Starting phenix.real_space_refine on Mon Jul 6 15:18:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fca_28978/07_2026/8fca_28978_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fca_28978/07_2026/8fca_28978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fca_28978/07_2026/8fca_28978_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fca_28978/07_2026/8fca_28978_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fca_28978/07_2026/8fca_28978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fca_28978/07_2026/8fca_28978.map" } resolution = 3.41 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= 0.011 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 88 5.16 5 C 12056 2.51 5 N 3068 2.21 5 O 3248 1.98 5 H 17476 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35936 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 8923 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 577} Chain breaks: 2 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 6, 'GLU:plan': 10, 'ASN:plan1': 2, 'GLN:plan1': 4, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 151 Chain: "B" Number of atoms: 8923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 8923 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 577} Chain breaks: 2 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 6, 'GLU:plan': 10, 'ASN:plan1': 2, 'GLN:plan1': 4, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 151 Chain: "C" Number of atoms: 8923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 8923 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 577} Chain breaks: 2 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 6, 'GLU:plan': 10, 'ASN:plan1': 2, 'GLN:plan1': 4, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 151 Chain: "D" Number of atoms: 8923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 8923 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 577} Chain breaks: 2 Unresolved non-hydrogen bonds: 285 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'ASP:plan': 10, 'ARG:plan': 6, 'GLU:plan': 10, 'ASN:plan1': 2, 'GLN:plan1': 4, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 151 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'XS9': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'XS9:plan-2': 1, 'XS9:plan-3': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'XS9': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'XS9:plan-2': 1, 'XS9:plan-3': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'XS9': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'XS9:plan-2': 1, 'XS9:plan-3': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'XS9': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'XS9:plan-2': 1, 'XS9:plan-3': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 5.90, per 1000 atoms: 0.16 Number of scatterers: 35936 At special positions: 0 Unit cell: (158.76, 158.76, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 O 3248 8.00 N 3068 7.00 C 12056 6.00 H 17476 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4528 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 69.7% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 193 through 201 Processing helix chain 'A' and resid 209 through 221 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 232 through 237 removed outlier: 4.371A pdb=" N TYR A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 250 through 260 removed outlier: 3.733A pdb=" N GLN A 260 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 335 through 357 removed outlier: 3.762A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 380 Processing helix chain 'A' and resid 382 through 391 removed outlier: 3.665A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 440 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.865A pdb=" N LEU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 466 removed outlier: 3.947A pdb=" N GLU A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 491 removed outlier: 3.732A pdb=" N SER A 470 " --> pdb=" O PHE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 534 Processing helix chain 'A' and resid 551 through 570 Processing helix chain 'A' and resid 572 through 588 removed outlier: 4.199A pdb=" N ALA A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.848A pdb=" N GLY A 595 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 636 removed outlier: 3.564A pdb=" N THR A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU A 623 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 679 Processing helix chain 'A' and resid 683 through 689 removed outlier: 4.011A pdb=" N LEU A 686 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER A 687 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A 688 " --> pdb=" O MET A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 708 removed outlier: 3.791A pdb=" N PHE A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 725 removed outlier: 3.505A pdb=" N ASN A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 748 removed outlier: 3.901A pdb=" N HIS A 731 " --> pdb=" O LYS A 727 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 757 Processing helix chain 'B' and resid 151 through 161 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 193 through 201 Processing helix chain 'B' and resid 209 through 221 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 232 through 237 removed outlier: 4.371A pdb=" N TYR B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 248 Processing helix chain 'B' and resid 250 through 260 removed outlier: 3.733A pdb=" N GLN B 260 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 335 through 357 removed outlier: 3.762A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'B' and resid 382 through 391 removed outlier: 3.665A pdb=" N HIS B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 391 " --> pdb=" O GLN B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 Processing helix chain 'B' and resid 445 through 450 removed outlier: 3.865A pdb=" N LEU B 450 " --> pdb=" O ARG B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 466 removed outlier: 3.947A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 491 removed outlier: 3.733A pdb=" N SER B 470 " --> pdb=" O PHE B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 534 Processing helix chain 'B' and resid 551 through 570 Processing helix chain 'B' and resid 572 through 588 removed outlier: 4.199A pdb=" N ALA B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.848A pdb=" N GLY B 595 " --> pdb=" O PHE B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 636 removed outlier: 3.564A pdb=" N THR B 601 " --> pdb=" O LYS B 597 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 615 " --> pdb=" O PHE B 611 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU B 623 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE B 624 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 679 Processing helix chain 'B' and resid 683 through 689 removed outlier: 4.011A pdb=" N LEU B 686 " --> pdb=" O LEU B 683 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER B 687 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER B 688 " --> pdb=" O MET B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 708 removed outlier: 3.790A pdb=" N PHE B 695 " --> pdb=" O TYR B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 725 removed outlier: 3.505A pdb=" N ASN B 712 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 748 removed outlier: 3.901A pdb=" N HIS B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 748 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 757 Processing helix chain 'C' and resid 151 through 161 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 209 through 221 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 232 through 237 removed outlier: 4.372A pdb=" N TYR C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 250 through 260 removed outlier: 3.733A pdb=" N GLN C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 335 through 357 removed outlier: 3.762A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 380 Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.665A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 440 Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.865A pdb=" N LEU C 450 " --> pdb=" O ARG C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 466 removed outlier: 3.947A pdb=" N GLU C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 491 removed outlier: 3.731A pdb=" N SER C 470 " --> pdb=" O PHE C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 534 Processing helix chain 'C' and resid 551 through 570 Processing helix chain 'C' and resid 572 through 588 removed outlier: 4.200A pdb=" N ALA C 576 " --> pdb=" O GLU C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 595 removed outlier: 3.848A pdb=" N GLY C 595 " --> pdb=" O PHE C 592 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 636 removed outlier: 3.563A pdb=" N THR C 601 " --> pdb=" O LYS C 597 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR C 602 " --> pdb=" O LEU C 598 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 615 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 623 " --> pdb=" O LEU C 619 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 663 through 679 Processing helix chain 'C' and resid 683 through 689 removed outlier: 4.011A pdb=" N LEU C 686 " --> pdb=" O LEU C 683 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER C 687 " --> pdb=" O GLU C 684 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 688 " --> pdb=" O MET C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 691 through 708 removed outlier: 3.791A pdb=" N PHE C 695 " --> pdb=" O TYR C 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 725 removed outlier: 3.505A pdb=" N ASN C 712 " --> pdb=" O VAL C 708 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET C 718 " --> pdb=" O LEU C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 748 removed outlier: 3.901A pdb=" N HIS C 731 " --> pdb=" O LYS C 727 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 757 Processing helix chain 'D' and resid 151 through 161 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 209 through 221 Processing helix chain 'D' and resid 222 through 227 Processing helix chain 'D' and resid 232 through 237 removed outlier: 4.371A pdb=" N TYR D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 248 Processing helix chain 'D' and resid 250 through 260 removed outlier: 3.733A pdb=" N GLN D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 331 Processing helix chain 'D' and resid 335 through 357 removed outlier: 3.763A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 380 Processing helix chain 'D' and resid 382 through 391 removed outlier: 3.665A pdb=" N HIS D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 440 Processing helix chain 'D' and resid 445 through 450 removed outlier: 3.865A pdb=" N LEU D 450 " --> pdb=" O ARG D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 466 removed outlier: 3.946A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 491 removed outlier: 3.731A pdb=" N SER D 470 " --> pdb=" O PHE D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 534 Processing helix chain 'D' and resid 551 through 570 Processing helix chain 'D' and resid 572 through 588 removed outlier: 4.199A pdb=" N ALA D 576 " --> pdb=" O GLU D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 595 removed outlier: 3.848A pdb=" N GLY D 595 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 596 through 636 removed outlier: 3.564A pdb=" N THR D 601 " --> pdb=" O LYS D 597 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TYR D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 615 " --> pdb=" O PHE D 611 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 616 " --> pdb=" O LYS D 612 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU D 623 " --> pdb=" O LEU D 619 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE D 624 " --> pdb=" O VAL D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 679 Processing helix chain 'D' and resid 683 through 689 removed outlier: 4.010A pdb=" N LEU D 686 " --> pdb=" O LEU D 683 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER D 687 " --> pdb=" O GLU D 684 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER D 688 " --> pdb=" O MET D 685 " (cutoff:3.500A) Processing helix chain 'D' and resid 691 through 708 removed outlier: 3.791A pdb=" N PHE D 695 " --> pdb=" O TYR D 691 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 725 removed outlier: 3.505A pdb=" N ASN D 712 " --> pdb=" O VAL D 708 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET D 718 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 727 through 748 removed outlier: 3.901A pdb=" N HIS D 731 " --> pdb=" O LYS D 727 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE D 748 " --> pdb=" O ILE D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 757 Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 411 removed outlier: 6.480A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 405 through 411 removed outlier: 6.481A pdb=" N LYS B 405 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASP B 420 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 405 through 411 removed outlier: 6.479A pdb=" N LYS C 405 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASP C 420 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LYS C 407 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU C 418 " --> pdb=" O LYS C 407 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 405 through 411 removed outlier: 6.480A pdb=" N LYS D 405 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ASP D 420 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) 1145 hydrogen bonds defined for protein. 3303 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: 8.11 Time building geometry restraints manager: 4.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17448 1.03 - 1.23: 44 1.23 - 1.42: 7904 1.42 - 1.61: 10828 1.61 - 1.81: 160 Bond restraints: 36384 Sorted by residual: bond pdb=" CAY Y01 A1002 " pdb=" OAW Y01 A1002 " ideal model delta sigma weight residual 1.332 1.429 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" CAY Y01 C1001 " pdb=" OAW Y01 C1001 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CAY Y01 B1002 " pdb=" OAW Y01 B1002 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" CAY Y01 D1001 " pdb=" OAW Y01 D1001 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C15 XS9 A1001 " pdb=" C21 XS9 A1001 " ideal model delta sigma weight residual 1.548 1.642 -0.094 2.00e-02 2.50e+03 2.20e+01 ... (remaining 36379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.04: 65361 6.04 - 12.09: 55 12.09 - 18.13: 4 18.13 - 24.17: 16 24.17 - 30.22: 16 Bond angle restraints: 65452 Sorted by residual: angle pdb=" HZ1 LYS D 197 " pdb=" NZ LYS D 197 " pdb=" HZ3 LYS D 197 " ideal model delta sigma weight residual 109.00 78.78 30.22 3.00e+00 1.11e-01 1.01e+02 angle pdb=" HZ1 LYS A 197 " pdb=" NZ LYS A 197 " pdb=" HZ3 LYS A 197 " ideal model delta sigma weight residual 109.00 78.84 30.16 3.00e+00 1.11e-01 1.01e+02 angle pdb=" HZ1 LYS B 197 " pdb=" NZ LYS B 197 " pdb=" HZ3 LYS B 197 " ideal model delta sigma weight residual 109.00 78.84 30.16 3.00e+00 1.11e-01 1.01e+02 angle pdb=" HZ1 LYS C 197 " pdb=" NZ LYS C 197 " pdb=" HZ3 LYS C 197 " ideal model delta sigma weight residual 109.00 78.89 30.11 3.00e+00 1.11e-01 1.01e+02 angle pdb=" HZ2 LYS C 197 " pdb=" NZ LYS C 197 " pdb=" HZ3 LYS C 197 " ideal model delta sigma weight residual 109.00 79.35 29.65 3.00e+00 1.11e-01 9.77e+01 ... (remaining 65447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 17343 35.85 - 71.71: 381 71.71 - 107.56: 28 107.56 - 143.42: 28 143.42 - 179.27: 24 Dihedral angle restraints: 17804 sinusoidal: 9356 harmonic: 8448 Sorted by residual: dihedral pdb=" C16 XS9 C1002 " pdb=" C30 XS9 C1002 " pdb=" C31 XS9 C1002 " pdb=" O35 XS9 C1002 " ideal model delta sinusoidal sigma weight residual -149.32 29.95 -179.27 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C16 XS9 B1001 " pdb=" C30 XS9 B1001 " pdb=" C31 XS9 B1001 " pdb=" O35 XS9 B1001 " ideal model delta sinusoidal sigma weight residual -149.32 29.93 -179.25 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C16 XS9 A1001 " pdb=" C30 XS9 A1001 " pdb=" C31 XS9 A1001 " pdb=" O35 XS9 A1001 " ideal model delta sinusoidal sigma weight residual -149.32 29.93 -179.25 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 17801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.229: 3016 0.229 - 0.458: 12 0.458 - 0.687: 0 0.687 - 0.916: 0 0.916 - 1.145: 4 Chirality restraints: 3032 Sorted by residual: chirality pdb=" C31 XS9 D1002 " pdb=" C13 XS9 D1002 " pdb=" C30 XS9 D1002 " pdb=" C32 XS9 D1002 " both_signs ideal model delta sigma weight residual True 2.32 -1.18 1.14 2.00e-01 2.50e+01 3.28e+01 chirality pdb=" C31 XS9 A1001 " pdb=" C13 XS9 A1001 " pdb=" C30 XS9 A1001 " pdb=" C32 XS9 A1001 " both_signs ideal model delta sigma weight residual True 2.32 -1.18 1.14 2.00e-01 2.50e+01 3.26e+01 chirality pdb=" C31 XS9 B1001 " pdb=" C13 XS9 B1001 " pdb=" C30 XS9 B1001 " pdb=" C32 XS9 B1001 " both_signs ideal model delta sigma weight residual True 2.32 -1.18 1.14 2.00e-01 2.50e+01 3.26e+01 ... (remaining 3029 not shown) Planarity restraints: 5512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 575 " 0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C LEU A 575 " -0.031 2.00e-02 2.50e+03 pdb=" O LEU A 575 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA A 576 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 575 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C LEU D 575 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU D 575 " -0.011 2.00e-02 2.50e+03 pdb=" N ALA D 576 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 578 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C MET B 578 " 0.031 2.00e-02 2.50e+03 pdb=" O MET B 578 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL B 579 " -0.010 2.00e-02 2.50e+03 ... (remaining 5509 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1438 2.17 - 2.77: 68935 2.77 - 3.38: 96638 3.38 - 3.99: 117769 3.99 - 4.60: 188244 Nonbonded interactions: 473024 Sorted by model distance: nonbonded pdb=" O ARG B 400 " pdb=" HG SER B 403 " model vdw 1.557 2.450 nonbonded pdb=" O ARG A 400 " pdb=" HG SER A 403 " model vdw 1.557 2.450 nonbonded pdb=" O ARG D 400 " pdb=" HG SER D 403 " model vdw 1.557 2.450 nonbonded pdb=" O ARG C 400 " pdb=" HG SER C 403 " model vdw 1.557 2.450 nonbonded pdb=" O GLU C 225 " pdb=" HG SER C 229 " model vdw 1.638 2.450 ... (remaining 473019 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and resid 150 through 787) selection = (chain 'B' and resid 150 through 787) selection = (chain 'C' and resid 150 through 787) selection = (chain 'D' and resid 150 through 787) } 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: 1.030 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: 0.270 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 32.760 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 18908 Z= 0.282 Angle : 0.841 22.870 25820 Z= 0.362 Chirality : 0.061 1.145 3032 Planarity : 0.004 0.037 3212 Dihedral : 18.162 179.272 6992 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.18 (0.17), residues: 2376 helix: 1.83 (0.13), residues: 1492 sheet: -1.64 (0.48), residues: 116 loop : -0.90 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 271 TYR 0.008 0.001 TYR B 478 PHE 0.012 0.001 PHE C 386 TRP 0.017 0.001 TRP A 737 HIS 0.004 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.28 (18908) covalent geometry : angle 0.84109 / 0.36 (25820) hydrogen bonds : bond 0.16548 / 11.37 ( 1145) hydrogen bonds : angle 5.78275 / 4.12 ( 3303) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 413 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 MET cc_start: 0.6942 (ptm) cc_final: 0.6691 (ptt) REVERT: B 197 LYS cc_start: 0.7179 (tttp) cc_final: 0.6893 (tptt) REVERT: B 605 MET cc_start: 0.5182 (tpp) cc_final: 0.4929 (tpt) REVERT: B 625 MET cc_start: 0.5604 (mmt) cc_final: 0.5358 (mmt) REVERT: B 633 VAL cc_start: 0.8427 (t) cc_final: 0.8211 (t) REVERT: C 197 LYS cc_start: 0.7093 (tttp) cc_final: 0.6790 (tptt) REVERT: C 260 GLN cc_start: 0.7825 (mm110) cc_final: 0.7407 (mp10) REVERT: C 605 MET cc_start: 0.5288 (tpp) cc_final: 0.5033 (tpt) REVERT: C 633 VAL cc_start: 0.8523 (t) cc_final: 0.8304 (t) REVERT: C 774 ARG cc_start: 0.6962 (mtp85) cc_final: 0.6632 (mmt180) REVERT: D 197 LYS cc_start: 0.7332 (tttp) cc_final: 0.7127 (tptt) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.3549 time to fit residues: 214.4240 Evaluate side-chains 309 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN B 239 GLN C 239 GLN D 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.203861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.154554 restraints weight = 73462.160| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.42 r_work: 0.3637 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18908 Z= 0.236 Angle : 0.767 17.447 25820 Z= 0.361 Chirality : 0.047 0.468 3032 Planarity : 0.005 0.063 3212 Dihedral : 20.810 179.150 3188 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.17 % Allowed : 9.80 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.28 (0.17), residues: 2376 helix: 1.87 (0.13), residues: 1516 sheet: -1.90 (0.55), residues: 84 loop : -0.88 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 151 TYR 0.019 0.002 TYR A 346 PHE 0.015 0.002 PHE A 273 TRP 0.017 0.002 TRP C 737 HIS 0.006 0.001 HIS C 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.24 (18908) covalent geometry : angle 0.76718 / 0.36 (25820) hydrogen bonds : bond 0.05070 / 3.46 ( 1145) hydrogen bonds : angle 5.02502 / 3.59 ( 3303) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 330 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 MET cc_start: 0.6802 (ptm) cc_final: 0.6580 (ptt) REVERT: B 197 LYS cc_start: 0.7503 (tttp) cc_final: 0.7126 (tptt) REVERT: C 197 LYS cc_start: 0.7515 (tttp) cc_final: 0.7003 (tptt) REVERT: C 260 GLN cc_start: 0.8059 (mm110) cc_final: 0.7711 (mp10) REVERT: C 482 MET cc_start: 0.8063 (mmt) cc_final: 0.7854 (mmt) REVERT: C 534 MET cc_start: 0.4494 (mmt) cc_final: 0.4294 (mpp) REVERT: C 605 MET cc_start: 0.5355 (tpp) cc_final: 0.4987 (tpt) REVERT: D 197 LYS cc_start: 0.7852 (tttp) cc_final: 0.7493 (tptt) REVERT: D 482 MET cc_start: 0.8142 (mmt) cc_final: 0.7906 (mmp) REVERT: D 685 MET cc_start: 0.5696 (tpt) cc_final: 0.5459 (tpt) outliers start: 21 outliers final: 13 residues processed: 341 average time/residue: 0.3073 time to fit residues: 161.4369 Evaluate side-chains 317 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 304 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 711 LEU Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 152 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 178 optimal weight: 0.0170 chunk 140 optimal weight: 0.6980 chunk 199 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 212 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 113 optimal weight: 30.0000 overall best weight: 0.6420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.207246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.157422 restraints weight = 72590.379| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.42 r_work: 0.3679 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18908 Z= 0.118 Angle : 0.660 18.019 25820 Z= 0.299 Chirality : 0.043 0.503 3032 Planarity : 0.004 0.053 3212 Dihedral : 20.213 179.568 3188 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.67 % Allowed : 9.69 % Favored : 89.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.72 (0.17), residues: 2376 helix: 2.29 (0.13), residues: 1516 sheet: -1.32 (0.57), residues: 84 loop : -0.94 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 464 TYR 0.009 0.001 TYR D 346 PHE 0.021 0.001 PHE C 357 TRP 0.014 0.001 TRP C 737 HIS 0.004 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (18908) covalent geometry : angle 0.66000 / 0.30 (25820) hydrogen bonds : bond 0.04224 / 2.90 ( 1145) hydrogen bonds : angle 4.52389 / 3.23 ( 3303) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 322 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 197 LYS cc_start: 0.7444 (tttp) cc_final: 0.7052 (tptt) REVERT: C 260 GLN cc_start: 0.8011 (mm110) cc_final: 0.7701 (mp10) REVERT: D 197 LYS cc_start: 0.7757 (tttp) cc_final: 0.7396 (tptt) REVERT: D 605 MET cc_start: 0.5408 (tpt) cc_final: 0.4595 (tpt) REVERT: D 685 MET cc_start: 0.5791 (tpt) cc_final: 0.5506 (tpt) outliers start: 12 outliers final: 6 residues processed: 329 average time/residue: 0.3214 time to fit residues: 163.1734 Evaluate side-chains 303 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 297 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain D residue 306 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.204946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154870 restraints weight = 71078.027| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.37 r_work: 0.3643 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18908 Z= 0.151 Angle : 0.664 17.370 25820 Z= 0.303 Chirality : 0.044 0.507 3032 Planarity : 0.004 0.054 3212 Dihedral : 20.031 179.864 3188 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.50 % Allowed : 10.08 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.83 (0.17), residues: 2376 helix: 2.41 (0.13), residues: 1516 sheet: -1.29 (0.59), residues: 84 loop : -0.99 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 464 TYR 0.014 0.001 TYR C 346 PHE 0.028 0.001 PHE D 357 TRP 0.015 0.002 TRP C 737 HIS 0.004 0.001 HIS D 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (18908) covalent geometry : angle 0.66445 / 0.30 (25820) hydrogen bonds : bond 0.03966 / 2.71 ( 1145) hydrogen bonds : angle 4.47540 / 3.20 ( 3303) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 338 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 311 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 685 MET cc_start: 0.5443 (tpt) cc_final: 0.5132 (tpt) REVERT: B 197 LYS cc_start: 0.7624 (tttp) cc_final: 0.7345 (tptp) REVERT: B 605 MET cc_start: 0.5692 (mmt) cc_final: 0.5351 (tpt) REVERT: B 685 MET cc_start: 0.5212 (tpt) cc_final: 0.4947 (tpt) REVERT: B 756 PHE cc_start: 0.7020 (m-80) cc_final: 0.6688 (m-80) REVERT: C 260 GLN cc_start: 0.8129 (mm110) cc_final: 0.7811 (mp10) REVERT: C 685 MET cc_start: 0.5549 (tpt) cc_final: 0.5322 (tpt) REVERT: D 154 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7162 (tt) REVERT: D 197 LYS cc_start: 0.7908 (tttp) cc_final: 0.7537 (tptt) REVERT: D 605 MET cc_start: 0.5492 (tpt) cc_final: 0.4715 (tpt) REVERT: D 685 MET cc_start: 0.5770 (tpt) cc_final: 0.5495 (tpt) outliers start: 27 outliers final: 14 residues processed: 327 average time/residue: 0.3099 time to fit residues: 157.7730 Evaluate side-chains 314 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 299 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 783 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 151 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 177 optimal weight: 0.3980 chunk 186 optimal weight: 0.9990 chunk 200 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.206849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.157295 restraints weight = 71110.238| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.40 r_work: 0.3666 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18908 Z= 0.109 Angle : 0.638 17.168 25820 Z= 0.286 Chirality : 0.043 0.494 3032 Planarity : 0.004 0.064 3212 Dihedral : 19.866 179.914 3188 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.95 % Allowed : 11.08 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.05 (0.17), residues: 2376 helix: 2.62 (0.13), residues: 1520 sheet: -1.16 (0.58), residues: 84 loop : -1.02 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 464 TYR 0.011 0.001 TYR B 346 PHE 0.028 0.001 PHE B 357 TRP 0.013 0.001 TRP C 737 HIS 0.005 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (18908) covalent geometry : angle 0.63806 / 0.29 (25820) hydrogen bonds : bond 0.03544 / 2.43 ( 1145) hydrogen bonds : angle 4.20047 / 3.00 ( 3303) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 337 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 320 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 685 MET cc_start: 0.5189 (tpt) cc_final: 0.4880 (tpt) REVERT: B 756 PHE cc_start: 0.6920 (m-80) cc_final: 0.6569 (m-80) REVERT: C 154 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6840 (tt) REVERT: C 260 GLN cc_start: 0.8120 (mm110) cc_final: 0.7821 (mp10) REVERT: C 685 MET cc_start: 0.5509 (tpt) cc_final: 0.5190 (tpt) REVERT: C 710 LEU cc_start: 0.7837 (mt) cc_final: 0.7538 (mt) REVERT: D 154 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7137 (tt) REVERT: D 197 LYS cc_start: 0.7878 (tttp) cc_final: 0.7488 (tptt) REVERT: D 605 MET cc_start: 0.5535 (tpt) cc_final: 0.4573 (tpt) REVERT: D 685 MET cc_start: 0.5669 (tpt) cc_final: 0.5395 (tpt) outliers start: 17 outliers final: 13 residues processed: 327 average time/residue: 0.3221 time to fit residues: 162.7704 Evaluate side-chains 314 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 299 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 306 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 214 optimal weight: 0.9990 chunk 68 optimal weight: 0.0010 chunk 188 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 53 optimal weight: 30.0000 chunk 204 optimal weight: 0.6980 chunk 223 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.205023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.152427 restraints weight = 70726.163| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.38 r_work: 0.3644 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18908 Z= 0.134 Angle : 0.650 17.016 25820 Z= 0.293 Chirality : 0.043 0.493 3032 Planarity : 0.004 0.077 3212 Dihedral : 19.833 179.888 3188 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.39 % Allowed : 11.08 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.17 (0.17), residues: 2376 helix: 2.79 (0.13), residues: 1492 sheet: -1.33 (0.57), residues: 84 loop : -0.96 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 464 TYR 0.017 0.001 TYR C 346 PHE 0.027 0.001 PHE A 611 TRP 0.013 0.001 TRP C 737 HIS 0.005 0.001 HIS A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (18908) covalent geometry : angle 0.65048 / 0.29 (25820) hydrogen bonds : bond 0.03551 / 2.43 ( 1145) hydrogen bonds : angle 4.21044 / 3.01 ( 3303) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 341 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 316 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 685 MET cc_start: 0.5197 (tpt) cc_final: 0.4884 (tpt) REVERT: B 756 PHE cc_start: 0.6956 (m-80) cc_final: 0.6624 (m-80) REVERT: C 154 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6869 (tt) REVERT: C 197 LYS cc_start: 0.7471 (tttp) cc_final: 0.7042 (tptp) REVERT: C 260 GLN cc_start: 0.8377 (mm110) cc_final: 0.8078 (mp10) REVERT: C 605 MET cc_start: 0.5847 (mmm) cc_final: 0.5509 (mmt) REVERT: C 685 MET cc_start: 0.5757 (tpt) cc_final: 0.5434 (tpt) REVERT: D 154 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7249 (tt) REVERT: D 605 MET cc_start: 0.5559 (tpt) cc_final: 0.4891 (tpt) REVERT: D 685 MET cc_start: 0.5626 (tpt) cc_final: 0.5361 (tpt) outliers start: 25 outliers final: 18 residues processed: 327 average time/residue: 0.2875 time to fit residues: 146.3033 Evaluate side-chains 319 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 299 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 306 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 135 optimal weight: 2.9990 chunk 238 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 128 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 216 optimal weight: 9.9990 chunk 232 optimal weight: 7.9990 chunk 234 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.203668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.151672 restraints weight = 71097.607| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.52 r_work: 0.3614 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18908 Z= 0.157 Angle : 0.656 16.827 25820 Z= 0.297 Chirality : 0.043 0.491 3032 Planarity : 0.004 0.064 3212 Dihedral : 19.834 179.984 3188 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.45 % Allowed : 11.36 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.17), residues: 2376 helix: 2.76 (0.13), residues: 1492 sheet: -1.60 (0.56), residues: 84 loop : -0.99 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 464 TYR 0.017 0.001 TYR C 346 PHE 0.025 0.001 PHE A 611 TRP 0.013 0.001 TRP C 737 HIS 0.005 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (18908) covalent geometry : angle 0.65599 / 0.30 (25820) hydrogen bonds : bond 0.03598 / 2.47 ( 1145) hydrogen bonds : angle 4.22941 / 3.04 ( 3303) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 334 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 308 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7164 (tt) REVERT: A 745 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7394 (tm-30) REVERT: B 685 MET cc_start: 0.5207 (tpt) cc_final: 0.4879 (tpt) REVERT: C 154 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6921 (tt) REVERT: C 197 LYS cc_start: 0.7570 (tttp) cc_final: 0.7139 (tptp) REVERT: C 260 GLN cc_start: 0.8406 (mm110) cc_final: 0.8125 (mp10) REVERT: C 685 MET cc_start: 0.5658 (tpt) cc_final: 0.5420 (tpt) REVERT: D 154 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7247 (tt) REVERT: D 356 LEU cc_start: 0.7886 (tt) cc_final: 0.7032 (mp) REVERT: D 605 MET cc_start: 0.5583 (tpt) cc_final: 0.4791 (tpt) REVERT: D 685 MET cc_start: 0.5685 (tpt) cc_final: 0.5434 (tpt) outliers start: 26 outliers final: 22 residues processed: 320 average time/residue: 0.2969 time to fit residues: 147.9077 Evaluate side-chains 328 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 303 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 747 SER Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 783 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 306 GLU Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 509 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 747 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 306 GLU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 306 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 80 optimal weight: 0.3980 chunk 152 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 238 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 210 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.205614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3810 r_free = 0.3810 target = 0.153466 restraints weight = 70970.236| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.45 r_work: 0.3639 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18908 Z= 0.103 Angle : 0.633 16.801 25820 Z= 0.282 Chirality : 0.042 0.481 3032 Planarity : 0.004 0.073 3212 Dihedral : 19.746 179.877 3188 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.06 % Allowed : 12.36 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.17), residues: 2376 helix: 2.95 (0.13), residues: 1492 sheet: -1.43 (0.56), residues: 84 loop : -0.91 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 464 TYR 0.010 0.001 TYR C 346 PHE 0.026 0.001 PHE A 611 TRP 0.011 0.001 TRP C 737 HIS 0.005 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (18908) covalent geometry : angle 0.63270 / 0.28 (25820) hydrogen bonds : bond 0.03300 / 2.26 ( 1145) hydrogen bonds : angle 4.01260 / 2.88 ( 3303) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 320 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7084 (tt) REVERT: A 363 GLU cc_start: 0.8136 (mt-10) cc_final: 0.6960 (tt0) REVERT: B 363 GLU cc_start: 0.8132 (mt-10) cc_final: 0.6765 (tt0) REVERT: B 685 MET cc_start: 0.5121 (tpt) cc_final: 0.4885 (tpt) REVERT: C 154 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6832 (tt) REVERT: C 197 LYS cc_start: 0.7565 (tttp) cc_final: 0.7139 (tptp) REVERT: C 260 GLN cc_start: 0.8417 (mm110) cc_final: 0.8152 (mp10) REVERT: C 363 GLU cc_start: 0.8119 (mt-10) cc_final: 0.6945 (tt0) REVERT: C 685 MET cc_start: 0.5612 (tpt) cc_final: 0.5387 (tpt) REVERT: D 154 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7169 (tt) REVERT: D 356 LEU cc_start: 0.7847 (tt) cc_final: 0.7015 (mp) REVERT: D 363 GLU cc_start: 0.8127 (mt-10) cc_final: 0.6933 (tt0) REVERT: D 605 MET cc_start: 0.5388 (tpt) cc_final: 0.4739 (tpt) REVERT: D 685 MET cc_start: 0.5633 (tpt) cc_final: 0.5393 (tpt) outliers start: 19 outliers final: 12 residues processed: 325 average time/residue: 0.3110 time to fit residues: 157.0144 Evaluate side-chains 314 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 299 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 306 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 39 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.204764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.156958 restraints weight = 71204.779| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.63 r_work: 0.3639 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18908 Z= 0.120 Angle : 0.642 16.831 25820 Z= 0.287 Chirality : 0.043 0.485 3032 Planarity : 0.004 0.076 3212 Dihedral : 19.733 179.770 3188 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.95 % Allowed : 12.81 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.38 (0.17), residues: 2376 helix: 2.97 (0.13), residues: 1492 sheet: -1.57 (0.56), residues: 84 loop : -0.88 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 464 TYR 0.013 0.001 TYR C 346 PHE 0.026 0.001 PHE A 611 TRP 0.011 0.001 TRP C 737 HIS 0.006 0.001 HIS B 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (18908) covalent geometry : angle 0.64156 / 0.29 (25820) hydrogen bonds : bond 0.03307 / 2.26 ( 1145) hydrogen bonds : angle 4.03185 / 2.89 ( 3303) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 327 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 310 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7135 (tt) REVERT: A 745 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7620 (tm-30) REVERT: B 685 MET cc_start: 0.5187 (tpt) cc_final: 0.4946 (tpt) REVERT: C 154 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7229 (tt) REVERT: C 197 LYS cc_start: 0.7560 (tttp) cc_final: 0.7130 (tptp) REVERT: C 260 GLN cc_start: 0.8478 (mm110) cc_final: 0.8186 (mp10) REVERT: C 363 GLU cc_start: 0.8126 (mt-10) cc_final: 0.6922 (tt0) REVERT: C 685 MET cc_start: 0.5651 (tpt) cc_final: 0.5414 (tpt) REVERT: D 154 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7266 (tt) REVERT: D 363 GLU cc_start: 0.8137 (mt-10) cc_final: 0.6943 (tt0) REVERT: D 605 MET cc_start: 0.5385 (tpt) cc_final: 0.4829 (mmm) REVERT: D 685 MET cc_start: 0.5692 (tpt) cc_final: 0.5448 (tpt) outliers start: 17 outliers final: 13 residues processed: 316 average time/residue: 0.3106 time to fit residues: 153.3515 Evaluate side-chains 322 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 306 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 306 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 126 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 139 optimal weight: 0.4980 chunk 200 optimal weight: 0.6980 chunk 160 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.204680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154967 restraints weight = 71491.918| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.66 r_work: 0.3622 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18908 Z= 0.123 Angle : 0.645 16.706 25820 Z= 0.289 Chirality : 0.043 0.482 3032 Planarity : 0.004 0.076 3212 Dihedral : 19.721 179.885 3188 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.89 % Allowed : 13.36 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.44 (0.17), residues: 2376 helix: 3.08 (0.13), residues: 1468 sheet: -1.62 (0.55), residues: 84 loop : -0.86 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 464 TYR 0.013 0.001 TYR C 346 PHE 0.027 0.001 PHE A 611 TRP 0.012 0.001 TRP C 737 HIS 0.006 0.001 HIS C 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (18908) covalent geometry : angle 0.64469 / 0.29 (25820) hydrogen bonds : bond 0.03274 / 2.23 ( 1145) hydrogen bonds : angle 4.01307 / 2.87 ( 3303) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4752 Ramachandran restraints generated. 2376 Oldfield, 0 Emsley, 2376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Residue ILE 153 is missing expected H atoms. Skipping. Residue LEU 170 is missing expected H atoms. Skipping. Residue LEU 173 is missing expected H atoms. Skipping. Residue LEU 174 is missing expected H atoms. Skipping. Residue THR 175 is missing expected H atoms. Skipping. Residue LYS 177 is missing expected H atoms. Skipping. Residue LYS 178 is missing expected H atoms. Skipping. Residue THR 193 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LYS 276 is missing expected H atoms. Skipping. Residue VAL 301 is missing expected H atoms. Skipping. Residue MET 375 is missing expected H atoms. Skipping. Residue THR 426 is missing expected H atoms. Skipping. Residue LYS 442 is missing expected H atoms. Skipping. Residue LEU 494 is missing expected H atoms. Skipping. Residue TYR 500 is missing expected H atoms. Skipping. Residue TYR 502 is missing expected H atoms. Skipping. Residue TYR 508 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue SER 563 is missing expected H atoms. Skipping. Residue LEU 568 is missing expected H atoms. Skipping. Residue ILE 571 is missing expected H atoms. Skipping. Residue MET 587 is missing expected H atoms. Skipping. Residue LYS 597 is missing expected H atoms. Skipping. Residue LEU 598 is missing expected H atoms. Skipping. Residue THR 599 is missing expected H atoms. Skipping. Residue THR 601 is missing expected H atoms. Skipping. Residue TYR 602 is missing expected H atoms. Skipping. Residue SER 603 is missing expected H atoms. Skipping. Residue ILE 604 is missing expected H atoms. Skipping. Residue ILE 606 is missing expected H atoms. Skipping. Residue LYS 608 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue LYS 612 is missing expected H atoms. Skipping. Residue LEU 614 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue LEU 622 is missing expected H atoms. Skipping. Residue LEU 676 is missing expected H atoms. Skipping. Residue LEU 683 is missing expected H atoms. Skipping. Residue SER 688 is missing expected H atoms. Skipping. Residue VAL 722 is missing expected H atoms. Skipping. Residue VAL 725 is missing expected H atoms. Skipping. Residue SER 726 is missing expected H atoms. Skipping. Residue LYS 727 is missing expected H atoms. Skipping. Residue SER 729 is missing expected H atoms. Skipping. Residue LYS 730 is missing expected H atoms. Skipping. Residue ILE 732 is missing expected H atoms. Skipping. Residue LYS 766 is missing expected H atoms. Skipping. Evaluate side-chains 330 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 314 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7162 (tt) REVERT: A 745 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7633 (tm-30) REVERT: B 363 GLU cc_start: 0.8095 (mt-10) cc_final: 0.6829 (tt0) REVERT: B 685 MET cc_start: 0.5296 (tpt) cc_final: 0.5064 (tpt) REVERT: C 154 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7274 (tt) REVERT: C 197 LYS cc_start: 0.7619 (tttp) cc_final: 0.7115 (tttp) REVERT: C 260 GLN cc_start: 0.8526 (mm110) cc_final: 0.8206 (mp10) REVERT: C 363 GLU cc_start: 0.8135 (mt-10) cc_final: 0.6933 (tt0) REVERT: C 685 MET cc_start: 0.5616 (tpt) cc_final: 0.5379 (tpt) REVERT: D 154 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7281 (tt) REVERT: D 356 LEU cc_start: 0.7834 (tt) cc_final: 0.7076 (mp) REVERT: D 363 GLU cc_start: 0.8155 (mt-10) cc_final: 0.6956 (tt0) REVERT: D 605 MET cc_start: 0.5411 (tpt) cc_final: 0.4781 (mmm) REVERT: D 685 MET cc_start: 0.5761 (tpt) cc_final: 0.5520 (tpt) outliers start: 16 outliers final: 13 residues processed: 320 average time/residue: 0.3036 time to fit residues: 151.7948 Evaluate side-chains 327 residues out of total 2116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 311 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain B residue 575 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 747 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 306 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 50 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 210 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 218 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.203400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.151335 restraints weight = 72645.741| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.23 r_work: 0.3613 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18908 Z= 0.119 Angle : 0.642 16.650 25820 Z= 0.287 Chirality : 0.042 0.480 3032 Planarity : 0.004 0.076 3212 Dihedral : 19.701 179.975 3188 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.00 % Allowed : 13.47 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.32 (0.17), residues: 2376 helix: 2.93 (0.13), residues: 1520 sheet: -1.58 (0.55), residues: 84 loop : -1.07 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 464 TYR 0.013 0.001 TYR D 346 PHE 0.027 0.001 PHE A 611 TRP 0.011 0.001 TRP C 737 HIS 0.007 0.001 HIS B 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (18908) covalent geometry : angle 0.64181 / 0.29 (25820) hydrogen bonds : bond 0.03213 / 2.19 ( 1145) hydrogen bonds : angle 3.97772 / 2.85 ( 3303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10048.91 seconds wall clock time: 171 minutes 0.29 seconds (10260.29 seconds total)