A 5 7 " pdb=" C1' A 5 7 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" P A 5 8 " pdb=" OP1 A 5 8 " pdb=" OP2 A 5 8 " pdb=" O5' A 5 8 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.31 2.00e-01 2.50e+01 2.44e+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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.010 Find NCS groups from input model: 0.140 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.630 ------------------------------------------------------------------------------- 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 : 1.144 10.572 25058 Z= 0.634 Chirality : 0.069 0.339 2790 Planarity : 0.007 0.060 3100 Dihedral : 12.666 79.878 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 0.00919 / 0.43 (18453) covalent geometry : angle 1.14443 / 0.63 (25058) hydrogen bonds : bond 0.30222 / 15.59 ( 575) hydrogen bonds : angle 10.48436 / 4.85 ( 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 : 0.692 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: 0.1580 time to fit residues: 126.1963 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 : 0.601 ------------------------------------------------------------------------------- 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 = 0.4406 r_free = 0.4406 target = 0.185861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.143205 restraints weight = 32230.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.140845 restraints weight = 22305.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.142361 restraints weight = 20554.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.142233 restraints weight = 15762.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.142595 restraints weight = 13436.284| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18453 Z= 0.159 Angle : 0.826 17.923 25058 Z= 0.404 Chirality : 0.058 1.048 2790 Planarity : 0.005 0.056 3100 Dihedral : 10.962 146.437 2811 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.57 % Allowed : 12.00 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.15), residues: 2147 helix: -2.62 (0.14), residues: 852 sheet: -2.16 (0.32), residues: 232 loop : -2.48 (0.17), residues: 1063 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 0.037 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 0.00341 / 0.16 (18453) covalent geometry : angle 0.82624 / 0.40 (25058) hydrogen bonds : bond 0.04981 / 2.61 ( 575) hydrogen bonds : angle 6.10392 / 3.02 ( 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 453 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 404 time to evaluate : 0.669 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: A 12 MET cc_start: 0.4832 (ptp) cc_final: 0.4426 (mtm) REVERT: A 358 LYS cc_start: 0.8306 (tptm) cc_final: 0.8087 (tptt) REVERT: A 540 TYR cc_start: 0.9064 (m-80) cc_final: 0.8849 (m-80) REVERT: A 674 ASP cc_start: 0.6522 (t0) cc_final: 0.6056 (t0) REVERT: B 41 ASP cc_start: 0.7919 (t0) cc_final: 0.7656 (t0) REVERT: B 87 CYS cc_start: 0.7939 (m) cc_final: 0.7623 (m) REVERT: B 126 ARG cc_start: 0.7445 (mtm110) cc_final: 0.7008 (ptm160) REVERT: B 277 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7352 (mt-10) REVERT: B 284 ASN cc_start: 0.7913 (m-40) cc_final: 0.7617 (m110) REVERT: B 303 THR cc_start: 0.9121 (m) cc_final: 0.8862 (p) REVERT: B 443 SER cc_start: 0.8770 (t) cc_final: 0.8527 (p) REVERT: B 478 SER cc_start: 0.8784 (t) cc_final: 0.8310 (p) REVERT: B 537 ASN cc_start: 0.8347 (m-40) cc_final: 0.8038 (t0) REVERT: B 601 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8655 (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: 0.8232 (t) REVERT: B 694 ASN cc_start: 0.7914 (m110) cc_final: 0.7645 (t0) REVERT: C 3 ARG cc_start: 0.7595 (mtm180) cc_final: 0.7338 (mtp180) REVERT: C 28 MET cc_start: 0.7449 (tmm) cc_final: 0.7205 (tmm) REVERT: C 47 MET cc_start: 0.7261 (tpp) cc_final: 0.6754 (tpp) REVERT: C 51 MET cc_start: 0.8163 (mmm) cc_final: 0.7626 (mmm) REVERT: C 136 ARG cc_start: 0.5628 (ppt170) cc_final: 0.5110 (mmt90) REVERT: C 160 GLN cc_start: 0.7963 (mt0) cc_final: 0.7634 (tt0) REVERT: C 171 GLU cc_start: 0.7974 (mp0) cc_final: 0.7726 (pm20) REVERT: C 217 PHE cc_start: 0.5678 (p90) cc_final: 0.5421 (p90) REVERT: C 230 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7265 (mm-30) REVERT: C 402 MET cc_start: -0.0230 (mtt) cc_final: -0.0649 (mtp) REVERT: C 405 SER cc_start: 0.4223 (p) cc_final: 0.3701 (t) REVERT: C 428 LEU cc_start: 0.3196 (OUTLIER) cc_final: 0.2989 (mp) REVERT: C 432 HIS cc_start: 0.4992 (m90) cc_final: 0.4750 (m90) REVERT: C 526 LYS cc_start: 0.7505 (mmtm) cc_final: 0.7293 (mttm) REVERT: C 595 PHE cc_start: 0.6002 (p90) cc_final: 0.5497 (t80) outliers start: 49 outliers final: 20 residues processed: 429 average time/residue: 0.1448 time to fit residues: 92.2747 Evaluate side-chains 347 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 324 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 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 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: 6.9990 chunk 130 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 208 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 184 HIS ** 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 B 569 GLN B 629 ASN B 676 ASN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN C 556 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.178062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.134874 restraints weight = 32163.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130172 restraints weight = 21942.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131619 restraints weight = 20177.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132155 restraints weight = 14778.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132408 restraints weight = 13410.719| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 18453 Z= 0.265 Angle : 0.838 12.215 25058 Z= 0.415 Chirality : 0.056 0.553 2790 Planarity : 0.005 0.044 3100 Dihedral : 10.566 153.402 2796 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 3.40 % Allowed : 13.62 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.17 (0.17), residues: 2147 helix: -1.90 (0.16), residues: 857 sheet: -2.13 (0.30), residues: 253 loop : -2.20 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 563 TYR 0.027 0.002 TYR B 689 PHE 0.035 0.002 PHE C 595 TRP 0.024 0.002 TRP A 537 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.27 (18453) covalent geometry : angle 0.83844 / 0.41 (25058) hydrogen bonds : bond 0.04398 / 2.30 ( 575) hydrogen bonds : angle 5.71403 / 2.81 ( 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 406 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 341 time to evaluate : 0.680 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: 0.4889 (ptp) cc_final: 0.4438 (mtm) REVERT: A 211 MET cc_start: 0.8375 (mmm) cc_final: 0.8163 (mmm) REVERT: A 257 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9083 (mp) REVERT: A 512 ARG cc_start: 0.7537 (ttp80) cc_final: 0.7180 (ttp-110) REVERT: A 537 TRP cc_start: 0.8197 (m-90) cc_final: 0.7373 (m-10) REVERT: A 548 MET cc_start: 0.7483 (pmm) cc_final: 0.7202 (pmm) REVERT: A 609 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7220 (tptt) REVERT: A 661 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7973 (pm20) REVERT: A 674 ASP cc_start: 0.6872 (t0) cc_final: 0.6530 (t0) REVERT: B 176 LYS cc_start: 0.8268 (mppt) cc_final: 0.7905 (mtmt) REVERT: B 284 ASN cc_start: 0.8022 (m-40) cc_final: 0.7730 (m110) REVERT: B 303 THR cc_start: 0.9219 (m) cc_final: 0.8923 (p) REVERT: B 537 ASN cc_start: 0.8691 (m-40) cc_final: 0.8090 (t0) REVERT: B 601 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8747 (tt) REVERT: B 665 SER cc_start: 0.8699 (m) cc_final: 0.8222 (t) REVERT: B 689 TYR cc_start: 0.3556 (m-80) cc_final: 0.3331 (m-80) REVERT: B 699 PHE cc_start: 0.6920 (t80) cc_final: 0.6041 (t80) REVERT: B 705 TYR cc_start: 0.8567 (t80) cc_final: 0.8292 (t80) REVERT: B 740 PHE cc_start: 0.5598 (t80) cc_final: 0.5336 (t80) REVERT: B 744 MET cc_start: 0.7104 (mtp) cc_final: 0.6797 (mtm) REVERT: C 47 MET cc_start: 0.7425 (tpp) cc_final: 0.6736 (tpp) REVERT: C 51 MET cc_start: 0.8206 (mmm) cc_final: 0.7937 (mmm) REVERT: C 160 GLN cc_start: 0.7958 (mt0) cc_final: 0.7561 (tt0) REVERT: C 164 MET cc_start: 0.8224 (mmt) cc_final: 0.8009 (mmp) REVERT: C 171 GLU cc_start: 0.8065 (mp0) cc_final: 0.7586 (pm20) REVERT: C 217 PHE cc_start: 0.5749 (p90) cc_final: 0.5074 (p90) REVERT: C 230 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7544 (mm-30) REVERT: C 294 MET cc_start: 0.6985 (ppp) cc_final: 0.6583 (ppp) REVERT: C 312 LYS cc_start: 0.7514 (mttt) cc_final: 0.7166 (mmtt) REVERT: C 407 GLU cc_start: 0.5262 (OUTLIER) cc_final: 0.4545 (mp0) REVERT: C 467 MET cc_start: 0.3610 (mpp) cc_final: 0.3266 (mpp) REVERT: C 535 MET cc_start: 0.5334 (mmm) cc_final: 0.4974 (mmm) REVERT: C 551 GLN cc_start: 0.7529 (pt0) cc_final: 0.7241 (pm20) outliers start: 65 outliers final: 36 residues processed: 381 average time/residue: 0.1516 time to fit residues: 85.4811 Evaluate side-chains 345 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 224 SER 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 394 ASP 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 571 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 B residue 20 THR Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 113 ILE 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 493 THR Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 512 PHE Chi-restraints excluded: chain B residue 538 ASP Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 601 ILE Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 165 GLU 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 407 GLU 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: 10.0000 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 78 optimal weight: 0.0470 chunk 177 optimal weight: 5.9990 chunk 52 optimal weight: 0.0870 overall best weight: 1.3660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN ** A 670 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** 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 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 432 HIS ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 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 = 0.4330 r_free = 0.4330 target = 0.179168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.136254 restraints weight = 32209.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.134065 restraints weight = 21108.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135167 restraints weight = 18391.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135573 restraints weight = 13437.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135759 restraints weight = 12531.414| |-----------------------------------------------------------------------------| r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18453 Z= 0.176 Angle : 0.746 12.294 25058 Z= 0.362 Chirality : 0.051 0.410 2790 Planarity : 0.004 0.066 3100 Dihedral : 10.201 152.174 2793 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.88 % Allowed : 15.09 % 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: -2.73 (0.17), residues: 2147 helix: -1.45 (0.17), residues: 845 sheet: -2.16 (0.30), residues: 257 loop : -1.96 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 563 TYR 0.020 0.002 TYR C 592 PHE 0.027 0.002 PHE C 595 TRP 0.016 0.001 TRP A 537 HIS 0.004 0.001 HIS C 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (18453) covalent geometry : angle 0.74620 / 0.36 (25058) hydrogen bonds : bond 0.03687 / 1.93 ( 575) hydrogen bonds : angle 5.27238 / 2.61 ( 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 401 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 327 time to evaluate : 0.601 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: A 12 MET cc_start: 0.4552 (ptp) cc_final: 0.4028 (mtm) REVERT: A 257 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.8993 (mp) REVERT: A 335 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8578 (tt) REVERT: A 512 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7141 (ttp-110) REVERT: A 537 TRP cc_start: 0.8288 (m-90) cc_final: 0.7487 (m-10) REVERT: A 609 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7269 (tptt) REVERT: A 670 GLN cc_start: 0.7911 (tm-30) cc_final: 0.6656 (tm-30) REVERT: B 126 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7212 (ptm160) REVERT: B 176 LYS cc_start: 0.8336 (mppt) cc_final: 0.7903 (mtmt) REVERT: B 284 ASN cc_start: 0.7777 (m-40) cc_final: 0.7456 (m110) REVERT: B 303 THR cc_start: 0.9157 (m) cc_final: 0.8828 (p) REVERT: B 497 TYR cc_start: 0.8264 (t80) cc_final: 0.8006 (t80) REVERT: B 537 ASN cc_start: 0.8652 (m-40) cc_final: 0.7627 (t0) REVERT: B 601 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8789 (tt) REVERT: B 611 LEU cc_start: 0.9415 (tp) cc_final: 0.9195 (tp) REVERT: B 665 SER cc_start: 0.8800 (m) cc_final: 0.8396 (t) REVERT: B 679 GLN cc_start: 0.7461 (mm-40) cc_final: 0.6943 (tp-100) REVERT: B 694 ASN cc_start: 0.8194 (m110) cc_final: 0.7847 (t0) REVERT: B 699 PHE cc_start: 0.6362 (t80) cc_final: 0.5706 (t80) REVERT: B 744 MET cc_start: 0.7089 (mtp) cc_final: 0.6763 (mtm) REVERT: C 47 MET cc_start: 0.7417 (tpp) cc_final: 0.6677 (tpp) REVERT: C 51 MET cc_start: 0.8207 (mmm) cc_final: 0.7888 (mmm) REVERT: C 160 GLN cc_start: 0.7924 (mt0) cc_final: 0.7359 (tt0) REVERT: C 163 ILE cc_start: 0.8876 (mm) cc_final: 0.8573 (mm) REVERT: C 164 MET cc_start: 0.8118 (mmt) cc_final: 0.7768 (mmp) REVERT: C 294 MET cc_start: 0.6833 (ppp) cc_final: 0.6515 (ppp) REVERT: C 312 LYS cc_start: 0.7463 (mttt) cc_final: 0.7068 (mttt) REVERT: C 467 MET cc_start: 0.3652 (mpp) cc_final: 0.3213 (mpp) REVERT: C 551 GLN cc_start: 0.7338 (pt0) cc_final: 0.7042 (pm20) REVERT: C 592 TYR cc_start: 0.5766 (m-10) cc_final: 0.5394 (m-10) REVERT: C 595 PHE cc_start: 0.5723 (p90) cc_final: 0.5006 (t80) outliers start: 74 outliers final: 40 residues processed: 368 average time/residue: 0.1336 time to fit residues: 73.9655 Evaluate side-chains 338 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 294 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 571 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 592 ILE Chi-restraints excluded: chain A residue 609 LYS Chi-restraints excluded: chain A residue 652 SER 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 336 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 450 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 601 ILE Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 165 GLU 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 269 ARG Chi-restraints excluded: chain C residue 407 GLU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 633 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 190 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 170 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 213 optimal weight: 0.4980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS A 499 ASN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.178525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134843 restraints weight = 32146.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132894 restraints weight = 20025.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.133916 restraints weight = 18881.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134313 restraints weight = 13632.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134536 restraints weight = 12638.680| |-----------------------------------------------------------------------------| r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18453 Z= 0.182 Angle : 0.744 11.492 25058 Z= 0.362 Chirality : 0.051 0.418 2790 Planarity : 0.004 0.043 3100 Dihedral : 10.108 151.516 2793 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.19 % Allowed : 16.24 % Favored : 79.57 % 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: -2.47 (0.17), residues: 2147 helix: -1.25 (0.17), residues: 832 sheet: -1.99 (0.31), residues: 256 loop : -1.81 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 454 TYR 0.038 0.002 TYR C 360 PHE 0.027 0.002 PHE B 740 TRP 0.018 0.001 TRP C 552 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (18453) covalent geometry : angle 0.74362 / 0.36 (25058) hydrogen bonds : bond 0.03674 / 1.91 ( 575) hydrogen bonds : angle 5.22540 / 2.57 ( 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 395 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 315 time to evaluate : 0.460 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: 0.4505 (ptp) cc_final: 0.4013 (mtm) REVERT: A 257 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.8998 (mp) REVERT: A 410 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7762 (mt-10) REVERT: A 512 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7181 (ttp-110) REVERT: A 536 LYS cc_start: 0.8969 (tttt) cc_final: 0.8735 (ttmt) REVERT: A 566 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7215 (ttt-90) REVERT: A 595 MET cc_start: 0.8376 (mtm) cc_final: 0.8040 (mtm) REVERT: A 609 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7323 (tptt) REVERT: A 661 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7836 (pm20) REVERT: B 20 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8685 (m) REVERT: B 126 ARG cc_start: 0.7610 (mtm110) cc_final: 0.7289 (ptm160) REVERT: B 176 LYS cc_start: 0.8340 (mppt) cc_final: 0.8119 (mtmt) REVERT: B 284 ASN cc_start: 0.7796 (m-40) cc_final: 0.7456 (m110) REVERT: B 303 THR cc_start: 0.9171 (m) cc_final: 0.8838 (p) REVERT: B 470 CYS cc_start: 0.8149 (m) cc_final: 0.7831 (m) REVERT: B 497 TYR cc_start: 0.8264 (t80) cc_final: 0.7935 (t80) REVERT: B 537 ASN cc_start: 0.8550 (m-40) cc_final: 0.7767 (t0) REVERT: B 578 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6901 (tmtt) REVERT: B 601 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8768 (tt) REVERT: B 611 LEU cc_start: 0.9405 (tp) cc_final: 0.9160 (tp) REVERT: B 679 GLN cc_start: 0.7319 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: B 694 ASN cc_start: 0.8301 (m-40) cc_final: 0.7859 (t0) REVERT: C 47 MET cc_start: 0.7436 (tpp) cc_final: 0.7111 (tpp) REVERT: C 160 GLN cc_start: 0.7955 (mt0) cc_final: 0.7636 (mm-40) REVERT: C 163 ILE cc_start: 0.8937 (mm) cc_final: 0.8695 (mm) REVERT: C 164 MET cc_start: 0.8053 (mmt) cc_final: 0.7728 (mmp) REVERT: C 187 LYS cc_start: 0.8400 (pptt) cc_final: 0.7602 (mtmt) REVERT: C 190 LYS cc_start: 0.7371 (pptt) cc_final: 0.6853 (pptt) REVERT: C 269 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7105 (tmm160) REVERT: C 294 MET cc_start: 0.7042 (ppp) cc_final: 0.6714 (ppp) REVERT: C 312 LYS cc_start: 0.7488 (mttt) cc_final: 0.7178 (mttt) REVERT: C 536 MET cc_start: 0.2360 (pmm) cc_final: 0.1056 (ptt) REVERT: C 551 GLN cc_start: 0.7576 (pt0) cc_final: 0.7108 (pm20) REVERT: C 570 MET cc_start: 0.7262 (ppp) cc_final: 0.6990 (ppp) REVERT: C 575 MET cc_start: 0.5108 (ppp) cc_final: 0.4624 (ttp) REVERT: C 595 PHE cc_start: 0.5852 (p90) cc_final: 0.5303 (t80) REVERT: C 607 LEU cc_start: 0.5030 (OUTLIER) cc_final: 0.4742 (mt) outliers start: 80 outliers final: 45 residues processed: 365 average time/residue: 0.1392 time to fit residues: 75.8391 Evaluate side-chains 354 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 298 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR 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 261 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 566 ARG 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 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 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 153 ASN Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 411 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 523 MET 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 635 LYS Chi-restraints excluded: chain B residue 679 GLN 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 165 GLU Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 269 ARG Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 564 TRP Chi-restraints excluded: chain C residue 607 LEU 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: 0.0670 chunk 112 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 135 optimal weight: 0.0670 chunk 202 optimal weight: 5.9990 chunk 168 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS ** A 412 ASN ** 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 641 ASN ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.180982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.137486 restraints weight = 31997.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.133168 restraints weight = 22515.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134666 restraints weight = 17081.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135051 restraints weight = 14034.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.135214 restraints weight = 12880.031| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5403 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= 0.127 Angle : 0.712 11.116 25058 Z= 0.342 Chirality : 0.049 0.401 2790 Planarity : 0.004 0.039 3100 Dihedral : 9.910 153.681 2793 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.14 % Allowed : 17.97 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.27 (0.17), residues: 2147 helix: -1.03 (0.17), residues: 833 sheet: -1.85 (0.32), residues: 248 loop : -1.76 (0.18), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 563 TYR 0.029 0.001 TYR C 360 PHE 0.030 0.002 PHE C 323 TRP 0.021 0.001 TRP C 552 HIS 0.003 0.001 HIS A 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (18453) covalent geometry : angle 0.71223 / 0.34 (25058) hydrogen bonds : bond 0.03422 / 1.77 ( 575) hydrogen bonds : angle 5.08262 / 2.52 ( 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 394 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 334 time to evaluate : 0.661 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: 0.4805 (ptp) cc_final: 0.4336 (mtm) REVERT: A 410 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: A 512 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7214 (ttp-110) REVERT: A 524 GLU cc_start: 0.8332 (mp0) cc_final: 0.8096 (mp0) REVERT: A 536 LYS cc_start: 0.8914 (tttt) cc_final: 0.8474 (ttmt) REVERT: A 564 TYR cc_start: 0.8654 (m-80) cc_final: 0.8109 (m-80) REVERT: A 583 ARG cc_start: 0.8306 (mtm110) cc_final: 0.8093 (mtm180) REVERT: A 609 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7298 (tptt) REVERT: B 126 ARG cc_start: 0.7630 (mtm110) cc_final: 0.7325 (ptm160) REVERT: B 133 LEU cc_start: 0.9008 (mm) cc_final: 0.8720 (mp) REVERT: B 176 LYS cc_start: 0.8357 (mppt) cc_final: 0.8034 (mtmt) REVERT: B 284 ASN cc_start: 0.7750 (m-40) cc_final: 0.7379 (m110) REVERT: B 303 THR cc_start: 0.9099 (m) cc_final: 0.8689 (p) REVERT: B 358 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7030 (tm-30) REVERT: B 497 TYR cc_start: 0.8330 (t80) cc_final: 0.8021 (t80) REVERT: B 537 ASN cc_start: 0.8626 (m-40) cc_final: 0.7798 (t0) REVERT: B 578 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6628 (tmmt) REVERT: B 611 LEU cc_start: 0.9370 (tp) cc_final: 0.9123 (tp) REVERT: B 656 GLU cc_start: 0.7832 (pm20) cc_final: 0.7617 (pm20) REVERT: B 665 SER cc_start: 0.8677 (m) cc_final: 0.8452 (t) REVERT: B 679 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6635 (tm-30) REVERT: B 694 ASN cc_start: 0.8300 (m-40) cc_final: 0.7880 (t0) REVERT: B 705 TYR cc_start: 0.8345 (t80) cc_final: 0.7427 (t80) REVERT: C 4 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6984 (mp) REVERT: C 89 VAL cc_start: 0.8228 (m) cc_final: 0.7946 (p) REVERT: C 97 THR cc_start: 0.8013 (p) cc_final: 0.7812 (p) REVERT: C 187 LYS cc_start: 0.8439 (pptt) cc_final: 0.7672 (mtmt) REVERT: C 190 LYS cc_start: 0.7402 (pptt) cc_final: 0.6906 (pptt) REVERT: C 208 GLU cc_start: 0.8127 (pt0) cc_final: 0.7768 (pt0) REVERT: C 294 MET cc_start: 0.7066 (ppp) cc_final: 0.6771 (ppp) REVERT: C 312 LYS cc_start: 0.7391 (mttt) cc_final: 0.7122 (mtmm) REVERT: C 551 GLN cc_start: 0.7922 (pt0) cc_final: 0.7561 (pm20) REVERT: C 570 MET cc_start: 0.7102 (ppp) cc_final: 0.6842 (ppp) REVERT: C 595 PHE cc_start: 0.6065 (OUTLIER) cc_final: 0.5637 (p90) REVERT: C 607 LEU cc_start: 0.5387 (OUTLIER) cc_final: 0.5133 (mt) outliers start: 60 outliers final: 30 residues processed: 364 average time/residue: 0.1455 time to fit residues: 79.8379 Evaluate side-chains 347 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 310 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 410 GLU 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 609 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 688 GLU 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 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 578 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain B residue 679 GLN 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 165 GLU 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 235 THR 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 607 LEU 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: 3.9990 chunk 26 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 156 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 57 optimal weight: 30.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN B 47 HIS B 136 ASN B 276 ASN ** 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** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.175062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.132783 restraints weight = 32642.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128094 restraints weight = 22177.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129617 restraints weight = 20011.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.130001 restraints weight = 14969.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130193 restraints weight = 13861.480| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 18453 Z= 0.261 Angle : 0.819 13.275 25058 Z= 0.399 Chirality : 0.054 0.523 2790 Planarity : 0.005 0.065 3100 Dihedral : 10.143 149.596 2793 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.72 % Allowed : 17.86 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.17), residues: 2147 helix: -1.19 (0.17), residues: 845 sheet: -1.92 (0.31), residues: 242 loop : -1.87 (0.18), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 563 TYR 0.025 0.002 TYR B 559 PHE 0.024 0.002 PHE B 740 TRP 0.020 0.002 TRP A 706 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.26 (18453) covalent geometry : angle 0.81912 / 0.40 (25058) hydrogen bonds : bond 0.04046 / 2.11 ( 575) hydrogen bonds : angle 5.36688 / 2.59 ( 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 365 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 294 time to evaluate : 0.592 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: 0.4787 (ptp) cc_final: 0.4313 (mtm) REVERT: A 155 MET cc_start: 0.1178 (pmm) cc_final: 0.0485 (pmm) REVERT: A 257 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9054 (mp) REVERT: A 410 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7751 (mt-10) REVERT: A 512 ARG cc_start: 0.7416 (ttp80) cc_final: 0.7149 (ttp-110) REVERT: A 547 ASP cc_start: 0.6436 (t0) cc_final: 0.6121 (t0) REVERT: A 566 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7439 (ttt-90) REVERT: A 584 CYS cc_start: 0.8259 (m) cc_final: 0.8059 (m) REVERT: A 595 MET cc_start: 0.8461 (mtm) cc_final: 0.8129 (mtm) REVERT: A 609 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7465 (tptt) REVERT: A 661 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7945 (pm20) REVERT: B 126 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7258 (ptm160) REVERT: B 284 ASN cc_start: 0.7814 (m-40) cc_final: 0.7463 (m110) REVERT: B 303 THR cc_start: 0.9199 (m) cc_final: 0.8878 (p) REVERT: B 358 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7274 (tm-30) REVERT: B 497 TYR cc_start: 0.8373 (t80) cc_final: 0.8104 (t80) REVERT: B 537 ASN cc_start: 0.8601 (m-40) cc_final: 0.7798 (t0) REVERT: B 578 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6942 (tmtt) REVERT: B 604 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8282 (mp) REVERT: B 611 LEU cc_start: 0.9388 (tp) cc_final: 0.9079 (tp) REVERT: B 656 GLU cc_start: 0.7851 (pm20) cc_final: 0.7646 (pm20) REVERT: B 679 GLN cc_start: 0.7077 (mm-40) cc_final: 0.6553 (tm-30) REVERT: C 4 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7184 (mp) REVERT: C 97 THR cc_start: 0.8187 (p) cc_final: 0.7970 (p) REVERT: C 187 LYS cc_start: 0.8558 (pptt) cc_final: 0.8132 (pptt) REVERT: C 190 LYS cc_start: 0.7337 (pptt) cc_final: 0.6878 (pptt) REVERT: C 230 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7499 (mm-30) REVERT: C 294 MET cc_start: 0.7017 (ppp) cc_final: 0.6491 (ppp) REVERT: C 312 LYS cc_start: 0.7571 (mttt) cc_final: 0.7253 (mttt) REVERT: C 365 MET cc_start: 0.2116 (OUTLIER) cc_final: 0.1884 (mmm) REVERT: C 551 GLN cc_start: 0.8104 (pt0) cc_final: 0.7403 (pt0) REVERT: C 570 MET cc_start: 0.7095 (ppp) cc_final: 0.6815 (ppp) REVERT: C 595 PHE cc_start: 0.6020 (OUTLIER) cc_final: 0.5354 (t80) outliers start: 71 outliers final: 43 residues processed: 342 average time/residue: 0.1467 time to fit residues: 76.0784 Evaluate side-chains 329 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 276 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR 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 261 LEU Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 566 ARG 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 30 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 153 ASN 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 336 VAL Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 392 ILE 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 578 LYS Chi-restraints excluded: chain B residue 604 LEU 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 67 ILE Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 595 PHE 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: 0.8980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 0.0870 chunk 44 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 GLN B 16 ASN ** 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** ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.178940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.136762 restraints weight = 32058.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134071 restraints weight = 19851.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.135343 restraints weight = 17656.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.135820 restraints weight = 12741.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.136069 restraints weight = 11793.100| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18453 Z= 0.139 Angle : 0.743 10.794 25058 Z= 0.358 Chirality : 0.050 0.413 2790 Planarity : 0.004 0.066 3100 Dihedral : 9.919 153.979 2793 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.72 % Allowed : 18.60 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.17), residues: 2147 helix: -1.00 (0.18), residues: 837 sheet: -1.88 (0.32), residues: 245 loop : -1.75 (0.18), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 680 TYR 0.023 0.002 TYR C 360 PHE 0.026 0.002 PHE B 740 TRP 0.015 0.001 TRP A 706 HIS 0.003 0.001 HIS C 233 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (18453) covalent geometry : angle 0.74256 / 0.36 (25058) hydrogen bonds : bond 0.03517 / 1.82 ( 575) hydrogen bonds : angle 5.14456 / 2.51 ( 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 364 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 312 time to evaluate : 0.676 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: A 12 MET cc_start: 0.4687 (ptp) cc_final: 0.4224 (mtm) REVERT: A 410 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7770 (mt-10) REVERT: A 512 ARG cc_start: 0.7397 (ttp80) cc_final: 0.7141 (ttp-110) REVERT: A 548 MET cc_start: 0.7257 (pmm) cc_final: 0.6660 (pmm) REVERT: A 564 TYR cc_start: 0.8674 (m-80) cc_final: 0.8396 (m-80) REVERT: A 566 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7267 (ttt-90) REVERT: A 595 MET cc_start: 0.8123 (mtm) cc_final: 0.7755 (mtm) REVERT: A 609 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7304 (tptt) REVERT: A 661 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: B 284 ASN cc_start: 0.7891 (m-40) cc_final: 0.7546 (m110) REVERT: B 303 THR cc_start: 0.9117 (m) cc_final: 0.8728 (p) REVERT: B 356 MET cc_start: 0.7488 (tpp) cc_final: 0.7187 (tpp) REVERT: B 358 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7126 (tm-30) REVERT: B 497 TYR cc_start: 0.8302 (t80) cc_final: 0.8018 (t80) REVERT: B 537 ASN cc_start: 0.8524 (m-40) cc_final: 0.7797 (t0) REVERT: B 611 LEU cc_start: 0.9351 (tp) cc_final: 0.9082 (tp) REVERT: B 665 SER cc_start: 0.8783 (m) cc_final: 0.8420 (t) REVERT: B 679 GLN cc_start: 0.7121 (mm-40) cc_final: 0.6555 (tm-30) REVERT: C 46 ARG cc_start: 0.8733 (tpp80) cc_final: 0.7959 (tpp80) REVERT: C 97 THR cc_start: 0.8068 (p) cc_final: 0.7855 (p) REVERT: C 187 LYS cc_start: 0.8467 (pptt) cc_final: 0.8064 (pptt) REVERT: C 190 LYS cc_start: 0.7342 (pptt) cc_final: 0.6898 (pptt) REVERT: C 208 GLU cc_start: 0.7876 (pt0) cc_final: 0.7173 (pt0) REVERT: C 266 ILE cc_start: 0.7709 (mm) cc_final: 0.7428 (mm) REVERT: C 294 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6587 (ppp) REVERT: C 312 LYS cc_start: 0.7558 (mttt) cc_final: 0.7250 (mttt) REVERT: C 365 MET cc_start: 0.2002 (OUTLIER) cc_final: 0.1679 (mmm) REVERT: C 536 MET cc_start: 0.2240 (pmm) cc_final: 0.1001 (ptt) REVERT: C 570 MET cc_start: 0.7138 (ppp) cc_final: 0.6875 (ppp) REVERT: C 595 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.5536 (p90) outliers start: 52 outliers final: 35 residues processed: 342 average time/residue: 0.1473 time to fit residues: 75.3686 Evaluate side-chains 328 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 224 SER 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 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 VAL 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 B residue 30 TYR 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 379 LYS 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 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 243 MET Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 365 MET Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 595 PHE Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 209 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.177351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135219 restraints weight = 32012.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.132379 restraints weight = 21146.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133643 restraints weight = 18751.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134141 restraints weight = 13563.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.134319 restraints weight = 12402.387| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18453 Z= 0.176 Angle : 0.783 23.374 25058 Z= 0.373 Chirality : 0.051 0.428 2790 Planarity : 0.004 0.058 3100 Dihedral : 9.911 152.881 2793 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.62 % Allowed : 19.22 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.17), residues: 2147 helix: -1.01 (0.17), residues: 839 sheet: -1.89 (0.31), residues: 246 loop : -1.69 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 563 TYR 0.021 0.002 TYR C 360 PHE 0.025 0.002 PHE B 740 TRP 0.011 0.001 TRP A 706 HIS 0.007 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (18453) covalent geometry : angle 0.78341 / 0.37 (25058) hydrogen bonds : bond 0.03617 / 1.87 ( 575) hydrogen bonds : angle 5.15148 / 2.50 ( 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 344 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 294 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: A 12 MET cc_start: 0.4695 (ptp) cc_final: 0.4238 (mtm) REVERT: A 257 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8904 (mp) REVERT: A 410 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7887 (mt-10) REVERT: A 512 ARG cc_start: 0.7422 (ttp80) cc_final: 0.7139 (ttp-110) REVERT: A 548 MET cc_start: 0.7370 (pmm) cc_final: 0.6676 (pmm) REVERT: A 564 TYR cc_start: 0.8833 (m-80) cc_final: 0.8513 (m-80) REVERT: A 566 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7399 (ttt-90) REVERT: A 609 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7372 (tptt) REVERT: A 661 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: B 278 LYS cc_start: 0.8861 (ttmm) cc_final: 0.8578 (tttp) REVERT: B 284 ASN cc_start: 0.7746 (m-40) cc_final: 0.7464 (m110) REVERT: B 303 THR cc_start: 0.9147 (m) cc_final: 0.8725 (p) REVERT: B 356 MET cc_start: 0.7544 (tpp) cc_final: 0.7281 (tpp) REVERT: B 358 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7135 (tm-30) REVERT: B 464 ASP cc_start: 0.7898 (p0) cc_final: 0.7694 (p0) REVERT: B 470 CYS cc_start: 0.8139 (m) cc_final: 0.7854 (m) REVERT: B 497 TYR cc_start: 0.8382 (t80) cc_final: 0.8147 (t80) REVERT: B 537 ASN cc_start: 0.8524 (m-40) cc_final: 0.7793 (t0) REVERT: B 578 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6968 (tmtt) REVERT: B 611 LEU cc_start: 0.9375 (tp) cc_final: 0.9094 (tp) REVERT: B 679 GLN cc_start: 0.7144 (mm-40) cc_final: 0.6583 (tp-100) REVERT: B 680 ARG cc_start: 0.6034 (mtp-110) cc_final: 0.5823 (mtp180) REVERT: C 41 LYS cc_start: 0.8437 (mmmt) cc_final: 0.7766 (mtmm) REVERT: C 46 ARG cc_start: 0.8730 (tpp80) cc_final: 0.7841 (tpp80) REVERT: C 170 ASN cc_start: 0.7741 (m110) cc_final: 0.6873 (t0) REVERT: C 187 LYS cc_start: 0.8488 (pptt) cc_final: 0.8084 (pptt) REVERT: C 190 LYS cc_start: 0.7508 (pptt) cc_final: 0.7149 (pptt) REVERT: C 205 TYR cc_start: 0.7352 (p90) cc_final: 0.6881 (p90) REVERT: C 208 GLU cc_start: 0.7900 (pt0) cc_final: 0.7177 (pt0) REVERT: C 266 ILE cc_start: 0.7665 (mm) cc_final: 0.7409 (mm) REVERT: C 294 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6477 (ppp) REVERT: C 312 LYS cc_start: 0.7561 (mttt) cc_final: 0.7237 (mttt) REVERT: C 536 MET cc_start: 0.2535 (pmm) cc_final: 0.1993 (ppp) REVERT: C 570 MET cc_start: 0.7031 (ppp) cc_final: 0.6724 (ppp) REVERT: C 595 PHE cc_start: 0.5797 (OUTLIER) cc_final: 0.5522 (p90) outliers start: 50 outliers final: 39 residues processed: 326 average time/residue: 0.1445 time to fit residues: 70.6936 Evaluate side-chains 325 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 278 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 VAL 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 370 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 VAL 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 B residue 30 TYR Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 171 MET 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 379 LYS Chi-restraints excluded: chain B residue 409 MET 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 578 LYS Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 635 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 THR 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 595 PHE Chi-restraints excluded: chain C residue 633 PHE Chi-restraints excluded: chain C residue 668 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 166 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 212 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 HIS ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B 641 ASN ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 GLN 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 = 0.179188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136026 restraints weight = 31976.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135133 restraints weight = 19260.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135928 restraints weight = 16266.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136364 restraints weight = 12311.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136547 restraints weight = 11352.212| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18453 Z= 0.146 Angle : 0.766 17.634 25058 Z= 0.366 Chirality : 0.050 0.412 2790 Planarity : 0.004 0.053 3100 Dihedral : 9.819 153.457 2793 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.51 % Allowed : 19.49 % Favored : 78.00 % 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: -2.10 (0.17), residues: 2147 helix: -0.92 (0.18), residues: 840 sheet: -1.87 (0.32), residues: 229 loop : -1.62 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 204 TYR 0.021 0.002 TYR C 360 PHE 0.031 0.002 PHE B 740 TRP 0.020 0.001 TRP A 537 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (18453) covalent geometry : angle 0.76585 / 0.37 (25058) hydrogen bonds : bond 0.03526 / 1.81 ( 575) hydrogen bonds : angle 5.17651 / 2.55 ( 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: 48 poor density : 298 time to evaluate : 0.590 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: 0.4656 (ptp) cc_final: 0.4192 (mtm) REVERT: A 84 ARG cc_start: 0.8266 (mmm160) cc_final: 0.7899 (mmm160) REVERT: A 257 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8872 (mp) REVERT: A 410 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: A 512 ARG cc_start: 0.7335 (ttp80) cc_final: 0.7076 (ttp-110) REVERT: A 548 MET cc_start: 0.7270 (pmm) cc_final: 0.6856 (pmm) REVERT: A 564 TYR cc_start: 0.8731 (m-80) cc_final: 0.8448 (m-80) REVERT: A 583 ARG cc_start: 0.8260 (mtm110) cc_final: 0.8042 (mtm180) REVERT: A 609 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7356 (tptt) REVERT: A 661 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: B 284 ASN cc_start: 0.7701 (m-40) cc_final: 0.7492 (m110) REVERT: B 303 THR cc_start: 0.9109 (m) cc_final: 0.8644 (p) REVERT: B 356 MET cc_start: 0.7493 (tpp) cc_final: 0.7229 (tpp) REVERT: B 358 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7144 (tm-30) REVERT: B 464 ASP cc_start: 0.7893 (p0) cc_final: 0.7690 (p0) REVERT: B 470 CYS cc_start: 0.8035 (m) cc_final: 0.7773 (m) REVERT: B 497 TYR cc_start: 0.8360 (t80) cc_final: 0.8094 (t80) REVERT: B 537 ASN cc_start: 0.8539 (m-40) cc_final: 0.7730 (t0) REVERT: B 578 LYS cc_start: 0.7166 (OUTLIER) cc_final: 0.6867 (tmtt) REVERT: B 611 LEU cc_start: 0.9349 (tp) cc_final: 0.9074 (tp) REVERT: B 679 GLN cc_start: 0.7181 (mm-40) cc_final: 0.6654 (tp-100) REVERT: B 680 ARG cc_start: 0.5897 (mtp-110) cc_final: 0.5372 (mtp180) REVERT: B 683 LEU cc_start: 0.7690 (tp) cc_final: 0.6916 (pp) REVERT: B 714 MET cc_start: 0.5645 (ttt) cc_final: 0.5431 (ttt) REVERT: C 41 LYS cc_start: 0.8432 (mmmt) cc_final: 0.7753 (mtmm) REVERT: C 46 ARG cc_start: 0.8651 (tpp80) cc_final: 0.7761 (tpp80) REVERT: C 53 MET cc_start: 0.5476 (mmt) cc_final: 0.5159 (mmt) REVERT: C 170 ASN cc_start: 0.7738 (m110) cc_final: 0.6887 (t0) REVERT: C 187 LYS cc_start: 0.8473 (pptt) cc_final: 0.8084 (pptt) REVERT: C 190 LYS cc_start: 0.7491 (pptt) cc_final: 0.7079 (pptt) REVERT: C 205 TYR cc_start: 0.7357 (p90) cc_final: 0.6849 (p90) REVERT: C 208 GLU cc_start: 0.7915 (pt0) cc_final: 0.7258 (pt0) REVERT: C 257 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7815 (tm-30) REVERT: C 266 ILE cc_start: 0.7668 (mm) cc_final: 0.7374 (mm) REVERT: C 294 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6492 (ppp) REVERT: C 312 LYS cc_start: 0.7568 (mttt) cc_final: 0.7234 (mttt) REVERT: C 536 MET cc_start: 0.2592 (pmm) cc_final: 0.1431 (ptt) REVERT: C 550 TYR cc_start: 0.6056 (m-80) cc_final: 0.5761 (m-80) REVERT: C 570 MET cc_start: 0.7016 (ppp) cc_final: 0.6717 (ppp) REVERT: C 595 PHE cc_start: 0.5755 (OUTLIER) cc_final: 0.5479 (p90) outliers start: 48 outliers final: 36 residues processed: 328 average time/residue: 0.1462 time to fit residues: 72.0600 Evaluate side-chains 333 residues out of total 1909 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 290 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 127 VAL 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 345 LEU Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 410 GLU Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 428 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 570 THR 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 B residue 8 LEU Chi-restraints excluded: chain B residue 30 TYR Chi-restraints excluded: chain B residue 171 MET 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 321 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 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 635 LYS Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 50 MET Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 235 THR 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 595 PHE 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: 3.9990 chunk 157 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 143 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 chunk 127 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** C 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 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 = 0.4308 r_free = 0.4308 target = 0.177050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.133986 restraints weight = 32107.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132054 restraints weight = 19603.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133549 restraints weight = 19100.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.133462 restraints weight = 13811.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134294 restraints weight = 12665.327| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18453 Z= 0.174 Angle : 0.786 18.611 25058 Z= 0.376 Chirality : 0.051 0.424 2790 Planarity : 0.004 0.049 3100 Dihedral : 9.822 152.362 2793 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.62 % Allowed : 19.28 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.17), residues: 2147 helix: -0.96 (0.18), residues: 848 sheet: -1.84 (0.33), residues: 227 loop : -1.63 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 204 TYR 0.021 0.002 TYR C 360 PHE 0.027 0.002 PHE B 740 TRP 0.016 0.001 TRP A 537 HIS 0.005 0.001 HIS A 437 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (18453) covalent geometry : angle 0.78558 / 0.38 (25058) hydrogen bonds : bond 0.03600 / 1.85 ( 575) hydrogen bonds : angle 5.19973 / 2.53 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2942.03 seconds wall clock time: 51 minutes 57.02 seconds (3117.02 seconds total)