Starting phenix.real_space_refine on Sat Jun 28 09:09:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tdl_41166/06_2025/8tdl_41166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tdl_41166/06_2025/8tdl_41166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tdl_41166/06_2025/8tdl_41166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tdl_41166/06_2025/8tdl_41166.map" model { file = "/net/cci-nas-00/data/ceres_data/8tdl_41166/06_2025/8tdl_41166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tdl_41166/06_2025/8tdl_41166.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.007 sd= 0.080 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 70 5.16 5 C 11200 2.51 5 N 3052 2.21 5 O 3213 1.98 5 H 15197 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 32732 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 4676 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 9, 'TRANS': 354} Chain breaks: 2 Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 632 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 6, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 216 Chain: "B" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 4676 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 9, 'TRANS': 354} Chain breaks: 2 Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 632 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 6, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 216 Chain: "C" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 4676 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 9, 'TRANS': 354} Chain breaks: 2 Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 632 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 6, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 216 Chain: "D" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 4676 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 9, 'TRANS': 354} Chain breaks: 2 Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 632 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 6, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 216 Chain: "E" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 4676 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 9, 'TRANS': 354} Chain breaks: 2 Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 632 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 6, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 216 Chain: "F" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 4676 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 9, 'TRANS': 354} Chain breaks: 2 Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 632 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 6, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 216 Chain: "G" Number of atoms: 4676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 4676 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 9, 'TRANS': 354} Chain breaks: 2 Unresolved non-hydrogen bonds: 484 Unresolved non-hydrogen angles: 632 Unresolved non-hydrogen dihedrals: 409 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 6, 'HIS:plan': 4, 'PHE:plan': 10, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 216 Time building chain proxies: 15.67, per 1000 atoms: 0.48 Number of scatterers: 32732 At special positions: 0 Unit cell: (135.3, 136.4, 140.8, 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 70 16.00 O 3213 8.00 N 3052 7.00 C 11200 6.00 H 15197 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: 8.27 Conformation dependent library (CDL) restraints added in 2.9 seconds 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4984 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 9 sheets defined 64.6% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.73 Creating SS restraints... Processing helix chain 'A' and resid 166 through 179 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'A' and resid 200 through 232 removed outlier: 4.732A pdb=" N MET A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU A 216 " --> pdb=" O PHE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 270 removed outlier: 4.748A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 312 removed outlier: 3.546A pdb=" N LYS A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 534 Processing helix chain 'A' and resid 537 through 571 removed outlier: 3.602A pdb=" N PHE A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 558 " --> pdb=" O ILE A 554 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 removed outlier: 3.631A pdb=" N THR A 617 " --> pdb=" O ALA A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 660 Processing helix chain 'A' and resid 695 through 717 Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 189 through 193 Processing helix chain 'B' and resid 200 through 232 removed outlier: 4.732A pdb=" N MET B 215 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU B 216 " --> pdb=" O PHE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 270 removed outlier: 4.749A pdb=" N LYS B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 312 removed outlier: 3.546A pdb=" N LYS B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 534 Processing helix chain 'B' and resid 537 through 571 removed outlier: 3.602A pdb=" N PHE B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 554 " --> pdb=" O ALA B 550 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 558 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 617 removed outlier: 3.631A pdb=" N THR B 617 " --> pdb=" O ALA B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 660 Processing helix chain 'B' and resid 695 through 717 Processing helix chain 'C' and resid 167 through 179 Processing helix chain 'C' and resid 189 through 193 Processing helix chain 'C' and resid 200 through 232 removed outlier: 4.732A pdb=" N MET C 215 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU C 216 " --> pdb=" O PHE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 270 removed outlier: 4.749A pdb=" N LYS C 248 " --> pdb=" O HIS C 244 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 312 removed outlier: 3.546A pdb=" N LYS C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 534 Processing helix chain 'C' and resid 537 through 571 removed outlier: 3.602A pdb=" N PHE C 553 " --> pdb=" O VAL C 549 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE C 554 " --> pdb=" O ALA C 550 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR C 558 " --> pdb=" O ILE C 554 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 617 removed outlier: 3.632A pdb=" N THR C 617 " --> pdb=" O ALA C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 642 through 660 Processing helix chain 'C' and resid 695 through 717 Processing helix chain 'D' and resid 167 through 179 Processing helix chain 'D' and resid 189 through 193 Processing helix chain 'D' and resid 200 through 232 removed outlier: 4.732A pdb=" N MET D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU D 216 " --> pdb=" O PHE D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 270 removed outlier: 4.748A pdb=" N LYS D 248 " --> pdb=" O HIS D 244 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 312 removed outlier: 3.546A pdb=" N LYS D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 534 Processing helix chain 'D' and resid 537 through 571 removed outlier: 3.602A pdb=" N PHE D 553 " --> pdb=" O VAL D 549 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR D 558 " --> pdb=" O ILE D 554 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 617 removed outlier: 3.631A pdb=" N THR D 617 " --> pdb=" O ALA D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 642 through 660 Processing helix chain 'D' and resid 695 through 717 Processing helix chain 'E' and resid 167 through 179 Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'E' and resid 200 through 232 removed outlier: 4.732A pdb=" N MET E 215 " --> pdb=" O ILE E 211 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU E 216 " --> pdb=" O PHE E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 270 removed outlier: 4.749A pdb=" N LYS E 248 " --> pdb=" O HIS E 244 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 312 removed outlier: 3.546A pdb=" N LYS E 279 " --> pdb=" O PRO E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 534 Processing helix chain 'E' and resid 537 through 571 removed outlier: 3.602A pdb=" N PHE E 553 " --> pdb=" O VAL E 549 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE E 554 " --> pdb=" O ALA E 550 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR E 558 " --> pdb=" O ILE E 554 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN E 561 " --> pdb=" O SER E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 617 removed outlier: 3.631A pdb=" N THR E 617 " --> pdb=" O ALA E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 642 through 660 Processing helix chain 'E' and resid 695 through 717 Processing helix chain 'F' and resid 167 through 179 Processing helix chain 'F' and resid 189 through 193 Processing helix chain 'F' and resid 200 through 232 removed outlier: 4.732A pdb=" N MET F 215 " --> pdb=" O ILE F 211 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU F 216 " --> pdb=" O PHE F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 270 removed outlier: 4.749A pdb=" N LYS F 248 " --> pdb=" O HIS F 244 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER F 249 " --> pdb=" O GLY F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 312 removed outlier: 3.546A pdb=" N LYS F 279 " --> pdb=" O PRO F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 534 Processing helix chain 'F' and resid 537 through 571 removed outlier: 3.602A pdb=" N PHE F 553 " --> pdb=" O VAL F 549 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE F 554 " --> pdb=" O ALA F 550 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR F 558 " --> pdb=" O ILE F 554 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN F 561 " --> pdb=" O SER F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 617 removed outlier: 3.631A pdb=" N THR F 617 " --> pdb=" O ALA F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 660 Processing helix chain 'F' and resid 695 through 717 Processing helix chain 'G' and resid 167 through 179 Processing helix chain 'G' and resid 189 through 193 Processing helix chain 'G' and resid 200 through 232 removed outlier: 4.731A pdb=" N MET G 215 " --> pdb=" O ILE G 211 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU G 216 " --> pdb=" O PHE G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 270 removed outlier: 4.748A pdb=" N LYS G 248 " --> pdb=" O HIS G 244 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N SER G 249 " --> pdb=" O GLY G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 312 removed outlier: 3.546A pdb=" N LYS G 279 " --> pdb=" O PRO G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 534 Processing helix chain 'G' and resid 537 through 571 removed outlier: 3.602A pdb=" N PHE G 553 " --> pdb=" O VAL G 549 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE G 554 " --> pdb=" O ALA G 550 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR G 558 " --> pdb=" O ILE G 554 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN G 561 " --> pdb=" O SER G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 612 through 617 removed outlier: 3.631A pdb=" N THR G 617 " --> pdb=" O ALA G 613 " (cutoff:3.500A) Processing helix chain 'G' and resid 642 through 660 Processing helix chain 'G' and resid 695 through 717 Processing sheet with id=AA1, first strand: chain 'A' and resid 580 through 583 removed outlier: 3.591A pdb=" N GLU A 591 " --> pdb=" O VAL A 599 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A 599 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N MET A 593 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS A 607 " --> pdb=" O ASN G 622 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE G 620 " --> pdb=" O TYR A 609 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU G 591 " --> pdb=" O VAL G 599 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL G 599 " --> pdb=" O GLU G 591 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N MET G 593 " --> pdb=" O THR G 597 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR G 597 " --> pdb=" O MET G 593 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS G 607 " --> pdb=" O ASN F 622 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE F 620 " --> pdb=" O TYR G 609 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU F 591 " --> pdb=" O VAL F 599 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL F 599 " --> pdb=" O GLU F 591 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N MET F 593 " --> pdb=" O THR F 597 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR F 597 " --> pdb=" O MET F 593 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS F 607 " --> pdb=" O ASN E 622 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE E 620 " --> pdb=" O TYR F 609 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU E 591 " --> pdb=" O VAL E 599 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL E 599 " --> pdb=" O GLU E 591 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N MET E 593 " --> pdb=" O THR E 597 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR E 597 " --> pdb=" O MET E 593 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS E 607 " --> pdb=" O ASN D 622 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE D 620 " --> pdb=" O TYR E 609 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU D 591 " --> pdb=" O VAL D 599 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL D 599 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N MET D 593 " --> pdb=" O THR D 597 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR D 597 " --> pdb=" O MET D 593 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS D 607 " --> pdb=" O ASN C 622 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 620 " --> pdb=" O TYR D 609 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU C 591 " --> pdb=" O VAL C 599 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL C 599 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N MET C 593 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR C 597 " --> pdb=" O MET C 593 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS C 607 " --> pdb=" O ASN B 622 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 620 " --> pdb=" O TYR C 609 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 591 " --> pdb=" O VAL B 599 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL B 599 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N MET B 593 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LYS B 607 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 620 " --> pdb=" O TYR B 609 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 630 through 638 removed outlier: 6.403A pdb=" N LYS A 680 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 675 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS A 682 " --> pdb=" O LYS A 673 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP A 688 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 667 " --> pdb=" O ASP A 688 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 726 through 731 removed outlier: 6.566A pdb=" N ASP A 727 " --> pdb=" O GLN B 726 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE B 728 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN A 729 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU B 730 " --> pdb=" O ASN A 729 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR A 731 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP B 727 " --> pdb=" O GLN C 726 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE C 728 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN B 729 " --> pdb=" O ILE C 728 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU C 730 " --> pdb=" O ASN B 729 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N THR B 731 " --> pdb=" O LEU C 730 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP C 727 " --> pdb=" O GLN D 726 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE D 728 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN C 729 " --> pdb=" O ILE D 728 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU D 730 " --> pdb=" O ASN C 729 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR C 731 " --> pdb=" O LEU D 730 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP D 727 " --> pdb=" O GLN E 726 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE E 728 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN D 729 " --> pdb=" O ILE E 728 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU E 730 " --> pdb=" O ASN D 729 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR D 731 " --> pdb=" O LEU E 730 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASP E 727 " --> pdb=" O GLN F 726 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE F 728 " --> pdb=" O ASP E 727 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASN E 729 " --> pdb=" O ILE F 728 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU F 730 " --> pdb=" O ASN E 729 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR E 731 " --> pdb=" O LEU F 730 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP F 727 " --> pdb=" O GLN G 726 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ILE G 728 " --> pdb=" O ASP F 727 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASN F 729 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU G 730 " --> pdb=" O ASN F 729 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR F 731 " --> pdb=" O LEU G 730 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 630 through 638 removed outlier: 6.404A pdb=" N LYS B 680 " --> pdb=" O ILE B 675 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE B 675 " --> pdb=" O LYS B 680 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS B 682 " --> pdb=" O LYS B 673 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP B 688 " --> pdb=" O VAL B 667 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL B 667 " --> pdb=" O ASP B 688 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 630 through 638 removed outlier: 6.403A pdb=" N LYS C 680 " --> pdb=" O ILE C 675 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE C 675 " --> pdb=" O LYS C 680 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS C 682 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP C 688 " --> pdb=" O VAL C 667 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL C 667 " --> pdb=" O ASP C 688 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 630 through 638 removed outlier: 6.403A pdb=" N LYS D 680 " --> pdb=" O ILE D 675 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE D 675 " --> pdb=" O LYS D 680 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS D 682 " --> pdb=" O LYS D 673 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP D 688 " --> pdb=" O VAL D 667 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL D 667 " --> pdb=" O ASP D 688 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 630 through 638 removed outlier: 6.404A pdb=" N LYS E 680 " --> pdb=" O ILE E 675 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE E 675 " --> pdb=" O LYS E 680 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS E 682 " --> pdb=" O LYS E 673 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP E 688 " --> pdb=" O VAL E 667 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL E 667 " --> pdb=" O ASP E 688 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 630 through 638 removed outlier: 6.404A pdb=" N LYS F 680 " --> pdb=" O ILE F 675 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE F 675 " --> pdb=" O LYS F 680 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS F 682 " --> pdb=" O LYS F 673 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP F 688 " --> pdb=" O VAL F 667 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL F 667 " --> pdb=" O ASP F 688 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 630 through 638 removed outlier: 6.403A pdb=" N LYS G 680 " --> pdb=" O ILE G 675 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE G 675 " --> pdb=" O LYS G 680 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS G 682 " --> pdb=" O LYS G 673 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP G 688 " --> pdb=" O VAL G 667 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL G 667 " --> pdb=" O ASP G 688 " (cutoff:3.500A) 1490 hydrogen bonds defined for protein. 4446 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: 12.06 Time building geometry restraints manager: 10.05 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: 15176 1.03 - 1.23: 34 1.23 - 1.42: 7190 1.42 - 1.62: 10486 1.62 - 1.82: 119 Bond restraints: 33005 Sorted by residual: bond pdb=" CB MET F 629 " pdb=" CG MET F 629 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.40e+00 bond pdb=" CB MET E 629 " pdb=" CG MET E 629 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.37e+00 bond pdb=" CB MET A 629 " pdb=" CG MET A 629 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.37e+00 bond pdb=" CB MET C 629 " pdb=" CG MET C 629 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.36e+00 bond pdb=" CB MET G 629 " pdb=" CG MET G 629 " ideal model delta sigma weight residual 1.520 1.465 0.055 3.00e-02 1.11e+03 3.36e+00 ... (remaining 33000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.46: 59160 9.46 - 18.92: 20 18.92 - 28.38: 26 28.38 - 37.84: 18 37.84 - 47.30: 3 Bond angle restraints: 59227 Sorted by residual: angle pdb=" SD MET B 713 " pdb=" CG MET B 713 " pdb=" HG3 MET B 713 " ideal model delta sigma weight residual 108.00 60.70 47.30 3.00e+00 1.11e-01 2.49e+02 angle pdb=" CB MET B 713 " pdb=" CG MET B 713 " pdb=" HG3 MET B 713 " ideal model delta sigma weight residual 109.00 64.91 44.09 3.00e+00 1.11e-01 2.16e+02 angle pdb=" SD MET B 713 " pdb=" CE MET B 713 " pdb=" HE3 MET B 713 " ideal model delta sigma weight residual 109.00 148.50 -39.50 3.00e+00 1.11e-01 1.73e+02 angle pdb="HD22 LEU A 562 " pdb=" CD2 LEU A 562 " pdb="HD23 LEU A 562 " ideal model delta sigma weight residual 110.00 76.93 33.07 3.00e+00 1.11e-01 1.21e+02 angle pdb="HD21 LEU F 562 " pdb=" CD2 LEU F 562 " pdb="HD23 LEU F 562 " ideal model delta sigma weight residual 110.00 76.98 33.02 3.00e+00 1.11e-01 1.21e+02 ... (remaining 59222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.41: 14653 13.41 - 26.83: 934 26.83 - 40.24: 232 40.24 - 53.65: 197 53.65 - 67.07: 77 Dihedral angle restraints: 16093 sinusoidal: 7595 harmonic: 8498 Sorted by residual: dihedral pdb=" CA TYR C 610 " pdb=" C TYR C 610 " pdb=" N PRO C 611 " pdb=" CA PRO C 611 " ideal model delta harmonic sigma weight residual 180.00 161.06 18.94 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA TYR B 610 " pdb=" C TYR B 610 " pdb=" N PRO B 611 " pdb=" CA PRO B 611 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA TYR G 610 " pdb=" C TYR G 610 " pdb=" N PRO G 611 " pdb=" CA PRO G 611 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 16090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1820 0.025 - 0.049: 704 0.049 - 0.074: 313 0.074 - 0.099: 137 0.099 - 0.124: 106 Chirality restraints: 3080 Sorted by residual: chirality pdb=" CA ILE A 675 " pdb=" N ILE A 675 " pdb=" C ILE A 675 " pdb=" CB ILE A 675 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA VAL A 670 " pdb=" N VAL A 670 " pdb=" C VAL A 670 " pdb=" CB VAL A 670 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE E 675 " pdb=" N ILE E 675 " pdb=" C ILE E 675 " pdb=" CB ILE E 675 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 3077 not shown) Planarity restraints: 5593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 274 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.30e+00 pdb=" N PRO A 275 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 275 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 275 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 274 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.30e+00 pdb=" N PRO F 275 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO F 275 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 275 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 274 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO D 275 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 275 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 275 " -0.032 5.00e-02 4.00e+02 ... (remaining 5590 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.02: 329 2.02 - 2.67: 43789 2.67 - 3.31: 91381 3.31 - 3.96: 109587 3.96 - 4.60: 170390 Nonbonded interactions: 415476 Sorted by model distance: nonbonded pdb=" HB2 MET B 713 " pdb=" HG3 MET B 713 " model vdw 1.377 1.952 nonbonded pdb=" HG LEU G 562 " pdb="HD22 LEU G 562 " model vdw 1.671 1.952 nonbonded pdb=" HG LEU B 562 " pdb="HD22 LEU B 562 " model vdw 1.671 1.952 nonbonded pdb=" HG LEU D 562 " pdb="HD22 LEU D 562 " model vdw 1.671 1.952 nonbonded pdb=" HG LEU C 562 " pdb="HD22 LEU C 562 " model vdw 1.672 1.952 ... (remaining 415471 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.630 Extract box with map and model: 1.250 Check model and map are aligned: 0.220 Set scattering table: 0.330 Process input model: 66.290 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.140 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.003 0.055 17808 Z= 0.128 Angle : 0.487 7.662 24381 Z= 0.269 Chirality : 0.039 0.124 3080 Planarity : 0.004 0.058 3129 Dihedral : 11.612 63.935 5663 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.17), residues: 2506 helix: 4.19 (0.12), residues: 1512 sheet: 0.02 (0.30), residues: 322 loop : 0.04 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 529 HIS 0.004 0.001 HIS D 689 PHE 0.032 0.002 PHE A 544 TYR 0.005 0.001 TYR F 575 ARG 0.001 0.000 ARG B 712 Details of bonding type rmsd hydrogen bonds : bond 0.12533 ( 1490) hydrogen bonds : angle 5.31090 ( 4446) covalent geometry : bond 0.00292 (17808) covalent geometry : angle 0.48735 (24381) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 555 ILE cc_start: 0.9128 (mp) cc_final: 0.8820 (mp) REVERT: A 559 CYS cc_start: 0.8329 (m) cc_final: 0.7870 (m) REVERT: B 720 ASP cc_start: 0.7283 (p0) cc_final: 0.7069 (p0) REVERT: C 629 MET cc_start: 0.7522 (mtt) cc_final: 0.6905 (mtt) REVERT: F 629 MET cc_start: 0.7660 (mtt) cc_final: 0.7337 (mtt) REVERT: G 297 PHE cc_start: 0.9259 (m-80) cc_final: 0.9050 (m-80) REVERT: G 555 ILE cc_start: 0.9116 (mp) cc_final: 0.8872 (mp) REVERT: G 559 CYS cc_start: 0.8526 (m) cc_final: 0.8204 (m) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.4323 time to fit residues: 208.6949 Evaluate side-chains 240 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 197 optimal weight: 20.0000 chunk 76 optimal weight: 50.0000 chunk 120 optimal weight: 9.9990 chunk 147 optimal weight: 50.0000 chunk 228 optimal weight: 0.8980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.088303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.063511 restraints weight = 198451.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.065075 restraints weight = 73448.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.065936 restraints weight = 40170.942| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17808 Z= 0.179 Angle : 0.519 16.728 24381 Z= 0.289 Chirality : 0.040 0.147 3080 Planarity : 0.004 0.055 3129 Dihedral : 3.624 15.345 2632 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.60 % Allowed : 5.55 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.82 (0.17), residues: 2506 helix: 3.98 (0.12), residues: 1589 sheet: 0.05 (0.30), residues: 322 loop : -0.33 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP G 664 HIS 0.004 0.001 HIS B 668 PHE 0.038 0.001 PHE B 297 TYR 0.013 0.002 TYR G 610 ARG 0.001 0.000 ARG B 702 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 1490) hydrogen bonds : angle 4.17849 ( 4446) covalent geometry : bond 0.00364 (17808) covalent geometry : angle 0.51897 (24381) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 259 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8932 (pp) REVERT: A 555 ILE cc_start: 0.9215 (mp) cc_final: 0.8996 (mp) REVERT: A 559 CYS cc_start: 0.8825 (m) cc_final: 0.8361 (m) REVERT: B 542 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8920 (pp) REVERT: C 542 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8900 (pp) REVERT: D 542 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8920 (pp) REVERT: D 588 MET cc_start: 0.7977 (ptp) cc_final: 0.7686 (ptp) REVERT: D 629 MET cc_start: 0.8207 (mtt) cc_final: 0.7753 (mtt) REVERT: E 542 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9024 (pp) REVERT: E 629 MET cc_start: 0.7980 (mtt) cc_final: 0.7461 (mtt) REVERT: F 542 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9038 (pp) REVERT: F 629 MET cc_start: 0.8095 (mtt) cc_final: 0.7828 (mtt) REVERT: G 542 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8909 (pp) REVERT: G 555 ILE cc_start: 0.9192 (mp) cc_final: 0.8977 (mp) REVERT: G 559 CYS cc_start: 0.8890 (m) cc_final: 0.8542 (m) outliers start: 23 outliers final: 13 residues processed: 266 average time/residue: 0.4355 time to fit residues: 196.0259 Evaluate side-chains 260 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 240 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 562 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 542 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 610 TYR Chi-restraints excluded: chain G residue 296 PHE Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 562 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 114 optimal weight: 6.9990 chunk 151 optimal weight: 30.0000 chunk 165 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 116 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.088382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.062942 restraints weight = 203040.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064513 restraints weight = 73409.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.065346 restraints weight = 39694.986| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17808 Z= 0.153 Angle : 0.487 23.065 24381 Z= 0.265 Chirality : 0.039 0.153 3080 Planarity : 0.004 0.050 3129 Dihedral : 3.510 14.280 2632 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.53 % Allowed : 6.59 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.98 (0.18), residues: 2506 helix: 4.15 (0.12), residues: 1589 sheet: -0.26 (0.30), residues: 322 loop : -0.15 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 664 HIS 0.003 0.001 HIS D 689 PHE 0.030 0.001 PHE G 297 TYR 0.013 0.002 TYR G 610 ARG 0.001 0.000 ARG C 712 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 1490) hydrogen bonds : angle 3.81961 ( 4446) covalent geometry : bond 0.00324 (17808) covalent geometry : angle 0.48714 (24381) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Evaluate side-chains 275 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8935 (pp) REVERT: A 555 ILE cc_start: 0.9177 (mp) cc_final: 0.8933 (mp) REVERT: A 559 CYS cc_start: 0.8825 (m) cc_final: 0.8378 (m) REVERT: B 542 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8946 (pp) REVERT: B 588 MET cc_start: 0.8395 (ptp) cc_final: 0.8141 (ptp) REVERT: C 542 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8889 (pp) REVERT: C 629 MET cc_start: 0.8384 (mtt) cc_final: 0.8145 (mtt) REVERT: D 542 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8929 (pp) REVERT: D 727 ASP cc_start: 0.8801 (p0) cc_final: 0.8449 (p0) REVERT: E 542 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9014 (pp) REVERT: E 610 TYR cc_start: 0.9263 (OUTLIER) cc_final: 0.9026 (t80) REVERT: E 629 MET cc_start: 0.8223 (mtt) cc_final: 0.7791 (mtt) REVERT: F 542 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9059 (pp) REVERT: F 629 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8121 (mtt) REVERT: G 542 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8907 (pp) REVERT: G 555 ILE cc_start: 0.9184 (mp) cc_final: 0.8964 (mp) REVERT: G 559 CYS cc_start: 0.8906 (m) cc_final: 0.8594 (m) outliers start: 22 outliers final: 8 residues processed: 260 average time/residue: 0.4298 time to fit residues: 190.5923 Evaluate side-chains 257 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 542 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 562 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 40.0000 chunk 203 optimal weight: 3.9990 chunk 43 optimal weight: 30.0000 chunk 160 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 241 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 196 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.087376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062729 restraints weight = 197706.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.064304 restraints weight = 72252.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065144 restraints weight = 38933.938| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17808 Z= 0.200 Angle : 0.503 20.811 24381 Z= 0.274 Chirality : 0.039 0.151 3080 Planarity : 0.004 0.047 3129 Dihedral : 3.454 14.112 2632 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.53 % Allowed : 6.38 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.99 (0.17), residues: 2506 helix: 4.22 (0.12), residues: 1589 sheet: -0.45 (0.30), residues: 322 loop : -0.24 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 664 HIS 0.004 0.001 HIS A 668 PHE 0.038 0.001 PHE G 297 TYR 0.014 0.001 TYR G 610 ARG 0.001 0.000 ARG A 712 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 1490) hydrogen bonds : angle 3.80044 ( 4446) covalent geometry : bond 0.00429 (17808) covalent geometry : angle 0.50334 (24381) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8947 (pp) REVERT: A 555 ILE cc_start: 0.9195 (mp) cc_final: 0.8955 (mp) REVERT: A 559 CYS cc_start: 0.8779 (m) cc_final: 0.8356 (m) REVERT: B 542 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8985 (pp) REVERT: C 297 PHE cc_start: 0.9336 (m-80) cc_final: 0.9089 (m-80) REVERT: C 542 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8921 (pp) REVERT: C 555 ILE cc_start: 0.9320 (mp) cc_final: 0.9080 (mp) REVERT: C 559 CYS cc_start: 0.8901 (m) cc_final: 0.8597 (m) REVERT: D 542 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8952 (pp) REVERT: D 727 ASP cc_start: 0.8743 (p0) cc_final: 0.8440 (p0) REVERT: E 542 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9015 (pp) REVERT: E 629 MET cc_start: 0.8428 (mtt) cc_final: 0.8071 (mtt) REVERT: F 542 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9093 (pp) REVERT: F 629 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8308 (mtt) REVERT: G 542 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8913 (pp) REVERT: G 555 ILE cc_start: 0.9194 (mp) cc_final: 0.8930 (mp) REVERT: G 559 CYS cc_start: 0.8856 (m) cc_final: 0.8477 (m) outliers start: 22 outliers final: 11 residues processed: 258 average time/residue: 0.4451 time to fit residues: 195.7110 Evaluate side-chains 259 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain E residue 542 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 562 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 28 optimal weight: 2.9990 chunk 231 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 173 optimal weight: 0.2980 chunk 126 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.088069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.062618 restraints weight = 201169.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.064198 restraints weight = 72527.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.065038 restraints weight = 39070.024| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17808 Z= 0.105 Angle : 0.463 22.052 24381 Z= 0.250 Chirality : 0.039 0.139 3080 Planarity : 0.004 0.044 3129 Dihedral : 3.328 14.000 2632 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.32 % Allowed : 7.84 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.19 (0.17), residues: 2506 helix: 4.36 (0.12), residues: 1589 sheet: -0.40 (0.30), residues: 322 loop : -0.06 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 664 HIS 0.003 0.001 HIS B 689 PHE 0.028 0.001 PHE C 297 TYR 0.011 0.001 TYR D 623 ARG 0.001 0.000 ARG G 712 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 1490) hydrogen bonds : angle 3.57324 ( 4446) covalent geometry : bond 0.00223 (17808) covalent geometry : angle 0.46278 (24381) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Evaluate side-chains 265 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 2.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8956 (pp) REVERT: A 555 ILE cc_start: 0.9225 (mp) cc_final: 0.8986 (mp) REVERT: A 559 CYS cc_start: 0.8759 (m) cc_final: 0.8341 (m) REVERT: A 629 MET cc_start: 0.8491 (mtt) cc_final: 0.8054 (mtt) REVERT: B 542 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8983 (pp) REVERT: C 542 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8928 (pp) REVERT: C 555 ILE cc_start: 0.9315 (mp) cc_final: 0.9088 (mp) REVERT: C 559 CYS cc_start: 0.8888 (m) cc_final: 0.8605 (m) REVERT: C 593 MET cc_start: 0.8976 (mtp) cc_final: 0.8727 (mtt) REVERT: D 542 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8961 (pp) REVERT: D 727 ASP cc_start: 0.8725 (p0) cc_final: 0.8411 (p0) REVERT: E 542 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9038 (pp) REVERT: F 542 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9083 (pp) REVERT: F 629 MET cc_start: 0.8403 (mtt) cc_final: 0.8147 (mtt) REVERT: G 542 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8945 (pp) REVERT: G 555 ILE cc_start: 0.9254 (mp) cc_final: 0.8999 (mp) REVERT: G 559 CYS cc_start: 0.8798 (m) cc_final: 0.8414 (m) outliers start: 19 outliers final: 9 residues processed: 252 average time/residue: 0.4211 time to fit residues: 180.2999 Evaluate side-chains 252 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain E residue 542 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 562 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 116 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 0 optimal weight: 80.0000 chunk 54 optimal weight: 8.9990 chunk 146 optimal weight: 7.9990 chunk 167 optimal weight: 0.9980 chunk 113 optimal weight: 50.0000 chunk 213 optimal weight: 4.9990 chunk 153 optimal weight: 40.0000 chunk 221 optimal weight: 50.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 726 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.085669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.060627 restraints weight = 202555.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062134 restraints weight = 75519.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.062965 restraints weight = 41720.868| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 17808 Z= 0.304 Angle : 0.534 20.438 24381 Z= 0.294 Chirality : 0.040 0.138 3080 Planarity : 0.004 0.042 3129 Dihedral : 3.449 13.969 2632 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.60 % Allowed : 8.18 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.99 (0.17), residues: 2506 helix: 4.29 (0.12), residues: 1589 sheet: -0.60 (0.31), residues: 322 loop : -0.36 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 664 HIS 0.005 0.001 HIS A 668 PHE 0.045 0.002 PHE G 297 TYR 0.013 0.002 TYR C 575 ARG 0.002 0.000 ARG D 652 Details of bonding type rmsd hydrogen bonds : bond 0.03444 ( 1490) hydrogen bonds : angle 3.86067 ( 4446) covalent geometry : bond 0.00651 (17808) covalent geometry : angle 0.53367 (24381) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 245 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8978 (pp) REVERT: A 555 ILE cc_start: 0.9208 (mp) cc_final: 0.8973 (mp) REVERT: A 559 CYS cc_start: 0.8839 (m) cc_final: 0.8431 (m) REVERT: A 629 MET cc_start: 0.8664 (mtt) cc_final: 0.8249 (mtt) REVERT: B 542 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9013 (pp) REVERT: C 542 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8933 (pp) REVERT: C 555 ILE cc_start: 0.9312 (mp) cc_final: 0.9087 (mp) REVERT: C 559 CYS cc_start: 0.8879 (m) cc_final: 0.8589 (m) REVERT: D 542 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8963 (pp) REVERT: D 727 ASP cc_start: 0.8803 (p0) cc_final: 0.8570 (p0) REVERT: E 542 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9076 (pp) REVERT: F 542 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9101 (pp) REVERT: F 629 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8599 (mtt) REVERT: G 542 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8962 (pp) REVERT: G 555 ILE cc_start: 0.9253 (mp) cc_final: 0.8996 (mp) REVERT: G 559 CYS cc_start: 0.8879 (m) cc_final: 0.8507 (m) outliers start: 23 outliers final: 10 residues processed: 252 average time/residue: 0.4471 time to fit residues: 191.7248 Evaluate side-chains 252 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 2.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 566 ILE Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain E residue 542 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 542 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain G residue 296 PHE Chi-restraints excluded: chain G residue 542 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 137 optimal weight: 2.9990 chunk 112 optimal weight: 50.0000 chunk 23 optimal weight: 1.9990 chunk 229 optimal weight: 0.5980 chunk 0 optimal weight: 80.0000 chunk 36 optimal weight: 80.0000 chunk 116 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.087476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.061965 restraints weight = 199123.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.063528 restraints weight = 71282.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.064364 restraints weight = 38165.545| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17808 Z= 0.129 Angle : 0.471 21.433 24381 Z= 0.257 Chirality : 0.039 0.136 3080 Planarity : 0.003 0.041 3129 Dihedral : 3.359 13.793 2632 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.46 % Allowed : 8.95 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.09 (0.17), residues: 2506 helix: 4.31 (0.12), residues: 1603 sheet: -0.53 (0.30), residues: 322 loop : -0.25 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP F 664 HIS 0.002 0.001 HIS G 648 PHE 0.013 0.001 PHE A 297 TYR 0.012 0.001 TYR G 610 ARG 0.001 0.000 ARG C 703 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 1490) hydrogen bonds : angle 3.64031 ( 4446) covalent geometry : bond 0.00276 (17808) covalent geometry : angle 0.47092 (24381) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Evaluate side-chains 257 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8972 (pp) REVERT: A 555 ILE cc_start: 0.9246 (mp) cc_final: 0.8975 (mp) REVERT: A 559 CYS cc_start: 0.8775 (m) cc_final: 0.8390 (m) REVERT: A 629 MET cc_start: 0.8588 (mtt) cc_final: 0.8192 (mtt) REVERT: B 542 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9006 (pp) REVERT: C 542 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8976 (pp) REVERT: C 559 CYS cc_start: 0.8864 (m) cc_final: 0.8546 (m) REVERT: D 542 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8958 (pp) REVERT: D 727 ASP cc_start: 0.8739 (p0) cc_final: 0.8499 (p0) REVERT: E 542 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9085 (pp) REVERT: F 629 MET cc_start: 0.8693 (mtt) cc_final: 0.8380 (mtt) REVERT: G 542 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8955 (pp) REVERT: G 555 ILE cc_start: 0.9245 (mp) cc_final: 0.8966 (mp) REVERT: G 559 CYS cc_start: 0.8810 (m) cc_final: 0.8456 (m) outliers start: 21 outliers final: 13 residues processed: 243 average time/residue: 0.4135 time to fit residues: 170.6325 Evaluate side-chains 251 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain E residue 542 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain G residue 296 PHE Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 39 optimal weight: 50.0000 chunk 228 optimal weight: 10.0000 chunk 212 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 113 optimal weight: 50.0000 chunk 215 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.086317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.061637 restraints weight = 199483.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.063159 restraints weight = 73225.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.063986 restraints weight = 39560.104| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 17808 Z= 0.227 Angle : 0.499 20.940 24381 Z= 0.274 Chirality : 0.039 0.134 3080 Planarity : 0.004 0.040 3129 Dihedral : 3.361 13.982 2632 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.46 % Allowed : 9.15 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.96 (0.17), residues: 2506 helix: 4.24 (0.12), residues: 1603 sheet: -0.68 (0.30), residues: 322 loop : -0.35 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP F 664 HIS 0.004 0.001 HIS A 668 PHE 0.050 0.001 PHE E 297 TYR 0.012 0.001 TYR C 575 ARG 0.001 0.000 ARG E 712 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 1490) hydrogen bonds : angle 3.72657 ( 4446) covalent geometry : bond 0.00490 (17808) covalent geometry : angle 0.49948 (24381) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 2.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8983 (pp) REVERT: A 555 ILE cc_start: 0.9254 (mp) cc_final: 0.8983 (mp) REVERT: A 559 CYS cc_start: 0.8715 (m) cc_final: 0.8332 (m) REVERT: A 629 MET cc_start: 0.8622 (mtt) cc_final: 0.8252 (mtt) REVERT: B 542 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9028 (pp) REVERT: C 542 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8983 (pp) REVERT: C 559 CYS cc_start: 0.8880 (m) cc_final: 0.8564 (m) REVERT: D 542 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8955 (pp) REVERT: D 727 ASP cc_start: 0.8791 (p0) cc_final: 0.8557 (p0) REVERT: E 542 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9080 (pp) REVERT: F 629 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8432 (mtt) REVERT: G 542 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8971 (pp) REVERT: G 555 ILE cc_start: 0.9295 (mp) cc_final: 0.9049 (mp) REVERT: G 559 CYS cc_start: 0.8827 (m) cc_final: 0.8484 (m) outliers start: 21 outliers final: 13 residues processed: 243 average time/residue: 0.4281 time to fit residues: 177.4737 Evaluate side-chains 254 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 234 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain E residue 542 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 629 MET Chi-restraints excluded: chain G residue 296 PHE Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 231 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 232 optimal weight: 0.4980 chunk 76 optimal weight: 30.0000 chunk 134 optimal weight: 4.9990 chunk 180 optimal weight: 80.0000 chunk 212 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.087579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.061999 restraints weight = 198212.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.063556 restraints weight = 71246.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064392 restraints weight = 38050.731| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17808 Z= 0.113 Angle : 0.467 21.426 24381 Z= 0.254 Chirality : 0.039 0.135 3080 Planarity : 0.003 0.040 3129 Dihedral : 3.297 13.787 2632 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.53 % Allowed : 9.15 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.13 (0.17), residues: 2506 helix: 4.34 (0.12), residues: 1603 sheet: -0.59 (0.30), residues: 322 loop : -0.18 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP G 664 HIS 0.002 0.001 HIS B 689 PHE 0.013 0.001 PHE A 297 TYR 0.012 0.001 TYR G 610 ARG 0.001 0.000 ARG G 712 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 1490) hydrogen bonds : angle 3.55055 ( 4446) covalent geometry : bond 0.00242 (17808) covalent geometry : angle 0.46687 (24381) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9021 (pp) REVERT: A 555 ILE cc_start: 0.9265 (mp) cc_final: 0.8990 (mp) REVERT: A 559 CYS cc_start: 0.8785 (m) cc_final: 0.8413 (m) REVERT: A 629 MET cc_start: 0.8597 (mtt) cc_final: 0.8209 (mtt) REVERT: B 542 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9003 (pp) REVERT: C 542 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8983 (pp) REVERT: C 559 CYS cc_start: 0.8867 (m) cc_final: 0.8566 (m) REVERT: D 542 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8976 (pp) REVERT: D 727 ASP cc_start: 0.8785 (p0) cc_final: 0.8556 (p0) REVERT: E 542 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9089 (pp) REVERT: G 542 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8961 (pp) REVERT: G 555 ILE cc_start: 0.9245 (mp) cc_final: 0.8965 (mp) REVERT: G 559 CYS cc_start: 0.8827 (m) cc_final: 0.8476 (m) outliers start: 22 outliers final: 14 residues processed: 243 average time/residue: 0.4261 time to fit residues: 176.6245 Evaluate side-chains 253 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 233 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain E residue 542 LEU Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 132 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 115 optimal weight: 30.0000 chunk 183 optimal weight: 50.0000 chunk 248 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.086678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061906 restraints weight = 197871.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.063452 restraints weight = 72157.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.064306 restraints weight = 38790.821| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17808 Z= 0.168 Angle : 0.482 21.222 24381 Z= 0.263 Chirality : 0.039 0.140 3080 Planarity : 0.003 0.040 3129 Dihedral : 3.274 14.005 2632 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.46 % Allowed : 9.15 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.08 (0.17), residues: 2506 helix: 4.31 (0.12), residues: 1603 sheet: -0.62 (0.30), residues: 322 loop : -0.23 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 298 HIS 0.003 0.001 HIS A 668 PHE 0.012 0.001 PHE A 297 TYR 0.012 0.001 TYR G 610 ARG 0.001 0.000 ARG B 652 Details of bonding type rmsd hydrogen bonds : bond 0.03118 ( 1490) hydrogen bonds : angle 3.58844 ( 4446) covalent geometry : bond 0.00365 (17808) covalent geometry : angle 0.48210 (24381) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Residue THR 166 is missing expected H atoms. Skipping. Residue LEU 167 is missing expected H atoms. Skipping. Residue LEU 169 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue SER 172 is missing expected H atoms. Skipping. Residue VAL 176 is missing expected H atoms. Skipping. Residue VAL 177 is missing expected H atoms. Skipping. Residue ILE 178 is missing expected H atoms. Skipping. Residue LEU 179 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue VAL 190 is missing expected H atoms. Skipping. Residue LEU 191 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue THR 195 is missing expected H atoms. Skipping. Residue LEU 199 is missing expected H atoms. Skipping. Residue VAL 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue VAL 206 is missing expected H atoms. Skipping. Residue LEU 207 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue MET 209 is missing expected H atoms. Skipping. Residue VAL 210 is missing expected H atoms. Skipping. Residue ILE 211 is missing expected H atoms. Skipping. Residue SER 213 is missing expected H atoms. Skipping. Residue MET 215 is missing expected H atoms. Skipping. Residue LEU 216 is missing expected H atoms. Skipping. Residue VAL 217 is missing expected H atoms. Skipping. Residue THR 218 is missing expected H atoms. Skipping. Residue MET 222 is missing expected H atoms. Skipping. Residue LEU 224 is missing expected H atoms. Skipping. Residue ILE 225 is missing expected H atoms. Skipping. Residue VAL 226 is missing expected H atoms. Skipping. Residue LEU 228 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue THR 231 is missing expected H atoms. Skipping. Residue LEU 234 is missing expected H atoms. Skipping. Residue LEU 235 is missing expected H atoms. Skipping. Residue LYS 238 is missing expected H atoms. Skipping. Residue VAL 239 is missing expected H atoms. Skipping. Residue LEU 240 is missing expected H atoms. Skipping. Residue TYR 241 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LEU 246 is missing expected H atoms. Skipping. Residue LYS 247 is missing expected H atoms. Skipping. Residue SER 249 is missing expected H atoms. Skipping. Residue VAL 250 is missing expected H atoms. Skipping. Residue VAL 252 is missing expected H atoms. Skipping. Residue ILE 254 is missing expected H atoms. Skipping. Residue LEU 256 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 259 is missing expected H atoms. Skipping. Residue LEU 260 is missing expected H atoms. Skipping. Residue VAL 261 is missing expected H atoms. Skipping. Residue ILE 264 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 271 is missing expected H atoms. Skipping. Residue LYS 272 is missing expected H atoms. Skipping. Residue SER 274 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue VAL 280 is missing expected H atoms. Skipping. Residue LEU 281 is missing expected H atoms. Skipping. Residue LYS 282 is missing expected H atoms. Skipping. Residue ILE 284 is missing expected H atoms. Skipping. Residue THR 285 is missing expected H atoms. Skipping. Residue THR 287 is missing expected H atoms. Skipping. Residue LEU 288 is missing expected H atoms. Skipping. Residue ILE 289 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 293 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue LEU 303 is missing expected H atoms. Skipping. Residue LEU 305 is missing expected H atoms. Skipping. Residue LYS 511 is missing expected H atoms. Skipping. Residue LYS 515 is missing expected H atoms. Skipping. Residue MET 522 is missing expected H atoms. Skipping. Residue LEU 530 is missing expected H atoms. Skipping. Residue LEU 531 is missing expected H atoms. Skipping. Residue LEU 532 is missing expected H atoms. Skipping. Residue LEU 533 is missing expected H atoms. Skipping. Residue VAL 535 is missing expected H atoms. Skipping. Residue THR 537 is missing expected H atoms. Skipping. Residue LYS 539 is missing expected H atoms. Skipping. Residue VAL 540 is missing expected H atoms. Skipping. Residue LEU 541 is missing expected H atoms. Skipping. Residue LEU 548 is missing expected H atoms. Skipping. Evaluate side-chains 258 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 2.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9054 (pp) REVERT: A 555 ILE cc_start: 0.9271 (mp) cc_final: 0.8994 (mp) REVERT: A 559 CYS cc_start: 0.8795 (m) cc_final: 0.8435 (m) REVERT: A 629 MET cc_start: 0.8609 (mtt) cc_final: 0.8238 (mtt) REVERT: B 542 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9012 (pp) REVERT: C 542 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8992 (pp) REVERT: C 559 CYS cc_start: 0.8883 (m) cc_final: 0.8589 (m) REVERT: D 542 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9047 (pp) REVERT: D 727 ASP cc_start: 0.8789 (p0) cc_final: 0.8538 (p0) REVERT: E 542 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9080 (pp) REVERT: G 542 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8970 (pp) REVERT: G 555 ILE cc_start: 0.9292 (mp) cc_final: 0.9042 (mp) REVERT: G 559 CYS cc_start: 0.8863 (m) cc_final: 0.8530 (m) outliers start: 21 outliers final: 14 residues processed: 243 average time/residue: 0.4408 time to fit residues: 182.8383 Evaluate side-chains 255 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 610 TYR Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain C residue 542 LEU Chi-restraints excluded: chain C residue 610 TYR Chi-restraints excluded: chain D residue 521 LEU Chi-restraints excluded: chain D residue 542 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 562 LEU Chi-restraints excluded: chain D residue 610 TYR Chi-restraints excluded: chain D residue 629 MET Chi-restraints excluded: chain E residue 542 LEU Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 610 TYR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain G residue 542 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 610 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 101 optimal weight: 0.7980 chunk 251 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 137 optimal weight: 0.3980 chunk 76 optimal weight: 30.0000 chunk 121 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 232 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 238 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.087062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.061697 restraints weight = 200054.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.063223 restraints weight = 72442.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.064063 restraints weight = 39104.841| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17808 Z= 0.136 Angle : 0.469 21.400 24381 Z= 0.255 Chirality : 0.039 0.140 3080 Planarity : 0.003 0.040 3129 Dihedral : 3.239 13.768 2632 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.39 % Allowed : 9.57 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.16 (0.17), residues: 2506 helix: 4.36 (0.11), residues: 1603 sheet: -0.57 (0.29), residues: 322 loop : -0.19 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 298 HIS 0.002 0.001 HIS A 668 PHE 0.018 0.001 PHE D 296 TYR 0.013 0.001 TYR G 610 ARG 0.001 0.000 ARG D 712 Details of bonding type rmsd hydrogen bonds : bond 0.03048 ( 1490) hydrogen bonds : angle 3.50098 ( 4446) covalent geometry : bond 0.00294 (17808) covalent geometry : angle 0.46917 (24381) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9094.38 seconds wall clock time: 156 minutes 16.04 seconds (9376.04 seconds total)