Starting phenix.real_space_refine on Sat Jul 4 18:13:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9khk_62345/07_2026/9khk_62345.cif Found real_map, /net/cci-nas-00/data/ceres_data/9khk_62345/07_2026/9khk_62345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9khk_62345/07_2026/9khk_62345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9khk_62345/07_2026/9khk_62345.map" model { file = "/net/cci-nas-00/data/ceres_data/9khk_62345/07_2026/9khk_62345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9khk_62345/07_2026/9khk_62345.cif" } resolution = 2.9 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 8 5.49 5 S 116 5.16 5 C 14424 2.51 5 N 3544 2.21 5 O 3896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21996 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5342 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 24, 'TRANS': 640} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5342 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 24, 'TRANS': 640} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5342 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 24, 'TRANS': 640} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 5342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5342 Classifications: {'peptide': 665} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 24, 'TRANS': 640} Chain breaks: 4 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'PHE:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 55 Chain: "A" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 156 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "B" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 156 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "D" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 156 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 Chain: "C" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 156 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'POV': 1, 'PTY': 1, 'Y01': 1, 'YZY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 22 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1148 SG CYS A 176 33.663 32.558 74.477 1.00135.05 S ATOM 1162 SG CYS A 178 30.476 32.528 76.559 1.00144.58 S ATOM 1184 SG CYS A 181 32.732 35.541 76.831 1.00137.82 S ATOM 6490 SG CYS B 176 97.954 33.697 74.523 1.00135.05 S ATOM 6504 SG CYS B 178 97.976 30.513 76.610 1.00144.58 S ATOM 6526 SG CYS B 181 94.965 32.772 76.873 1.00137.82 S ATOM 11832 SG CYS D 176 32.637 96.895 74.523 1.00135.05 S ATOM 11846 SG CYS D 178 32.615 100.079 76.609 1.00144.58 S ATOM 11868 SG CYS D 181 35.626 97.819 76.873 1.00137.82 S ATOM 17174 SG CYS C 176 96.893 97.951 74.527 1.00135.05 S ATOM 17188 SG CYS C 178 100.077 97.973 76.614 1.00144.58 S ATOM 17210 SG CYS C 181 97.817 94.962 76.877 1.00137.82 S Time building chain proxies: 4.52, per 1000 atoms: 0.21 Number of scatterers: 21996 At special positions: 0 Unit cell: (131.44, 131.44, 138.224, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 116 16.00 P 8 15.00 O 3896 8.00 N 3544 7.00 C 14424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 553 " - pdb=" SG CYS A 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS D 553 " - pdb=" SG CYS D 558 " distance=2.03 Simple disulfide: pdb=" SG CYS C 553 " - pdb=" SG CYS C 558 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 804 " pdb="ZN ZN A 804 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 176 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 804 " - pdb=" SG CYS A 181 " pdb=" ZN B 805 " pdb="ZN ZN B 805 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 176 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 178 " pdb="ZN ZN B 805 " - pdb=" SG CYS B 181 " pdb=" ZN C 805 " pdb="ZN ZN C 805 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 178 " pdb="ZN ZN C 805 " - pdb=" SG CYS C 181 " pdb=" ZN D 804 " pdb="ZN ZN D 804 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 176 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 178 " pdb="ZN ZN D 804 " - pdb=" SG CYS D 181 " Number of angles added : 12 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5120 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 3 sheets defined 77.0% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 31 through 43 removed outlier: 3.628A pdb=" N LEU A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 59 Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 82 through 92 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 108 through 118 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 removed outlier: 3.609A pdb=" N HIS A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 215 through 234 removed outlier: 3.837A pdb=" N LYS A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 258 removed outlier: 3.676A pdb=" N GLN A 258 " --> pdb=" O ASP A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 271 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 298 through 303 Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 340 through 351 Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.935A pdb=" N ILE A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 386 removed outlier: 3.742A pdb=" N SER A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 386 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 426 Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.848A pdb=" N ASP A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 460 Processing helix chain 'A' and resid 473 through 492 Processing helix chain 'A' and resid 493 through 500 removed outlier: 3.875A pdb=" N THR A 498 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 499 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 540 removed outlier: 4.343A pdb=" N LEU A 515 " --> pdb=" O GLY A 511 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE A 523 " --> pdb=" O LYS A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 543 No H-bonds generated for 'chain 'A' and resid 541 through 543' Processing helix chain 'A' and resid 567 through 578 Processing helix chain 'A' and resid 579 through 581 No H-bonds generated for 'chain 'A' and resid 579 through 581' Processing helix chain 'A' and resid 594 through 614 Processing helix chain 'A' and resid 615 through 632 removed outlier: 3.682A pdb=" N LEU A 630 " --> pdb=" O ASN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 649 Processing helix chain 'A' and resid 658 through 663 removed outlier: 3.927A pdb=" N ILE A 663 " --> pdb=" O PRO A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 735 removed outlier: 4.084A pdb=" N HIS A 735 " --> pdb=" O ASN A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 Processing helix chain 'B' and resid 31 through 43 removed outlier: 3.628A pdb=" N LEU B 37 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 108 through 118 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 removed outlier: 3.609A pdb=" N HIS B 192 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 211 Processing helix chain 'B' and resid 215 through 234 removed outlier: 3.837A pdb=" N LYS B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 258 removed outlier: 3.676A pdb=" N GLN B 258 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 271 Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 340 through 351 Processing helix chain 'B' and resid 357 through 361 removed outlier: 3.935A pdb=" N ILE B 360 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 386 removed outlier: 3.742A pdb=" N SER B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 426 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 426 through 433 removed outlier: 3.847A pdb=" N ASP B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 460 Processing helix chain 'B' and resid 473 through 492 Processing helix chain 'B' and resid 493 through 500 removed outlier: 3.875A pdb=" N THR B 498 " --> pdb=" O SER B 495 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 499 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 540 removed outlier: 4.343A pdb=" N LEU B 515 " --> pdb=" O GLY B 511 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP B 516 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE B 523 " --> pdb=" O LYS B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 567 through 578 Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 594 through 614 Processing helix chain 'B' and resid 615 through 632 removed outlier: 3.682A pdb=" N LEU B 630 " --> pdb=" O ASN B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 649 Processing helix chain 'B' and resid 658 through 663 removed outlier: 3.927A pdb=" N ILE B 663 " --> pdb=" O PRO B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 735 removed outlier: 4.085A pdb=" N HIS B 735 " --> pdb=" O ASN B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 755 Processing helix chain 'D' and resid 31 through 43 removed outlier: 3.629A pdb=" N LEU D 37 " --> pdb=" O GLU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 59 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 82 through 92 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 108 through 118 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 removed outlier: 3.609A pdb=" N HIS D 192 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 211 Processing helix chain 'D' and resid 215 through 234 removed outlier: 3.836A pdb=" N LYS D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 258 removed outlier: 3.677A pdb=" N GLN D 258 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 271 Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 298 through 303 Processing helix chain 'D' and resid 304 through 316 Processing helix chain 'D' and resid 326 through 339 Processing helix chain 'D' and resid 340 through 351 Processing helix chain 'D' and resid 357 through 361 removed outlier: 3.935A pdb=" N ILE D 360 " --> pdb=" O GLY D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 386 removed outlier: 3.743A pdb=" N SER D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN D 386 " --> pdb=" O LEU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 426 Proline residue: D 409 - end of helix Processing helix chain 'D' and resid 426 through 433 removed outlier: 3.847A pdb=" N ASP D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 460 Processing helix chain 'D' and resid 473 through 492 Processing helix chain 'D' and resid 493 through 500 removed outlier: 3.874A pdb=" N THR D 498 " --> pdb=" O SER D 495 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 499 " --> pdb=" O LEU D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 540 removed outlier: 4.344A pdb=" N LEU D 515 " --> pdb=" O GLY D 511 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP D 516 " --> pdb=" O ARG D 512 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 522 " --> pdb=" O LEU D 518 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE D 523 " --> pdb=" O LYS D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 543 No H-bonds generated for 'chain 'D' and resid 541 through 543' Processing helix chain 'D' and resid 567 through 578 Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 594 through 614 Processing helix chain 'D' and resid 615 through 632 removed outlier: 3.682A pdb=" N LEU D 630 " --> pdb=" O ASN D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 649 Processing helix chain 'D' and resid 658 through 663 removed outlier: 3.927A pdb=" N ILE D 663 " --> pdb=" O PRO D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 735 removed outlier: 4.085A pdb=" N HIS D 735 " --> pdb=" O ASN D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 755 Processing helix chain 'C' and resid 31 through 43 removed outlier: 3.628A pdb=" N LEU C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 82 through 92 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 removed outlier: 3.609A pdb=" N HIS C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 Processing helix chain 'C' and resid 215 through 234 removed outlier: 3.837A pdb=" N LYS C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 258 removed outlier: 3.676A pdb=" N GLN C 258 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 271 Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 304 through 316 Processing helix chain 'C' and resid 326 through 339 Processing helix chain 'C' and resid 340 through 351 Processing helix chain 'C' and resid 357 through 361 removed outlier: 3.935A pdb=" N ILE C 360 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 386 removed outlier: 3.743A pdb=" N SER C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 426 Proline residue: C 409 - end of helix Processing helix chain 'C' and resid 426 through 433 removed outlier: 3.847A pdb=" N ASP C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 460 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'C' and resid 493 through 500 removed outlier: 3.874A pdb=" N THR C 498 " --> pdb=" O SER C 495 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 499 " --> pdb=" O LEU C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 540 removed outlier: 4.343A pdb=" N LEU C 515 " --> pdb=" O GLY C 511 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP C 516 " --> pdb=" O ARG C 512 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE C 522 " --> pdb=" O LEU C 518 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 543 No H-bonds generated for 'chain 'C' and resid 541 through 543' Processing helix chain 'C' and resid 567 through 578 Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 594 through 614 Processing helix chain 'C' and resid 615 through 632 removed outlier: 3.682A pdb=" N LEU C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 649 Processing helix chain 'C' and resid 658 through 663 removed outlier: 3.927A pdb=" N ILE C 663 " --> pdb=" O PRO C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 735 removed outlier: 4.085A pdb=" N HIS C 735 " --> pdb=" O ASN C 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 755 Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.576A pdb=" N ILE A 168 " --> pdb=" O ILE B 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.622A pdb=" N ILE B 168 " --> pdb=" O ILE C 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 18 through 19 removed outlier: 3.628A pdb=" N ILE C 168 " --> pdb=" O ILE D 18 " (cutoff:3.500A) 1407 hydrogen bonds defined for protein. 4164 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: 3.60 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3465 1.32 - 1.44: 5991 1.44 - 1.57: 12824 1.57 - 1.69: 20 1.69 - 1.81: 188 Bond restraints: 22488 Sorted by residual: bond pdb=" N LEU A 408 " pdb=" CA LEU A 408 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.94e+00 bond pdb=" N LEU B 408 " pdb=" CA LEU B 408 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.85e+00 bond pdb=" N LEU D 408 " pdb=" CA LEU D 408 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.85e+00 bond pdb=" C PRO D 658 " pdb=" N PRO D 659 " ideal model delta sigma weight residual 1.329 1.366 -0.037 1.18e-02 7.18e+03 9.84e+00 bond pdb=" C PRO C 658 " pdb=" N PRO C 659 " ideal model delta sigma weight residual 1.329 1.366 -0.037 1.18e-02 7.18e+03 9.84e+00 ... (remaining 22483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 29662 2.22 - 4.44: 701 4.44 - 6.66: 37 6.66 - 8.89: 12 8.89 - 11.11: 12 Bond angle restraints: 30424 Sorted by residual: angle pdb=" N PRO B 659 " pdb=" CA PRO B 659 " pdb=" C PRO B 659 " ideal model delta sigma weight residual 110.70 121.81 -11.11 1.22e+00 6.72e-01 8.29e+01 angle pdb=" N PRO D 659 " pdb=" CA PRO D 659 " pdb=" C PRO D 659 " ideal model delta sigma weight residual 110.70 121.81 -11.11 1.22e+00 6.72e-01 8.29e+01 angle pdb=" N PRO A 659 " pdb=" CA PRO A 659 " pdb=" C PRO A 659 " ideal model delta sigma weight residual 110.70 121.79 -11.09 1.22e+00 6.72e-01 8.26e+01 angle pdb=" N PRO C 659 " pdb=" CA PRO C 659 " pdb=" C PRO C 659 " ideal model delta sigma weight residual 110.70 121.77 -11.07 1.22e+00 6.72e-01 8.24e+01 angle pdb=" N PRO B 171 " pdb=" CA PRO B 171 " pdb=" C PRO B 171 " ideal model delta sigma weight residual 111.68 101.39 10.29 1.67e+00 3.59e-01 3.79e+01 ... (remaining 30419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 13184 35.91 - 71.82: 480 71.82 - 107.74: 24 107.74 - 143.65: 28 143.65 - 179.56: 4 Dihedral angle restraints: 13720 sinusoidal: 5852 harmonic: 7868 Sorted by residual: dihedral pdb=" C5 YZY A 806 " pdb=" C3 YZY A 806 " pdb=" C4 YZY A 806 " pdb=" O2 YZY A 806 " ideal model delta sinusoidal sigma weight residual 177.74 -1.82 179.56 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C5 YZY D 806 " pdb=" C3 YZY D 806 " pdb=" C4 YZY D 806 " pdb=" O2 YZY D 806 " ideal model delta sinusoidal sigma weight residual 177.74 -1.78 179.52 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C5 YZY C 801 " pdb=" C3 YZY C 801 " pdb=" C4 YZY C 801 " pdb=" O2 YZY C 801 " ideal model delta sinusoidal sigma weight residual 177.74 -1.78 179.52 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 13717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 3158 0.084 - 0.168: 242 0.168 - 0.252: 16 0.252 - 0.337: 0 0.337 - 0.421: 4 Chirality restraints: 3420 Sorted by residual: chirality pdb=" CA PRO A 659 " pdb=" N PRO A 659 " pdb=" C PRO A 659 " pdb=" CB PRO A 659 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA PRO D 659 " pdb=" N PRO D 659 " pdb=" C PRO D 659 " pdb=" CB PRO D 659 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" CA PRO B 659 " pdb=" N PRO B 659 " pdb=" C PRO B 659 " pdb=" CB PRO B 659 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 3417 not shown) Planarity restraints: 3748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C27 YZY D 806 " -0.066 2.00e-02 2.50e+03 6.62e-02 4.38e+01 pdb=" C28 YZY D 806 " 0.067 2.00e-02 2.50e+03 pdb=" C29 YZY D 806 " 0.065 2.00e-02 2.50e+03 pdb=" C30 YZY D 806 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY A 806 " -0.066 2.00e-02 2.50e+03 6.58e-02 4.34e+01 pdb=" C28 YZY A 806 " 0.067 2.00e-02 2.50e+03 pdb=" C29 YZY A 806 " 0.065 2.00e-02 2.50e+03 pdb=" C30 YZY A 806 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C27 YZY B 801 " 0.066 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C28 YZY B 801 " -0.067 2.00e-02 2.50e+03 pdb=" C29 YZY B 801 " -0.065 2.00e-02 2.50e+03 pdb=" C30 YZY B 801 " 0.066 2.00e-02 2.50e+03 ... (remaining 3745 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4721 2.79 - 3.32: 21066 3.32 - 3.84: 34994 3.84 - 4.37: 39486 4.37 - 4.90: 70755 Nonbonded interactions: 171022 Sorted by model distance: nonbonded pdb=" OD1 ASP D 67 " pdb=" N ARG D 71 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP B 67 " pdb=" N ARG B 71 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP C 67 " pdb=" N ARG C 71 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP A 67 " pdb=" N ARG A 71 " model vdw 2.262 3.120 nonbonded pdb=" NE ARG A 17 " pdb=" OG1 THR D 167 " model vdw 2.275 3.120 ... (remaining 171017 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 755) selection = (chain 'B' and resid 17 through 755) selection = (chain 'C' and resid 17 through 755) selection = (chain 'D' and resid 17 through 755) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.620 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 0.126 22508 Z= 0.320 Angle : 0.707 11.107 30444 Z= 0.447 Chirality : 0.046 0.421 3420 Planarity : 0.005 0.070 3748 Dihedral : 18.342 179.561 8588 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.35 % Allowed : 25.65 % Favored : 74.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.16), residues: 2620 helix: 2.04 (0.11), residues: 1940 sheet: None (None), residues: 0 loop : -0.84 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 170 TYR 0.009 0.001 TYR A 524 PHE 0.016 0.001 PHE C 341 TRP 0.012 0.001 TRP B 410 HIS 0.001 0.000 HIS B 370 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.32 (22488) covalent geometry : angle 0.70375 / 0.45 (30424) SS BOND : bond 0.00119 / 0.06 ( 4) SS BOND : angle 0.53161 / 0.35 ( 8) hydrogen bonds : bond 0.08427 / 5.72 ( 1407) hydrogen bonds : angle 3.60486 / 2.61 ( 4164) metal coordination : bond 0.02103 / 1.56 ( 16) metal coordination : angle 3.47540 / 2.46 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 307 time to evaluate : 0.632 Fit side-chains REVERT: A 181 CYS cc_start: 0.5599 (m) cc_final: 0.5257 (m) REVERT: A 624 MET cc_start: 0.8696 (mmm) cc_final: 0.8443 (mtt) outliers start: 8 outliers final: 4 residues processed: 311 average time/residue: 0.4430 time to fit residues: 162.0700 Evaluate side-chains 248 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 244 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain C residue 410 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN A 151 HIS ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN A 309 GLN B 38 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN B 309 GLN D 38 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN D 309 GLN D 629 GLN C 38 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 177 ASN C 309 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.173707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129955 restraints weight = 26150.804| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.17 r_work: 0.3319 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22508 Z= 0.122 Angle : 0.468 6.518 30444 Z= 0.244 Chirality : 0.036 0.159 3420 Planarity : 0.004 0.056 3748 Dihedral : 12.266 166.359 3552 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.80 % Allowed : 22.64 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.48 (0.16), residues: 2620 helix: 2.38 (0.12), residues: 1952 sheet: None (None), residues: 0 loop : -0.61 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 194 TYR 0.009 0.001 TYR C 524 PHE 0.018 0.001 PHE C 341 TRP 0.012 0.001 TRP B 315 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (22488) covalent geometry : angle 0.46718 / 0.24 (30424) SS BOND : bond 0.00147 / 0.07 ( 4) SS BOND : angle 0.48626 / 0.33 ( 8) hydrogen bonds : bond 0.04827 / 3.29 ( 1407) hydrogen bonds : angle 3.20991 / 2.34 ( 4164) metal coordination : bond 0.00704 / 0.65 ( 16) metal coordination : angle 1.80272 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 267 time to evaluate : 0.778 Fit side-chains REVERT: A 114 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7024 (tt) REVERT: A 343 MET cc_start: 0.7089 (OUTLIER) cc_final: 0.6787 (mmt) REVERT: A 552 ASN cc_start: 0.7520 (OUTLIER) cc_final: 0.7141 (t0) REVERT: A 664 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6910 (pt) REVERT: B 114 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.6907 (tt) REVERT: B 335 MET cc_start: 0.8061 (mpt) cc_final: 0.7665 (mpt) REVERT: B 404 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6543 (mt-10) REVERT: B 552 ASN cc_start: 0.7602 (OUTLIER) cc_final: 0.7214 (t0) REVERT: B 664 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6975 (pt) REVERT: D 114 LEU cc_start: 0.7416 (OUTLIER) cc_final: 0.6915 (tt) REVERT: D 162 VAL cc_start: 0.7522 (OUTLIER) cc_final: 0.7283 (p) REVERT: D 335 MET cc_start: 0.8066 (mpt) cc_final: 0.7672 (mpt) REVERT: D 404 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6609 (mt-10) REVERT: D 552 ASN cc_start: 0.7607 (OUTLIER) cc_final: 0.7224 (t0) REVERT: D 664 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6933 (pt) REVERT: C 114 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6881 (tt) REVERT: C 335 MET cc_start: 0.8040 (mpt) cc_final: 0.7642 (mpt) REVERT: C 404 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6592 (mt-10) REVERT: C 552 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7211 (t0) REVERT: C 664 ILE cc_start: 0.7158 (OUTLIER) cc_final: 0.6931 (pt) outliers start: 110 outliers final: 41 residues processed: 327 average time/residue: 0.4728 time to fit residues: 182.4646 Evaluate side-chains 302 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 244 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 664 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 263 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 258 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.167691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.123178 restraints weight = 26682.289| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.18 r_work: 0.3236 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22508 Z= 0.186 Angle : 0.530 7.570 30444 Z= 0.278 Chirality : 0.038 0.168 3420 Planarity : 0.004 0.057 3748 Dihedral : 10.887 153.973 3552 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.24 % Allowed : 20.94 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.16), residues: 2620 helix: 2.19 (0.11), residues: 1952 sheet: None (None), residues: 0 loop : -0.80 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 194 TYR 0.011 0.001 TYR A 524 PHE 0.024 0.002 PHE A 36 TRP 0.016 0.001 TRP A 315 HIS 0.005 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (22488) covalent geometry : angle 0.52947 / 0.28 (30424) SS BOND : bond 0.00266 / 0.13 ( 4) SS BOND : angle 0.66441 / 0.45 ( 8) hydrogen bonds : bond 0.06576 / 4.48 ( 1407) hydrogen bonds : angle 3.36046 / 2.45 ( 4164) metal coordination : bond 0.00513 / 0.50 ( 16) metal coordination : angle 0.85451 / 0.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 274 time to evaluate : 0.803 Fit side-chains REVERT: A 343 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6970 (mmt) REVERT: A 552 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7322 (t0) REVERT: A 664 ILE cc_start: 0.7144 (OUTLIER) cc_final: 0.6827 (pt) REVERT: B 105 ARG cc_start: 0.7777 (tmm-80) cc_final: 0.7503 (ttt90) REVERT: B 404 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6667 (mt-10) REVERT: B 552 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7473 (t0) REVERT: B 664 ILE cc_start: 0.7106 (OUTLIER) cc_final: 0.6791 (pt) REVERT: D 105 ARG cc_start: 0.7728 (tmm-80) cc_final: 0.7513 (tmm-80) REVERT: D 404 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6685 (mt-10) REVERT: D 552 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7498 (t0) REVERT: D 664 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6876 (pt) REVERT: C 404 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6667 (mt-10) REVERT: C 552 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7492 (t0) REVERT: C 664 ILE cc_start: 0.7156 (OUTLIER) cc_final: 0.6837 (pt) outliers start: 143 outliers final: 50 residues processed: 355 average time/residue: 0.5042 time to fit residues: 208.8765 Evaluate side-chains 316 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 707 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 139 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 212 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 256 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.168544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.124429 restraints weight = 26570.264| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.20 r_work: 0.3259 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22508 Z= 0.140 Angle : 0.484 6.989 30444 Z= 0.254 Chirality : 0.037 0.162 3420 Planarity : 0.004 0.060 3748 Dihedral : 10.549 156.376 3552 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 5.02 % Allowed : 23.34 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.16), residues: 2620 helix: 2.27 (0.12), residues: 1956 sheet: None (None), residues: 0 loop : -0.77 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 194 TYR 0.011 0.001 TYR C 524 PHE 0.019 0.001 PHE B 341 TRP 0.014 0.001 TRP A 315 HIS 0.003 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (22488) covalent geometry : angle 0.48327 / 0.25 (30424) SS BOND : bond 0.00220 / 0.11 ( 4) SS BOND : angle 0.73263 / 0.50 ( 8) hydrogen bonds : bond 0.05699 / 3.89 ( 1407) hydrogen bonds : angle 3.29725 / 2.40 ( 4164) metal coordination : bond 0.00358 / 0.31 ( 16) metal coordination : angle 0.91147 / 0.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 268 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 114 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7218 (tt) REVERT: A 272 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7801 (ptm160) REVERT: A 335 MET cc_start: 0.8269 (mpp) cc_final: 0.7640 (mpp) REVERT: A 552 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7299 (t0) REVERT: A 664 ILE cc_start: 0.7180 (OUTLIER) cc_final: 0.6871 (pt) REVERT: B 114 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6982 (tt) REVERT: B 160 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7738 (tt) REVERT: B 272 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7781 (ptm160) REVERT: B 404 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6672 (mt-10) REVERT: B 552 ASN cc_start: 0.7776 (OUTLIER) cc_final: 0.7470 (t0) REVERT: B 664 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6855 (pt) REVERT: D 114 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6988 (tt) REVERT: D 160 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7682 (tt) REVERT: D 404 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6699 (mt-10) REVERT: D 552 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7495 (t0) REVERT: D 664 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6887 (pt) REVERT: C 114 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.6951 (tt) REVERT: C 160 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7734 (tt) REVERT: C 272 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7782 (ptm160) REVERT: C 404 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6685 (mt-10) REVERT: C 552 ASN cc_start: 0.7803 (OUTLIER) cc_final: 0.7496 (t0) REVERT: C 664 ILE cc_start: 0.7179 (OUTLIER) cc_final: 0.6873 (pt) outliers start: 115 outliers final: 49 residues processed: 337 average time/residue: 0.5264 time to fit residues: 206.1833 Evaluate side-chains 311 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 241 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 648 MET Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 506 LEU Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 648 MET Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 648 MET Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 707 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 245 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 163 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 533 ASN A 731 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 GLN B 533 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN D 533 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN C 533 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.163193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117868 restraints weight = 26498.059| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.12 r_work: 0.3154 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 22508 Z= 0.281 Angle : 0.627 8.666 30444 Z= 0.328 Chirality : 0.042 0.173 3420 Planarity : 0.005 0.063 3748 Dihedral : 10.875 153.761 3544 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.37 % Allowed : 22.82 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.16), residues: 2620 helix: 1.87 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : -0.97 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 730 TYR 0.014 0.002 TYR C 524 PHE 0.026 0.002 PHE D 36 TRP 0.020 0.002 TRP B 315 HIS 0.005 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00700 / 0.28 (22488) covalent geometry : angle 0.62701 / 0.33 (30424) SS BOND : bond 0.00359 / 0.18 ( 4) SS BOND : angle 0.96001 / 0.64 ( 8) hydrogen bonds : bond 0.08197 / 5.58 ( 1407) hydrogen bonds : angle 3.57448 / 2.60 ( 4164) metal coordination : bond 0.00604 / 0.55 ( 16) metal coordination : angle 0.99725 / 0.58 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 263 time to evaluate : 0.855 Fit side-chains REVERT: A 36 PHE cc_start: 0.4087 (OUTLIER) cc_final: 0.3661 (p90) REVERT: A 533 ASN cc_start: 0.8403 (t0) cc_final: 0.8198 (t0) REVERT: A 552 ASN cc_start: 0.7834 (OUTLIER) cc_final: 0.7509 (t0) REVERT: A 560 LYS cc_start: 0.7955 (tppt) cc_final: 0.7699 (mmmm) REVERT: A 664 ILE cc_start: 0.7216 (OUTLIER) cc_final: 0.6895 (pt) REVERT: B 36 PHE cc_start: 0.4112 (OUTLIER) cc_final: 0.3582 (p90) REVERT: B 114 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7063 (tt) REVERT: B 404 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6824 (mt-10) REVERT: B 533 ASN cc_start: 0.8406 (t0) cc_final: 0.8197 (t0) REVERT: B 552 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.7599 (t0) REVERT: B 664 ILE cc_start: 0.7231 (OUTLIER) cc_final: 0.6907 (pt) REVERT: D 36 PHE cc_start: 0.4060 (OUTLIER) cc_final: 0.3532 (p90) REVERT: D 114 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7069 (tt) REVERT: D 404 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6830 (mt-10) REVERT: D 533 ASN cc_start: 0.8409 (t0) cc_final: 0.8204 (t0) REVERT: D 552 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7614 (t0) REVERT: D 664 ILE cc_start: 0.7241 (OUTLIER) cc_final: 0.6912 (pt) REVERT: C 36 PHE cc_start: 0.4117 (OUTLIER) cc_final: 0.3643 (p90) REVERT: C 114 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7050 (tt) REVERT: C 404 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6811 (mt-10) REVERT: C 533 ASN cc_start: 0.8410 (t0) cc_final: 0.8197 (t0) REVERT: C 552 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7607 (t0) REVERT: C 664 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6887 (pt) outliers start: 146 outliers final: 48 residues processed: 360 average time/residue: 0.4793 time to fit residues: 203.1015 Evaluate side-chains 318 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 252 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain D residue 36 PHE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 174 ILE Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 340 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 613 LEU Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 707 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 210 optimal weight: 0.9990 chunk 214 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 205 optimal weight: 8.9990 chunk 254 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.167514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123290 restraints weight = 26385.070| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.14 r_work: 0.3246 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22508 Z= 0.132 Angle : 0.502 8.487 30444 Z= 0.263 Chirality : 0.037 0.160 3420 Planarity : 0.005 0.058 3748 Dihedral : 10.402 156.289 3544 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.67 % Allowed : 24.78 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.16), residues: 2620 helix: 2.20 (0.12), residues: 1948 sheet: None (None), residues: 0 loop : -0.76 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 730 TYR 0.012 0.001 TYR B 524 PHE 0.020 0.001 PHE D 341 TRP 0.014 0.001 TRP A 315 HIS 0.003 0.000 HIS C 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22488) covalent geometry : angle 0.50124 / 0.26 (30424) SS BOND : bond 0.00203 / 0.10 ( 4) SS BOND : angle 0.65983 / 0.45 ( 8) hydrogen bonds : bond 0.05736 / 3.91 ( 1407) hydrogen bonds : angle 3.38830 / 2.46 ( 4164) metal coordination : bond 0.00273 / 0.27 ( 16) metal coordination : angle 0.99026 / 0.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 259 time to evaluate : 0.821 Fit side-chains REVERT: A 36 PHE cc_start: 0.3932 (OUTLIER) cc_final: 0.3541 (p90) REVERT: A 272 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7666 (ptm160) REVERT: A 335 MET cc_start: 0.8241 (mpp) cc_final: 0.7874 (mpt) REVERT: A 404 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: A 552 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7410 (t0) REVERT: A 664 ILE cc_start: 0.7116 (OUTLIER) cc_final: 0.6822 (pt) REVERT: B 114 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7052 (tt) REVERT: B 272 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7647 (ptm160) REVERT: B 404 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6681 (mt-10) REVERT: B 552 ASN cc_start: 0.7784 (OUTLIER) cc_final: 0.7482 (t0) REVERT: B 664 ILE cc_start: 0.7167 (OUTLIER) cc_final: 0.6869 (pt) REVERT: D 114 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7055 (tt) REVERT: D 404 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6704 (mt-10) REVERT: D 467 GLU cc_start: 0.8091 (pp20) cc_final: 0.7851 (mp0) REVERT: D 552 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7494 (t0) REVERT: D 664 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6844 (pt) REVERT: C 114 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7026 (tt) REVERT: C 272 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7643 (ptm160) REVERT: C 404 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6705 (mt-10) REVERT: C 467 GLU cc_start: 0.8098 (pp20) cc_final: 0.7869 (mp0) REVERT: C 552 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7506 (t0) REVERT: C 664 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6827 (pt) outliers start: 107 outliers final: 37 residues processed: 332 average time/residue: 0.5067 time to fit residues: 196.0184 Evaluate side-chains 298 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 242 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 707 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 25 optimal weight: 0.6980 chunk 222 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 174 optimal weight: 7.9990 chunk 134 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.168571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118267 restraints weight = 26324.876| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.08 r_work: 0.3254 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22508 Z= 0.124 Angle : 0.498 8.173 30444 Z= 0.260 Chirality : 0.036 0.158 3420 Planarity : 0.004 0.058 3748 Dihedral : 10.171 158.569 3544 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.36 % Allowed : 25.17 % Favored : 70.46 % 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 are not related in a simple way. whole: 2.35 (0.16), residues: 2620 helix: 2.29 (0.12), residues: 1948 sheet: None (None), residues: 0 loop : -0.67 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 730 TYR 0.011 0.001 TYR B 524 PHE 0.019 0.001 PHE C 341 TRP 0.014 0.001 TRP A 315 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (22488) covalent geometry : angle 0.49777 / 0.26 (30424) SS BOND : bond 0.00199 / 0.10 ( 4) SS BOND : angle 0.62215 / 0.42 ( 8) hydrogen bonds : bond 0.05343 / 3.64 ( 1407) hydrogen bonds : angle 3.35630 / 2.44 ( 4164) metal coordination : bond 0.00177 / 0.14 ( 16) metal coordination : angle 1.26975 / 0.84 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 255 time to evaluate : 0.814 Fit side-chains REVERT: A 36 PHE cc_start: 0.4025 (OUTLIER) cc_final: 0.3628 (p90) REVERT: A 185 SER cc_start: 0.7692 (OUTLIER) cc_final: 0.7404 (t) REVERT: A 331 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7066 (mm) REVERT: A 335 MET cc_start: 0.8067 (mpp) cc_final: 0.7709 (mpp) REVERT: A 361 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7811 (mptm) REVERT: A 404 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6589 (mt-10) REVERT: A 552 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7384 (t0) REVERT: A 664 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.6740 (pt) REVERT: B 36 PHE cc_start: 0.3966 (OUTLIER) cc_final: 0.2896 (m-10) REVERT: B 37 LEU cc_start: 0.4302 (OUTLIER) cc_final: 0.3858 (mp) REVERT: B 114 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6990 (tt) REVERT: B 335 MET cc_start: 0.8141 (mpp) cc_final: 0.7785 (mpt) REVERT: B 361 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7800 (mptm) REVERT: B 404 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6586 (mt-10) REVERT: B 552 ASN cc_start: 0.7693 (OUTLIER) cc_final: 0.7394 (t0) REVERT: B 664 ILE cc_start: 0.7005 (OUTLIER) cc_final: 0.6720 (pt) REVERT: D 17 ARG cc_start: 0.6477 (mmm-85) cc_final: 0.5838 (ttm-80) REVERT: D 36 PHE cc_start: 0.3966 (OUTLIER) cc_final: 0.2863 (m-10) REVERT: D 114 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.6968 (tt) REVERT: D 272 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7628 (ptm160) REVERT: D 335 MET cc_start: 0.8177 (mpp) cc_final: 0.7747 (mpt) REVERT: D 361 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7802 (mptm) REVERT: D 404 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6596 (mt-10) REVERT: D 552 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7407 (t0) REVERT: D 664 ILE cc_start: 0.7034 (OUTLIER) cc_final: 0.6738 (pt) REVERT: C 17 ARG cc_start: 0.6482 (mmm-85) cc_final: 0.5847 (ttm-80) REVERT: C 36 PHE cc_start: 0.3971 (OUTLIER) cc_final: 0.2895 (m-10) REVERT: C 37 LEU cc_start: 0.4329 (OUTLIER) cc_final: 0.3888 (mp) REVERT: C 105 ARG cc_start: 0.7696 (tmm-80) cc_final: 0.7298 (ttt-90) REVERT: C 114 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6942 (tt) REVERT: C 335 MET cc_start: 0.8146 (mpp) cc_final: 0.7710 (mpt) REVERT: C 361 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7802 (mptm) REVERT: C 404 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6593 (mt-10) REVERT: C 552 ASN cc_start: 0.7721 (OUTLIER) cc_final: 0.7423 (t0) REVERT: C 664 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.6732 (pt) outliers start: 100 outliers final: 39 residues processed: 324 average time/residue: 0.4706 time to fit residues: 178.3285 Evaluate side-chains 307 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 240 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 471 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 590 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 442 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain D residue 36 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 272 ARG Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 471 MET Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 590 VAL Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 442 MET Chi-restraints excluded: chain C residue 471 MET Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 707 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.1980 chunk 218 optimal weight: 0.9980 chunk 196 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 242 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 215 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 HIS ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 HIS ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.171709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.127791 restraints weight = 26160.201| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.15 r_work: 0.3307 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 22508 Z= 0.110 Angle : 0.488 8.864 30444 Z= 0.253 Chirality : 0.036 0.153 3420 Planarity : 0.004 0.058 3748 Dihedral : 9.888 161.501 3544 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.66 % Allowed : 26.35 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.16), residues: 2620 helix: 2.45 (0.12), residues: 1940 sheet: None (None), residues: 0 loop : -0.54 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 730 TYR 0.010 0.001 TYR C 524 PHE 0.018 0.001 PHE D 341 TRP 0.012 0.001 TRP A 315 HIS 0.001 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (22488) covalent geometry : angle 0.48523 / 0.25 (30424) SS BOND : bond 0.00116 / 0.06 ( 4) SS BOND : angle 0.47440 / 0.33 ( 8) hydrogen bonds : bond 0.04465 / 3.05 ( 1407) hydrogen bonds : angle 3.30143 / 2.39 ( 4164) metal coordination : bond 0.02341 / 1.24 ( 16) metal coordination : angle 2.80009 / 2.18 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 256 time to evaluate : 0.791 Fit side-chains REVERT: A 36 PHE cc_start: 0.4142 (OUTLIER) cc_final: 0.3768 (p90) REVERT: A 113 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7738 (mm-30) REVERT: A 185 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7484 (t) REVERT: A 331 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7112 (mm) REVERT: A 361 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7854 (mptm) REVERT: A 552 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7291 (t0) REVERT: A 664 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6786 (pt) REVERT: B 114 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.6963 (tt) REVERT: B 335 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7560 (mpt) REVERT: B 361 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7814 (mptm) REVERT: B 404 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6559 (mt-10) REVERT: B 552 ASN cc_start: 0.7672 (OUTLIER) cc_final: 0.7334 (t0) REVERT: B 664 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6828 (pt) REVERT: D 114 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7073 (tt) REVERT: D 335 MET cc_start: 0.8236 (mpp) cc_final: 0.7920 (mpt) REVERT: D 361 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7807 (mptm) REVERT: D 404 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: D 552 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7351 (t0) REVERT: D 623 MET cc_start: 0.8232 (ttp) cc_final: 0.8005 (mtp) REVERT: D 664 ILE cc_start: 0.7091 (OUTLIER) cc_final: 0.6828 (pt) REVERT: C 105 ARG cc_start: 0.7661 (tmm-80) cc_final: 0.7353 (ttt-90) REVERT: C 114 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7081 (tt) REVERT: C 335 MET cc_start: 0.8215 (mpp) cc_final: 0.7897 (mpt) REVERT: C 361 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7814 (mptm) REVERT: C 404 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6546 (mt-10) REVERT: C 552 ASN cc_start: 0.7671 (OUTLIER) cc_final: 0.7346 (t0) REVERT: C 664 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6828 (pt) outliers start: 84 outliers final: 28 residues processed: 311 average time/residue: 0.4467 time to fit residues: 163.4352 Evaluate side-chains 283 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 233 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 707 LEU Chi-restraints excluded: chain C residue 708 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 131 optimal weight: 9.9990 chunk 258 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 224 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 213 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 257 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.169631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.124917 restraints weight = 26370.392| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.11 r_work: 0.3275 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22508 Z= 0.126 Angle : 0.506 8.364 30444 Z= 0.262 Chirality : 0.037 0.156 3420 Planarity : 0.004 0.058 3748 Dihedral : 9.953 160.955 3544 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.36 % Allowed : 27.09 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.16), residues: 2620 helix: 2.41 (0.12), residues: 1948 sheet: None (None), residues: 0 loop : -0.53 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 730 TYR 0.011 0.001 TYR C 524 PHE 0.019 0.001 PHE D 341 TRP 0.013 0.001 TRP A 315 HIS 0.003 0.000 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (22488) covalent geometry : angle 0.50259 / 0.26 (30424) SS BOND : bond 0.00182 / 0.09 ( 4) SS BOND : angle 0.53654 / 0.36 ( 8) hydrogen bonds : bond 0.05078 / 3.47 ( 1407) hydrogen bonds : angle 3.31598 / 2.41 ( 4164) metal coordination : bond 0.00749 / 0.39 ( 16) metal coordination : angle 2.92759 / 2.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 248 time to evaluate : 0.953 Fit side-chains REVERT: A 36 PHE cc_start: 0.4135 (OUTLIER) cc_final: 0.3715 (p90) REVERT: A 185 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7505 (t) REVERT: A 272 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7634 (ptm160) REVERT: A 331 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7333 (tt) REVERT: A 335 MET cc_start: 0.8048 (mpp) cc_final: 0.7592 (mpt) REVERT: A 361 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7858 (mptm) REVERT: A 552 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7350 (t0) REVERT: A 664 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6840 (pt) REVERT: B 114 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7038 (tt) REVERT: B 272 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7644 (ptm160) REVERT: B 335 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7570 (mpt) REVERT: B 361 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7814 (mptm) REVERT: B 404 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6657 (mt-10) REVERT: B 552 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7390 (t0) REVERT: B 664 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6823 (pt) REVERT: B 708 ILE cc_start: 0.7475 (mp) cc_final: 0.7141 (mm) REVERT: D 36 PHE cc_start: 0.4146 (OUTLIER) cc_final: 0.3804 (p90) REVERT: D 114 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7065 (tt) REVERT: D 335 MET cc_start: 0.8282 (mpp) cc_final: 0.7900 (mpt) REVERT: D 361 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7811 (mptm) REVERT: D 404 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6652 (mt-10) REVERT: D 510 LEU cc_start: 0.7582 (mt) cc_final: 0.7370 (mp) REVERT: D 552 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7383 (t0) REVERT: D 664 ILE cc_start: 0.7085 (OUTLIER) cc_final: 0.6813 (pt) REVERT: D 708 ILE cc_start: 0.7472 (mp) cc_final: 0.7140 (mm) REVERT: C 105 ARG cc_start: 0.7734 (tmm-80) cc_final: 0.7278 (ttp-110) REVERT: C 114 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7073 (tt) REVERT: C 272 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7639 (ptm160) REVERT: C 335 MET cc_start: 0.8254 (mpp) cc_final: 0.7866 (mpt) REVERT: C 361 LYS cc_start: 0.8290 (OUTLIER) cc_final: 0.7816 (mptm) REVERT: C 404 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: C 552 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7411 (t0) REVERT: C 623 MET cc_start: 0.8268 (ttp) cc_final: 0.8014 (mtp) REVERT: C 664 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6804 (pt) REVERT: C 708 ILE cc_start: 0.7475 (mp) cc_final: 0.7145 (mm) outliers start: 77 outliers final: 40 residues processed: 303 average time/residue: 0.4910 time to fit residues: 172.7559 Evaluate side-chains 300 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 234 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain D residue 36 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 631 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 631 ILE Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 53 optimal weight: 0.9990 chunk 208 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 134 optimal weight: 20.0000 chunk 92 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.169609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125310 restraints weight = 26333.003| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.12 r_work: 0.3279 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22508 Z= 0.127 Angle : 0.513 7.707 30444 Z= 0.266 Chirality : 0.037 0.156 3420 Planarity : 0.004 0.058 3748 Dihedral : 9.956 160.096 3544 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.49 % Allowed : 27.40 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.17), residues: 2620 helix: 2.39 (0.12), residues: 1948 sheet: None (None), residues: 0 loop : -0.49 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 194 TYR 0.011 0.001 TYR D 524 PHE 0.019 0.001 PHE D 341 TRP 0.013 0.001 TRP A 315 HIS 0.003 0.000 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (22488) covalent geometry : angle 0.51003 / 0.27 (30424) SS BOND : bond 0.00177 / 0.09 ( 4) SS BOND : angle 0.50918 / 0.35 ( 8) hydrogen bonds : bond 0.05095 / 3.48 ( 1407) hydrogen bonds : angle 3.34897 / 2.43 ( 4164) metal coordination : bond 0.00691 / 0.43 ( 16) metal coordination : angle 2.60518 / 2.11 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 241 time to evaluate : 0.621 Fit side-chains REVERT: A 36 PHE cc_start: 0.4156 (OUTLIER) cc_final: 0.3655 (p90) REVERT: A 272 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7634 (ptm160) REVERT: A 331 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7294 (tt) REVERT: A 335 MET cc_start: 0.8117 (mpp) cc_final: 0.7746 (mpt) REVERT: A 361 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7862 (mptm) REVERT: A 404 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: A 552 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7377 (t0) REVERT: A 664 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6821 (pt) REVERT: A 708 ILE cc_start: 0.7418 (mp) cc_final: 0.7061 (mm) REVERT: B 36 PHE cc_start: 0.4013 (OUTLIER) cc_final: 0.2874 (m-10) REVERT: B 114 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7112 (tt) REVERT: B 272 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7640 (ptm160) REVERT: B 335 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7467 (mpt) REVERT: B 361 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7823 (mptm) REVERT: B 404 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6647 (mt-10) REVERT: B 552 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7415 (t0) REVERT: B 664 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6815 (pt) REVERT: D 17 ARG cc_start: 0.6479 (mmm-85) cc_final: 0.5355 (ttp-110) REVERT: D 36 PHE cc_start: 0.4109 (OUTLIER) cc_final: 0.3819 (p90) REVERT: D 114 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7190 (tt) REVERT: D 335 MET cc_start: 0.8277 (mpp) cc_final: 0.7937 (mpt) REVERT: D 361 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7809 (mptm) REVERT: D 404 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6626 (mt-10) REVERT: D 510 LEU cc_start: 0.7606 (mt) cc_final: 0.7350 (mp) REVERT: D 552 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7423 (t0) REVERT: D 664 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6807 (pt) REVERT: D 730 ARG cc_start: 0.6595 (ttp80) cc_final: 0.6329 (ttp80) REVERT: C 17 ARG cc_start: 0.6527 (mmm-85) cc_final: 0.5374 (ttp-110) REVERT: C 105 ARG cc_start: 0.7638 (tmm-80) cc_final: 0.7400 (ttt-90) REVERT: C 114 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7166 (tt) REVERT: C 272 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7647 (ptm160) REVERT: C 335 MET cc_start: 0.8249 (mpp) cc_final: 0.7899 (mpt) REVERT: C 361 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7826 (mptm) REVERT: C 404 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6645 (mt-10) REVERT: C 552 ASN cc_start: 0.7767 (OUTLIER) cc_final: 0.7428 (t0) REVERT: C 664 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6792 (pt) REVERT: C 730 ARG cc_start: 0.6604 (ttp80) cc_final: 0.6370 (ttp80) outliers start: 80 outliers final: 48 residues processed: 302 average time/residue: 0.4586 time to fit residues: 161.9974 Evaluate side-chains 306 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 231 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 178 CYS Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 361 LYS Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 TRP Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 548 ASP Chi-restraints excluded: chain A residue 552 ASN Chi-restraints excluded: chain A residue 566 SER Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain B residue 36 PHE Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 361 LYS Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 410 TRP Chi-restraints excluded: chain B residue 422 MET Chi-restraints excluded: chain B residue 471 MET Chi-restraints excluded: chain B residue 498 THR Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 548 ASP Chi-restraints excluded: chain B residue 552 ASN Chi-restraints excluded: chain B residue 566 SER Chi-restraints excluded: chain B residue 631 ILE Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 707 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 36 PHE Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 361 LYS Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 404 GLU Chi-restraints excluded: chain D residue 410 TRP Chi-restraints excluded: chain D residue 422 MET Chi-restraints excluded: chain D residue 498 THR Chi-restraints excluded: chain D residue 547 ILE Chi-restraints excluded: chain D residue 548 ASP Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 707 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 36 PHE Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 272 ARG Chi-restraints excluded: chain C residue 361 LYS Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 404 GLU Chi-restraints excluded: chain C residue 410 TRP Chi-restraints excluded: chain C residue 422 MET Chi-restraints excluded: chain C residue 498 THR Chi-restraints excluded: chain C residue 547 ILE Chi-restraints excluded: chain C residue 548 ASP Chi-restraints excluded: chain C residue 552 ASN Chi-restraints excluded: chain C residue 566 SER Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 707 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 51 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 255 optimal weight: 0.7980 chunk 250 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 ASN ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.169398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126520 restraints weight = 26302.486| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.25 r_work: 0.3281 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22508 Z= 0.127 Angle : 0.513 7.876 30444 Z= 0.266 Chirality : 0.037 0.156 3420 Planarity : 0.004 0.058 3748 Dihedral : 9.954 159.721 3544 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.80 % Allowed : 27.36 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.17), residues: 2620 helix: 2.39 (0.12), residues: 1948 sheet: None (None), residues: 0 loop : -0.49 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 730 TYR 0.011 0.001 TYR B 524 PHE 0.019 0.001 PHE D 341 TRP 0.013 0.001 TRP A 315 HIS 0.003 0.000 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (22488) covalent geometry : angle 0.51071 / 0.27 (30424) SS BOND : bond 0.00185 / 0.09 ( 4) SS BOND : angle 0.51178 / 0.34 ( 8) hydrogen bonds : bond 0.05122 / 3.50 ( 1407) hydrogen bonds : angle 3.36178 / 2.44 ( 4164) metal coordination : bond 0.00649 / 0.37 ( 16) metal coordination : angle 2.57069 / 2.05 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7016.38 seconds wall clock time: 120 minutes 17.32 seconds (7217.32 seconds total)