Starting phenix.real_space_refine on Wed Sep 17 15:59:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khs_62353/09_2025/9khs_62353.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khs_62353/09_2025/9khs_62353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9khs_62353/09_2025/9khs_62353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khs_62353/09_2025/9khs_62353.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9khs_62353/09_2025/9khs_62353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khs_62353/09_2025/9khs_62353.map" } resolution = 4.31 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= 0.005 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 5985 2.51 5 N 1547 2.21 5 O 1767 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9327 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1161 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 132} Chain: "D" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 606 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 591 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 538 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6431 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 802, 6414 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 36, 'TRANS': 765} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 54 Conformer: "B" Number of residues, atoms: 802, 6414 Classifications: {'peptide': 802} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 36, 'TRANS': 765} Chain breaks: 4 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 54 bond proxies already assigned to first conformer: 6534 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU D 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU D 73 " occ=0.45 residue: pdb=" N ARG D 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG D 74 " occ=0.45 residue: pdb=" N GLY D 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY D 75 " occ=0.25 residue: pdb=" N GLY D 76 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY D 76 " occ=0.25 Time building chain proxies: 3.41, per 1000 atoms: 0.37 Number of scatterers: 9327 At special positions: 0 Unit cell: (103.203, 116.377, 101.007, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1767 8.00 N 1547 7.00 C 5985 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: 0.82 Conformation dependent library (CDL) restraints added in 609.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 6 sheets defined 60.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 3 through 17 removed outlier: 3.536A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 99 through 114 removed outlier: 3.664A pdb=" N SER B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.591A pdb=" N ALA B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 removed outlier: 3.732A pdb=" N ALA B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 33 removed outlier: 3.568A pdb=" N LYS D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 35 Processing helix chain 'C' and resid 22 through 28 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 55 through 59 removed outlier: 4.073A pdb=" N ASP C 58 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR C 59 " --> pdb=" O LEU C 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 55 through 59' Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 126 through 131 removed outlier: 4.479A pdb=" N PHE A 130 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.738A pdb=" N ALA A 138 " --> pdb=" O ILE A 134 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 140 " --> pdb=" O GLN A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.313A pdb=" N LEU A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 172 through 186 removed outlier: 3.732A pdb=" N THR A 179 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N THR A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.718A pdb=" N LYS A 196 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A 197 " --> pdb=" O PHE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 193 through 197' Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.923A pdb=" N PHE A 211 " --> pdb=" O PRO A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 3.554A pdb=" N LEU A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 222' Processing helix chain 'A' and resid 227 through 235 Processing helix chain 'A' and resid 242 through 273 removed outlier: 3.656A pdb=" N ALA A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 249 " --> pdb=" O GLN A 245 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS A 250 " --> pdb=" O THR A 246 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 270 " --> pdb=" O PHE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 292 removed outlier: 3.780A pdb=" N ARG A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE A 283 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 289 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 292 " --> pdb=" O HIS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.732A pdb=" N ARG A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 297 " --> pdb=" O HIS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 324 removed outlier: 3.536A pdb=" N ASN A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE A 315 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 removed outlier: 4.313A pdb=" N ASP A 335 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 337 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 370 Processing helix chain 'A' and resid 380 through 395 removed outlier: 3.632A pdb=" N PHE A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 388 " --> pdb=" O ASP A 384 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR A 391 " --> pdb=" O PHE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 406 removed outlier: 3.677A pdb=" N SER A 402 " --> pdb=" O GLY A 398 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 406 " --> pdb=" O SER A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 422 removed outlier: 3.721A pdb=" N LYS A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 462 removed outlier: 3.774A pdb=" N ARG A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 440 " --> pdb=" O THR A 436 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A 457 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 485 removed outlier: 4.483A pdb=" N GLU A 468 " --> pdb=" O SER A 464 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 542 Proline residue: A 534 - end of helix removed outlier: 3.739A pdb=" N SER A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 555 through 568 removed outlier: 4.025A pdb=" N VAL A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 589 removed outlier: 3.652A pdb=" N LYS A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 609 through 625 removed outlier: 3.920A pdb=" N ASN A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU A 615 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N TYR A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 625 " --> pdb=" O PHE A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 655 removed outlier: 3.765A pdb=" N ILE A 646 " --> pdb=" O TYR A 642 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE A 655 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 669 removed outlier: 3.722A pdb=" N LYS A 659 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N SER A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 703 removed outlier: 4.035A pdb=" N ARG A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 676 " --> pdb=" O PHE A 672 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 684 " --> pdb=" O MET A 680 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N PHE A 686 " --> pdb=" O ASN A 682 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A 688 " --> pdb=" O LEU A 684 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 755 removed outlier: 3.584A pdb=" N GLN A 733 " --> pdb=" O SER A 729 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP A 754 " --> pdb=" O ILE A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 760 removed outlier: 4.127A pdb=" N PHE A 759 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 760 " --> pdb=" O PRO A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 760' Processing helix chain 'A' and resid 761 through 781 removed outlier: 4.154A pdb=" N TYR A 766 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG A 767 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA A 769 " --> pdb=" O VAL A 765 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 770 " --> pdb=" O TYR A 766 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 778 " --> pdb=" O TYR A 774 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 787 removed outlier: 3.710A pdb=" N GLY A 785 " --> pdb=" O GLY A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 removed outlier: 4.209A pdb=" N TYR A 795 " --> pdb=" O ASP A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 813 removed outlier: 3.878A pdb=" N LYS A 804 " --> pdb=" O LYS A 800 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 805 " --> pdb=" O ASP A 801 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TYR A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.598A pdb=" N ALA A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 845 removed outlier: 4.570A pdb=" N PHE A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 836 " --> pdb=" O ARG A 832 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP A 840 " --> pdb=" O VAL A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 877 removed outlier: 3.722A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 882 through 886 Processing helix chain 'A' and resid 909 through 917 Processing helix chain 'A' and resid 930 through 934 removed outlier: 3.537A pdb=" N VAL A 934 " --> pdb=" O LEU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 953 removed outlier: 3.645A pdb=" N ARG A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 943 " --> pdb=" O GLU A 939 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 27 removed outlier: 6.352A pdb=" N HIS B 33 " --> pdb=" O VAL B 27 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 36 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 16 removed outlier: 9.158A pdb=" N LEU D 67 " --> pdb=" O GLN D 2 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE D 4 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU D 69 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS D 6 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU D 71 " --> pdb=" O LYS D 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 12 through 16 Processing sheet with id=AA4, first strand: chain 'C' and resid 12 through 15 removed outlier: 4.162A pdb=" N VAL C 5 " --> pdb=" O ILE C 13 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU C 15 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 3 " --> pdb=" O LEU C 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 44 through 45 removed outlier: 3.775A pdb=" N LYS C 48 " --> pdb=" O PHE C 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 906 through 908 429 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2688 1.33 - 1.45: 1435 1.45 - 1.57: 5348 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 9517 Sorted by residual: bond pdb=" N VAL A 881 " pdb=" CA VAL A 881 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.57e+00 bond pdb=" C TYR B 61 " pdb=" O TYR B 61 " ideal model delta sigma weight residual 1.241 1.221 0.021 9.80e-03 1.04e+04 4.38e+00 bond pdb=" N ASN C 60 " pdb=" CA ASN C 60 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.36e+00 bond pdb=" N GLY A 879 " pdb=" CA GLY A 879 " ideal model delta sigma weight residual 1.449 1.477 -0.028 1.45e-02 4.76e+03 3.75e+00 bond pdb=" C ALA A 519 " pdb=" N PRO A 520 " ideal model delta sigma weight residual 1.332 1.356 -0.024 1.30e-02 5.92e+03 3.40e+00 ... (remaining 9512 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 12397 2.09 - 4.18: 421 4.18 - 6.28: 53 6.28 - 8.37: 12 8.37 - 10.46: 1 Bond angle restraints: 12884 Sorted by residual: angle pdb=" N VAL A 531 " pdb=" CA VAL A 531 " pdb=" C VAL A 531 " ideal model delta sigma weight residual 112.12 107.72 4.40 8.40e-01 1.42e+00 2.74e+01 angle pdb=" N VAL A 521 " pdb=" CA VAL A 521 " pdb=" C VAL A 521 " ideal model delta sigma weight residual 108.88 119.34 -10.46 2.16e+00 2.14e-01 2.35e+01 angle pdb=" C TYR B 61 " pdb=" N PRO B 62 " pdb=" CA PRO B 62 " ideal model delta sigma weight residual 119.82 115.20 4.62 9.80e-01 1.04e+00 2.22e+01 angle pdb=" N TYR B 61 " pdb=" CA TYR B 61 " pdb=" C TYR B 61 " ideal model delta sigma weight residual 113.25 118.68 -5.43 1.30e+00 5.92e-01 1.74e+01 angle pdb=" N ASP A 636 " pdb=" CA ASP A 636 " pdb=" C ASP A 636 " ideal model delta sigma weight residual 114.31 109.02 5.29 1.29e+00 6.01e-01 1.68e+01 ... (remaining 12879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 5602 15.84 - 31.69: 160 31.69 - 47.53: 48 47.53 - 63.38: 2 63.38 - 79.22: 6 Dihedral angle restraints: 5818 sinusoidal: 2338 harmonic: 3480 Sorted by residual: dihedral pdb=" CA ARG E 72 " pdb=" C ARG E 72 " pdb=" N LEU E 73 " pdb=" CA LEU E 73 " ideal model delta harmonic sigma weight residual -180.00 -152.60 -27.40 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA VAL A 172 " pdb=" C VAL A 172 " pdb=" N ILE A 173 " pdb=" CA ILE A 173 " ideal model delta harmonic sigma weight residual -180.00 -153.05 -26.95 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLN A 661 " pdb=" C GLN A 661 " pdb=" N LEU A 662 " pdb=" CA LEU A 662 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 5815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1083 0.051 - 0.102: 317 0.102 - 0.153: 63 0.153 - 0.204: 6 0.204 - 0.255: 1 Chirality restraints: 1470 Sorted by residual: chirality pdb=" CB ILE D 61 " pdb=" CA ILE D 61 " pdb=" CG1 ILE D 61 " pdb=" CG2 ILE D 61 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB VAL A 185 " pdb=" CA VAL A 185 " pdb=" CG1 VAL A 185 " pdb=" CG2 VAL A 185 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.79e-01 chirality pdb=" CA ASN C 60 " pdb=" N ASN C 60 " pdb=" C ASN C 60 " pdb=" CB ASN C 60 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.16e-01 ... (remaining 1467 not shown) Planarity restraints: 1661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 59 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.68e+00 pdb=" C THR B 59 " 0.041 2.00e-02 2.50e+03 pdb=" O THR B 59 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP B 60 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 132 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.97e+00 pdb=" N PRO B 133 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 655 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 656 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 656 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 656 " -0.029 5.00e-02 4.00e+02 ... (remaining 1658 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2225 2.78 - 3.31: 8892 3.31 - 3.84: 15213 3.84 - 4.37: 18156 4.37 - 4.90: 29054 Nonbonded interactions: 73540 Sorted by model distance: nonbonded pdb=" OE1 GLN A 466 " pdb=" OH TYR A 537 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 652 " pdb=" OD2 ASP A 754 " model vdw 2.265 3.040 nonbonded pdb=" OE1 GLU A 404 " pdb=" OH TYR A 540 " model vdw 2.286 3.040 nonbonded pdb=" O PRO B 41 " pdb=" OG SER B 44 " model vdw 2.348 3.040 nonbonded pdb=" OH TYR A 174 " pdb=" OE2 GLU A 256 " model vdw 2.349 3.040 ... (remaining 73535 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 Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 28 or resid 30 through 47 or resid 49 through 76 \ )) selection = (chain 'D' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 19 or (resid 20 and (name N or nam \ e CA or name C or name O or name CB )) or resid 21 through 28 or (resid 30 and ( \ name N or name CA or name C or name O or name CB )) or resid 31 through 33 or (r \ esid 34 and (name N or name CA or name C or name O or name CB )) or resid 35 or \ (resid 36 and (name N or name CA or name C or name O or name CB )) or resid 37 t \ hrough 38 or (resid 39 through 41 and (name N or name CA or name C or name O or \ name CB )) or resid 42 through 47 or resid 49 through 58 or (resid 59 and (name \ N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resid \ 63 and (name N or name CA or name C or name O or name CB )) or resid 64 through \ 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or resi \ d 68 through 70 or (resid 71 and (name N or name CA or name C or name O or name \ CB )) or resid 72 or (resid 73 through 74 and (name N or name CA or name C or na \ me O or name CB )) or resid 75 through 76)) selection = (chain 'E' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 14 or (resid 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 19 or (resid 20 and (name N or nam \ e CA or name C or name O or name CB )) or resid 21 through 28 or (resid 30 and ( \ name N or name CA or name C or name O or name CB )) or resid 31 through 33 or (r \ esid 34 and (name N or name CA or name C or name O or name CB )) or resid 35 or \ (resid 36 and (name N or name CA or name C or name O or name CB )) or resid 37 t \ hrough 38 or (resid 39 through 41 and (name N or name CA or name C or name O or \ name CB )) or resid 42 through 47 or resid 49 through 58 or (resid 59 and (name \ N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resid \ 63 and (name N or name CA or name C or name O or name CB )) or resid 64 through \ 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or resi \ d 68 through 70 or (resid 71 and (name N or name CA or name C or name O or name \ CB )) or resid 72 or (resid 73 through 74 and (name N or name CA or name C or na \ me O or name CB )) or resid 75 through 76)) } 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=0.25 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: 0.530 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.400 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4130 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 : 0.005 0.047 9517 Z= 0.247 Angle : 0.917 10.461 12884 Z= 0.542 Chirality : 0.048 0.255 1470 Planarity : 0.007 0.056 1661 Dihedral : 9.628 79.221 3546 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.70 % Favored : 96.21 % Rotamer: Outliers : 0.10 % Allowed : 2.93 % Favored : 96.97 % 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 aren not related in a simple way. whole: -3.81 (0.19), residues: 1161 helix: -3.07 (0.13), residues: 581 sheet: -2.25 (0.48), residues: 94 loop : -1.60 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 42 TYR 0.027 0.003 TYR A 368 PHE 0.023 0.002 PHE A 460 TRP 0.028 0.004 TRP B 34 HIS 0.008 0.002 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 9517) covalent geometry : angle 0.91700 (12884) hydrogen bonds : bond 0.29463 ( 429) hydrogen bonds : angle 9.20712 ( 1239) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 PHE cc_start: 0.4162 (m-10) cc_final: 0.3759 (m-10) REVERT: B 124 ILE cc_start: 0.7203 (mt) cc_final: 0.6943 (mt) REVERT: A 146 ASP cc_start: 0.6101 (m-30) cc_final: 0.5535 (t0) REVERT: A 338 ASP cc_start: 0.8472 (t0) cc_final: 0.8261 (t70) REVERT: A 356 ARG cc_start: 0.2270 (mmt90) cc_final: 0.1536 (mmm-85) REVERT: A 443 GLU cc_start: 0.6992 (mt-10) cc_final: 0.6621 (mm-30) REVERT: A 465 LEU cc_start: 0.4118 (mp) cc_final: 0.3826 (mp) REVERT: A 694 ASN cc_start: 0.5843 (m-40) cc_final: 0.5390 (m-40) REVERT: A 702 GLN cc_start: 0.8512 (tp-100) cc_final: 0.8234 (tm-30) REVERT: A 740 LEU cc_start: 0.4549 (tp) cc_final: 0.4220 (tt) REVERT: A 812 ASN cc_start: 0.5066 (m-40) cc_final: 0.3740 (p0) REVERT: A 858 LEU cc_start: 0.7628 (mt) cc_final: 0.7346 (tp) REVERT: A 913 LYS cc_start: 0.6588 (ttmt) cc_final: 0.6339 (tmtt) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1004 time to fit residues: 31.4126 Evaluate side-chains 123 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS C 49 GLN A 149 ASN A 162 HIS A 176 ASN ** A 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 257 HIS A 394 HIS A 494 GLN A 665 GLN A 682 ASN B Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.286548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.253180 restraints weight = 32875.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.257871 restraints weight = 28091.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.257592 restraints weight = 21065.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.257912 restraints weight = 16017.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.258679 restraints weight = 16259.064| |-----------------------------------------------------------------------------| r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4531 r_free = 0.4531 target_work(ls_wunit_k1) = 0.252 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4529 r_free = 0.4529 target_work(ls_wunit_k1) = 0.252 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.4529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5631 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9517 Z= 0.168 Angle : 0.689 8.349 12884 Z= 0.360 Chirality : 0.043 0.159 1470 Planarity : 0.005 0.057 1661 Dihedral : 5.379 25.009 1254 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.20 % Allowed : 2.35 % Favored : 97.46 % 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 aren not related in a simple way. whole: -1.80 (0.23), residues: 1161 helix: -1.21 (0.18), residues: 622 sheet: -1.72 (0.52), residues: 88 loop : -0.77 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 453 TYR 0.025 0.002 TYR A 331 PHE 0.021 0.002 PHE A 342 TRP 0.014 0.002 TRP B 34 HIS 0.008 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9517) covalent geometry : angle 0.68864 (12884) hydrogen bonds : bond 0.05151 ( 429) hydrogen bonds : angle 5.42935 ( 1239) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 164 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.5711 (tppt) cc_final: 0.5075 (mmtt) REVERT: A 604 PHE cc_start: 0.8306 (m-10) cc_final: 0.8082 (m-80) REVERT: A 618 LEU cc_start: 0.8662 (mt) cc_final: 0.8416 (mp) REVERT: A 777 GLU cc_start: 0.7525 (mt-10) cc_final: 0.6911 (tp30) outliers start: 2 outliers final: 0 residues processed: 166 average time/residue: 0.0806 time to fit residues: 19.7807 Evaluate side-chains 112 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 11 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 28 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 HIS ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN ** D 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.280145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.261947 restraints weight = 25315.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.252911 restraints weight = 30903.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.248101 restraints weight = 18975.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.248864 restraints weight = 15464.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.252450 restraints weight = 9449.101| |-----------------------------------------------------------------------------| r_work (final): 0.4466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4465 r_free = 0.4465 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4465 r_free = 0.4465 target_work(ls_wunit_k1) = 0.245 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.4465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9517 Z= 0.139 Angle : 0.589 7.380 12884 Z= 0.305 Chirality : 0.042 0.144 1470 Planarity : 0.005 0.054 1661 Dihedral : 4.797 23.459 1254 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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 aren not related in a simple way. whole: -0.73 (0.24), residues: 1161 helix: -0.17 (0.20), residues: 622 sheet: -1.45 (0.54), residues: 93 loop : -0.48 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 482 TYR 0.017 0.002 TYR A 810 PHE 0.015 0.002 PHE A 748 TRP 0.010 0.002 TRP B 34 HIS 0.008 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9517) covalent geometry : angle 0.58891 (12884) hydrogen bonds : bond 0.04768 ( 429) hydrogen bonds : angle 4.87956 ( 1239) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 134 LYS cc_start: 0.7976 (tttm) cc_final: 0.7685 (tttm) REVERT: A 161 LYS cc_start: 0.5747 (tppt) cc_final: 0.5201 (mmtt) REVERT: A 283 ILE cc_start: 0.6001 (mm) cc_final: 0.5538 (mm) REVERT: A 407 MET cc_start: 0.4496 (mmp) cc_final: 0.4157 (mmt) REVERT: A 680 MET cc_start: 0.8189 (tpp) cc_final: 0.7848 (tpp) REVERT: A 777 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6970 (tp30) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.0816 time to fit residues: 17.6661 Evaluate side-chains 108 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 25 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.268783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.257812 restraints weight = 23121.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.239078 restraints weight = 29854.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.233435 restraints weight = 19838.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.232831 restraints weight = 16579.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.234146 restraints weight = 13165.001| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4300 r_free = 0.4300 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4299 r_free = 0.4299 target_work(ls_wunit_k1) = 0.225 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.4299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9517 Z= 0.135 Angle : 0.599 12.317 12884 Z= 0.302 Chirality : 0.043 0.209 1470 Planarity : 0.005 0.088 1661 Dihedral : 4.529 21.759 1254 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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 aren not related in a simple way. whole: -0.20 (0.25), residues: 1161 helix: 0.37 (0.21), residues: 621 sheet: -1.01 (0.55), residues: 93 loop : -0.47 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 868 TYR 0.019 0.002 TYR A 368 PHE 0.023 0.002 PHE A 367 TRP 0.017 0.002 TRP B 94 HIS 0.009 0.001 HIS A 294 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9517) covalent geometry : angle 0.59900 (12884) hydrogen bonds : bond 0.03878 ( 429) hydrogen bonds : angle 4.56084 ( 1239) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 LYS cc_start: 0.7896 (tttm) cc_final: 0.7628 (tttm) REVERT: E 58 ASP cc_start: 0.7200 (m-30) cc_final: 0.6575 (t0) REVERT: A 161 LYS cc_start: 0.5730 (tppt) cc_final: 0.5224 (mmtt) REVERT: A 694 ASN cc_start: 0.8317 (m-40) cc_final: 0.7749 (t0) REVERT: A 777 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7077 (mt-10) REVERT: A 894 MET cc_start: 0.3497 (tpp) cc_final: 0.3056 (mmm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.0863 time to fit residues: 20.5208 Evaluate side-chains 113 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 6 optimal weight: 0.0020 chunk 50 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 75 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.0770 chunk 47 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 overall best weight: 0.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 250 HIS A 942 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.266858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.256223 restraints weight = 20784.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.231188 restraints weight = 25345.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.227953 restraints weight = 21319.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.227383 restraints weight = 17511.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.229144 restraints weight = 12673.251| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4259 r_free = 0.4259 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4259 r_free = 0.4259 target_work(ls_wunit_k1) = 0.220 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.4259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9517 Z= 0.109 Angle : 0.552 6.921 12884 Z= 0.280 Chirality : 0.041 0.137 1470 Planarity : 0.004 0.039 1661 Dihedral : 4.375 21.335 1254 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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 aren not related in a simple way. whole: 0.10 (0.25), residues: 1161 helix: 0.63 (0.21), residues: 622 sheet: -0.90 (0.54), residues: 93 loop : -0.35 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 837 TYR 0.016 0.001 TYR A 810 PHE 0.012 0.001 PHE A 460 TRP 0.007 0.001 TRP B 142 HIS 0.003 0.000 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9517) covalent geometry : angle 0.55234 (12884) hydrogen bonds : bond 0.03650 ( 429) hydrogen bonds : angle 4.28847 ( 1239) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 134 LYS cc_start: 0.7837 (tttm) cc_final: 0.7602 (tttm) REVERT: E 58 ASP cc_start: 0.7427 (m-30) cc_final: 0.6798 (t0) REVERT: A 694 ASN cc_start: 0.8349 (m-40) cc_final: 0.7818 (t0) REVERT: A 740 LEU cc_start: 0.7557 (tt) cc_final: 0.7230 (tt) REVERT: A 777 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6807 (tp30) REVERT: A 905 MET cc_start: 0.7736 (mtp) cc_final: 0.7516 (mtp) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.0797 time to fit residues: 17.1856 Evaluate side-chains 113 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 108 optimal weight: 0.0570 chunk 46 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS D 41 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.255645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.244872 restraints weight = 19278.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.219462 restraints weight = 23512.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.215962 restraints weight = 22198.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.216251 restraints weight = 17455.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.218258 restraints weight = 12607.595| |-----------------------------------------------------------------------------| r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4197 r_free = 0.4197 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4197 r_free = 0.4197 target_work(ls_wunit_k1) = 0.212 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.4197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.6694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9517 Z= 0.139 Angle : 0.603 18.474 12884 Z= 0.301 Chirality : 0.042 0.176 1470 Planarity : 0.004 0.035 1661 Dihedral : 4.293 20.878 1254 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.25), residues: 1161 helix: 0.70 (0.21), residues: 625 sheet: -0.82 (0.54), residues: 97 loop : -0.40 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 453 TYR 0.016 0.002 TYR A 392 PHE 0.013 0.001 PHE A 748 TRP 0.014 0.002 TRP B 94 HIS 0.003 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9517) covalent geometry : angle 0.60313 (12884) hydrogen bonds : bond 0.03754 ( 429) hydrogen bonds : angle 4.24893 ( 1239) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 ASP cc_start: 0.7342 (m-30) cc_final: 0.6846 (t0) REVERT: A 368 TYR cc_start: 0.7892 (m-80) cc_final: 0.7646 (m-80) REVERT: A 471 ASP cc_start: 0.7220 (m-30) cc_final: 0.7010 (m-30) REVERT: A 694 ASN cc_start: 0.8462 (m-40) cc_final: 0.8033 (t0) REVERT: A 777 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7039 (tp30) REVERT: A 894 MET cc_start: 0.2030 (mmm) cc_final: -0.0094 (mmm) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0772 time to fit residues: 17.2650 Evaluate side-chains 120 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 942 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.249687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.205984 restraints weight = 26509.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.209752 restraints weight = 21652.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.208241 restraints weight = 20814.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.208016 restraints weight = 15884.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.208267 restraints weight = 15298.684| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4037 r_free = 0.4037 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4037 r_free = 0.4037 target_work(ls_wunit_k1) = 0.194 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.4037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.7487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9517 Z= 0.128 Angle : 0.575 9.468 12884 Z= 0.289 Chirality : 0.042 0.159 1470 Planarity : 0.004 0.036 1661 Dihedral : 4.260 21.368 1254 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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 aren not related in a simple way. whole: 0.44 (0.25), residues: 1161 helix: 0.93 (0.21), residues: 609 sheet: -0.67 (0.51), residues: 102 loop : -0.21 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 832 TYR 0.016 0.002 TYR A 810 PHE 0.023 0.001 PHE B 57 TRP 0.012 0.002 TRP B 142 HIS 0.004 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9517) covalent geometry : angle 0.57503 (12884) hydrogen bonds : bond 0.03677 ( 429) hydrogen bonds : angle 4.05620 ( 1239) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.296 Fit side-chains revert: symmetry clash REVERT: B 7 ILE cc_start: 0.8149 (mt) cc_final: 0.7937 (mm) REVERT: E 49 GLN cc_start: 0.6708 (tt0) cc_final: 0.6304 (pt0) REVERT: A 468 GLU cc_start: 0.7613 (tt0) cc_final: 0.7251 (mt-10) REVERT: A 471 ASP cc_start: 0.7371 (m-30) cc_final: 0.7131 (m-30) REVERT: A 694 ASN cc_start: 0.8456 (m-40) cc_final: 0.7937 (t0) REVERT: A 748 PHE cc_start: 0.8302 (m-80) cc_final: 0.7943 (m-80) REVERT: A 777 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7442 (tp30) REVERT: A 905 MET cc_start: 0.7863 (mtp) cc_final: 0.7639 (mtp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0814 time to fit residues: 19.4188 Evaluate side-chains 126 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 77 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.247669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.232150 restraints weight = 26856.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.206954 restraints weight = 29965.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.201930 restraints weight = 20578.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.203230 restraints weight = 17019.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.204258 restraints weight = 10541.079| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3973 r_free = 0.3973 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3973 r_free = 0.3973 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.7944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9517 Z= 0.116 Angle : 0.587 15.693 12884 Z= 0.291 Chirality : 0.041 0.136 1470 Planarity : 0.004 0.031 1661 Dihedral : 4.252 21.548 1254 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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 aren not related in a simple way. whole: 0.68 (0.25), residues: 1161 helix: 1.12 (0.21), residues: 603 sheet: -0.54 (0.54), residues: 91 loop : -0.10 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 832 TYR 0.012 0.002 TYR A 810 PHE 0.033 0.001 PHE A 748 TRP 0.008 0.001 TRP B 94 HIS 0.004 0.001 HIS A 699 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9517) covalent geometry : angle 0.58735 (12884) hydrogen bonds : bond 0.03407 ( 429) hydrogen bonds : angle 4.01520 ( 1239) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: E 44 ILE cc_start: 0.7686 (mm) cc_final: 0.7453 (mm) REVERT: E 49 GLN cc_start: 0.6880 (tt0) cc_final: 0.6261 (pt0) REVERT: E 71 LEU cc_start: 0.9064 (tp) cc_final: 0.8771 (tp) REVERT: A 468 GLU cc_start: 0.7787 (tt0) cc_final: 0.7495 (mt-10) REVERT: A 690 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6753 (tm-30) REVERT: A 694 ASN cc_start: 0.8362 (m-40) cc_final: 0.7553 (t0) REVERT: A 763 GLU cc_start: 0.7473 (pt0) cc_final: 0.6904 (tt0) REVERT: A 777 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7359 (tp30) REVERT: A 808 THR cc_start: 0.8267 (m) cc_final: 0.7953 (p) REVERT: A 894 MET cc_start: 0.4462 (mmm) cc_final: 0.4078 (tpp) REVERT: A 905 MET cc_start: 0.7821 (mtp) cc_final: 0.7521 (mtp) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 0.0748 time to fit residues: 18.2021 Evaluate side-chains 133 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 82 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 chunk 29 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 111 optimal weight: 9.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN ** A 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.242930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.209964 restraints weight = 28256.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.211060 restraints weight = 35305.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.210865 restraints weight = 17632.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.211654 restraints weight = 13985.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.211682 restraints weight = 15179.323| |-----------------------------------------------------------------------------| r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.209 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.208 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.4160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.8257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9517 Z= 0.118 Angle : 0.573 11.963 12884 Z= 0.285 Chirality : 0.042 0.146 1470 Planarity : 0.004 0.033 1661 Dihedral : 4.183 20.378 1254 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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 aren not related in a simple way. whole: 0.75 (0.25), residues: 1161 helix: 1.22 (0.21), residues: 605 sheet: -0.43 (0.54), residues: 90 loop : -0.14 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 837 TYR 0.019 0.002 TYR A 341 PHE 0.015 0.001 PHE B 63 TRP 0.010 0.001 TRP B 142 HIS 0.004 0.001 HIS A 699 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9517) covalent geometry : angle 0.57305 (12884) hydrogen bonds : bond 0.03326 ( 429) hydrogen bonds : angle 3.97681 ( 1239) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 49 GLN cc_start: 0.6831 (tt0) cc_final: 0.6470 (pt0) REVERT: E 71 LEU cc_start: 0.9076 (tp) cc_final: 0.8755 (tp) REVERT: A 468 GLU cc_start: 0.7557 (tt0) cc_final: 0.7245 (tt0) REVERT: A 690 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7133 (tm-30) REVERT: A 694 ASN cc_start: 0.8278 (m-40) cc_final: 0.7586 (t0) REVERT: A 763 GLU cc_start: 0.7295 (pt0) cc_final: 0.6793 (tt0) REVERT: A 777 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7483 (tp30) REVERT: A 826 ASP cc_start: 0.7588 (p0) cc_final: 0.7111 (p0) REVERT: A 894 MET cc_start: 0.3719 (mmm) cc_final: 0.3134 (tpp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.0712 time to fit residues: 18.2866 Evaluate side-chains 141 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 50 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN D 41 GLN A 234 ASN A 288 HIS A 294 HIS 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 = 0.228039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.195905 restraints weight = 27072.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.196320 restraints weight = 38052.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.195542 restraints weight = 18255.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.195588 restraints weight = 17148.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.195655 restraints weight = 13280.692| |-----------------------------------------------------------------------------| r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4009 r_free = 0.4009 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4009 r_free = 0.4009 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.4009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.9270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9517 Z= 0.178 Angle : 0.696 11.630 12884 Z= 0.356 Chirality : 0.046 0.162 1470 Planarity : 0.004 0.033 1661 Dihedral : 4.633 21.301 1254 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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 aren not related in a simple way. whole: 0.35 (0.24), residues: 1161 helix: 0.81 (0.21), residues: 597 sheet: -0.45 (0.56), residues: 85 loop : -0.24 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 828 TYR 0.035 0.003 TYR B 32 PHE 0.045 0.002 PHE A 748 TRP 0.014 0.002 TRP B 94 HIS 0.009 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9517) covalent geometry : angle 0.69639 (12884) hydrogen bonds : bond 0.04435 ( 429) hydrogen bonds : angle 4.33328 ( 1239) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2322 Ramachandran restraints generated. 1161 Oldfield, 0 Emsley, 1161 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 303 PHE cc_start: 0.7977 (m-80) cc_final: 0.7762 (m-80) REVERT: A 331 TYR cc_start: 0.5841 (m-80) cc_final: 0.5364 (m-80) REVERT: A 359 SER cc_start: 0.9343 (t) cc_final: 0.9117 (p) REVERT: A 690 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7260 (tm-30) REVERT: A 694 ASN cc_start: 0.8400 (m-40) cc_final: 0.7739 (t0) REVERT: A 763 GLU cc_start: 0.7448 (pt0) cc_final: 0.6774 (tt0) REVERT: A 894 MET cc_start: 0.3628 (mmm) cc_final: 0.3123 (tpp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0799 time to fit residues: 21.8114 Evaluate side-chains 141 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 72 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.0040 chunk 93 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 41 GLN E 41 GLN E 49 GLN A 324 GLN A 488 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.231374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.205577 restraints weight = 25996.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.198850 restraints weight = 37875.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.194228 restraints weight = 16375.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.195447 restraints weight = 9967.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.196600 restraints weight = 6759.000| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3949 r_free = 0.3949 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.9457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9517 Z= 0.123 Angle : 0.614 11.959 12884 Z= 0.308 Chirality : 0.043 0.197 1470 Planarity : 0.004 0.034 1661 Dihedral : 4.394 24.378 1254 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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 aren not related in a simple way. whole: 0.68 (0.25), residues: 1161 helix: 1.13 (0.21), residues: 595 sheet: -0.40 (0.55), residues: 85 loop : -0.13 (0.30), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 372 TYR 0.021 0.002 TYR A 174 PHE 0.022 0.001 PHE B 63 TRP 0.006 0.001 TRP B 142 HIS 0.008 0.001 HIS B 33 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9517) covalent geometry : angle 0.61397 (12884) hydrogen bonds : bond 0.03585 ( 429) hydrogen bonds : angle 4.06184 ( 1239) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1547.10 seconds wall clock time: 27 minutes 27.91 seconds (1647.91 seconds total)