Starting phenix.real_space_refine on Tue Aug 26 03:05:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tdl_41166/08_2025/8tdl_41166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tdl_41166/08_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_41166/08_2025/8tdl_41166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tdl_41166/08_2025/8tdl_41166.map" model { file = "/net/cci-nas-00/data/ceres_data/8tdl_41166/08_2025/8tdl_41166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tdl_41166/08_2025/8tdl_41166.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'PHE:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 4, 'TRP:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} 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: {'GLU:plan': 6, 'PHE:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 4, 'TRP:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} 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: {'GLU:plan': 6, 'PHE:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 4, 'TRP:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} 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: {'GLU:plan': 6, 'PHE:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 4, 'TRP:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} 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: {'GLU:plan': 6, 'PHE:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 4, 'TRP:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} 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: {'GLU:plan': 6, 'PHE:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 4, 'TRP:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} 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: {'GLU:plan': 6, 'PHE:plan': 10, 'ASN:plan1': 5, 'HIS:plan': 4, 'TRP:plan': 6, 'ARG:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 216 Time building chain proxies: 5.93, per 1000 atoms: 0.18 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: 3.01 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.88 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: 7.63 Time building geometry restraints manager: 4.04 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 29.670 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.800 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.94 (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 ARG 0.001 0.000 ARG B 712 TYR 0.005 0.001 TYR F 575 PHE 0.032 0.002 PHE A 544 TRP 0.003 0.000 TRP A 529 HIS 0.004 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00292 (17808) covalent geometry : angle 0.48735 (24381) hydrogen bonds : bond 0.12533 ( 1490) hydrogen bonds : angle 5.31090 ( 4446) *********************** 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 : 0.910 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: 0.9026 (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: 0.1863 time to fit residues: 90.8893 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 : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 80.0000 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 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 = 0.3702 r_free = 0.3702 target = 0.088364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063573 restraints weight = 200880.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.065142 restraints weight = 73968.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.065993 restraints weight = 40283.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.066435 restraints weight = 29633.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.066631 restraints weight = 25786.086| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17808 Z= 0.184 Angle : 0.530 18.735 24381 Z= 0.293 Chirality : 0.040 0.155 3080 Planarity : 0.004 0.056 3129 Dihedral : 3.667 15.136 2632 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.60 % Allowed : 5.34 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.77 (0.17), residues: 2506 helix: 3.96 (0.12), residues: 1589 sheet: -0.02 (0.30), residues: 322 loop : -0.35 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 625 TYR 0.013 0.002 TYR G 610 PHE 0.042 0.002 PHE B 297 TRP 0.002 0.000 TRP G 664 HIS 0.005 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00381 (17808) covalent geometry : angle 0.53050 (24381) hydrogen bonds : bond 0.03849 ( 1490) hydrogen bonds : angle 4.12622 ( 4446) *********************** 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 283 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8959 (pp) REVERT: A 555 ILE cc_start: 0.9203 (mp) cc_final: 0.8973 (mp) REVERT: A 559 CYS cc_start: 0.8785 (m) cc_final: 0.8313 (m) REVERT: B 542 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8952 (pp) REVERT: C 542 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8896 (pp) REVERT: D 542 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8918 (pp) REVERT: D 588 MET cc_start: 0.8001 (ptp) cc_final: 0.7686 (ptp) REVERT: E 542 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9024 (pp) REVERT: E 629 MET cc_start: 0.8017 (mtt) cc_final: 0.7543 (mtt) REVERT: F 629 MET cc_start: 0.8129 (mtt) cc_final: 0.7860 (mtt) REVERT: G 542 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8912 (pp) REVERT: G 555 ILE cc_start: 0.9197 (mp) cc_final: 0.8986 (mp) REVERT: G 559 CYS cc_start: 0.8891 (m) cc_final: 0.8557 (m) outliers start: 23 outliers final: 14 residues processed: 267 average time/residue: 0.1916 time to fit residues: 88.4648 Evaluate side-chains 261 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 241 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 B residue 629 MET 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 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 139 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 151 optimal weight: 30.0000 chunk 229 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 199 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 227 optimal weight: 30.0000 chunk 181 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.088169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.062752 restraints weight = 200278.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064318 restraints weight = 72641.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.065153 restraints weight = 39180.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.065585 restraints weight = 28700.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065713 restraints weight = 24994.270| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17808 Z= 0.176 Angle : 0.484 19.629 24381 Z= 0.266 Chirality : 0.039 0.170 3080 Planarity : 0.004 0.049 3129 Dihedral : 3.512 14.402 2632 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.60 % Allowed : 6.17 % Favored : 92.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.95 (0.18), residues: 2506 helix: 4.16 (0.12), residues: 1589 sheet: -0.35 (0.30), residues: 322 loop : -0.21 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 712 TYR 0.016 0.002 TYR G 610 PHE 0.025 0.001 PHE C 297 TRP 0.003 0.000 TRP G 664 HIS 0.004 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00378 (17808) covalent geometry : angle 0.48432 (24381) hydrogen bonds : bond 0.03552 ( 1490) hydrogen bonds : angle 3.81932 ( 4446) *********************** 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 277 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 254 time to evaluate : 0.902 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: 0.9200 (OUTLIER) cc_final: 0.8908 (pp) REVERT: A 555 ILE cc_start: 0.9189 (mp) cc_final: 0.8954 (mp) REVERT: A 559 CYS cc_start: 0.8780 (m) cc_final: 0.8332 (m) REVERT: B 542 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8947 (pp) REVERT: C 542 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8901 (pp) REVERT: C 629 MET cc_start: 0.8449 (mtt) cc_final: 0.8229 (mtt) REVERT: D 542 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8929 (pp) REVERT: D 727 ASP cc_start: 0.8743 (p0) cc_final: 0.8414 (p0) REVERT: E 542 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9022 (pp) REVERT: E 629 MET cc_start: 0.8321 (mtt) cc_final: 0.7941 (mtt) REVERT: F 629 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8248 (mtt) REVERT: G 297 PHE cc_start: 0.9335 (m-80) cc_final: 0.9112 (m-80) REVERT: G 542 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8917 (pp) REVERT: G 555 ILE cc_start: 0.9193 (mp) cc_final: 0.8976 (mp) REVERT: G 559 CYS cc_start: 0.8857 (m) cc_final: 0.8541 (m) outliers start: 23 outliers final: 11 residues processed: 261 average time/residue: 0.1884 time to fit residues: 84.9065 Evaluate side-chains 256 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 238 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 18 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 152 optimal weight: 20.0000 chunk 72 optimal weight: 80.0000 chunk 51 optimal weight: 2.9990 chunk 230 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 = 0.3678 r_free = 0.3678 target = 0.087737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.062000 restraints weight = 202278.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.063558 restraints weight = 73045.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.064397 restraints weight = 39630.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.064816 restraints weight = 29265.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.064999 restraints weight = 25774.341| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17808 Z= 0.146 Angle : 0.474 18.639 24381 Z= 0.259 Chirality : 0.039 0.156 3080 Planarity : 0.004 0.046 3129 Dihedral : 3.403 14.060 2632 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.46 % Allowed : 6.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.05 (0.17), residues: 2506 helix: 4.27 (0.12), residues: 1589 sheet: -0.48 (0.30), residues: 322 loop : -0.15 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 712 TYR 0.013 0.001 TYR G 610 PHE 0.031 0.001 PHE C 297 TRP 0.003 0.000 TRP G 664 HIS 0.003 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00313 (17808) covalent geometry : angle 0.47361 (24381) hydrogen bonds : bond 0.03260 ( 1490) hydrogen bonds : angle 3.67403 ( 4446) *********************** 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 270 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.923 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: 0.9205 (OUTLIER) cc_final: 0.8967 (pp) REVERT: A 555 ILE cc_start: 0.9244 (mp) cc_final: 0.8998 (mp) REVERT: A 559 CYS cc_start: 0.8766 (m) cc_final: 0.8340 (m) REVERT: B 542 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8985 (pp) REVERT: C 297 PHE cc_start: 0.9345 (m-80) cc_final: 0.9113 (m-80) REVERT: C 542 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8912 (pp) REVERT: C 555 ILE cc_start: 0.9308 (mp) cc_final: 0.9067 (mp) REVERT: C 559 CYS cc_start: 0.8883 (m) cc_final: 0.8577 (m) REVERT: D 542 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8965 (pp) REVERT: D 727 ASP cc_start: 0.8668 (p0) cc_final: 0.8364 (p0) REVERT: E 542 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9013 (pp) REVERT: E 629 MET cc_start: 0.8404 (mtt) cc_final: 0.8035 (mtt) REVERT: F 629 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8208 (mtt) REVERT: G 297 PHE cc_start: 0.9348 (m-80) cc_final: 0.9103 (m-80) REVERT: G 542 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8917 (pp) REVERT: G 555 ILE cc_start: 0.9209 (mp) cc_final: 0.8937 (mp) REVERT: G 559 CYS cc_start: 0.8837 (m) cc_final: 0.8450 (m) outliers start: 21 outliers final: 10 residues processed: 256 average time/residue: 0.1976 time to fit residues: 87.1444 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 : 0.920 ------------------------------------------------------------------------------- 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 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 82 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 chunk 195 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 134 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 207 optimal weight: 0.9980 chunk 226 optimal weight: 6.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- 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 = 0.087436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062963 restraints weight = 198260.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.064518 restraints weight = 72540.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.065358 restraints weight = 38946.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.065792 restraints weight = 28277.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.065927 restraints weight = 24535.599| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 17808 Z= 0.174 Angle : 0.467 18.882 24381 Z= 0.257 Chirality : 0.039 0.132 3080 Planarity : 0.004 0.043 3129 Dihedral : 3.344 13.847 2632 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.39 % Allowed : 7.70 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.11 (0.17), residues: 2506 helix: 4.32 (0.12), residues: 1603 sheet: -0.44 (0.30), residues: 322 loop : -0.29 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 712 TYR 0.011 0.001 TYR G 610 PHE 0.025 0.001 PHE C 297 TRP 0.003 0.000 TRP F 664 HIS 0.003 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00374 (17808) covalent geometry : angle 0.46724 (24381) hydrogen bonds : bond 0.03206 ( 1490) hydrogen bonds : angle 3.61293 ( 4446) *********************** 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 263 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 542 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8967 (pp) REVERT: A 555 ILE cc_start: 0.9239 (mp) cc_final: 0.8993 (mp) REVERT: A 559 CYS cc_start: 0.8777 (m) cc_final: 0.8374 (m) REVERT: A 629 MET cc_start: 0.8572 (mtt) cc_final: 0.8149 (mtt) REVERT: B 542 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8993 (pp) REVERT: B 588 MET cc_start: 0.8434 (ptp) cc_final: 0.8026 (ptp) REVERT: C 542 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8935 (pp) REVERT: C 555 ILE cc_start: 0.9295 (mp) cc_final: 0.9033 (mp) REVERT: C 559 CYS cc_start: 0.8882 (m) cc_final: 0.8605 (m) REVERT: D 542 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8949 (pp) REVERT: D 727 ASP cc_start: 0.8700 (p0) cc_final: 0.8404 (p0) REVERT: E 542 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9052 (pp) REVERT: F 629 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8428 (mtt) REVERT: G 297 PHE cc_start: 0.9327 (m-80) cc_final: 0.9031 (m-80) REVERT: G 542 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8958 (pp) REVERT: G 555 ILE cc_start: 0.9173 (mp) cc_final: 0.8912 (mp) REVERT: G 559 CYS cc_start: 0.8840 (m) cc_final: 0.8472 (m) outliers start: 20 outliers final: 11 residues processed: 249 average time/residue: 0.1930 time to fit residues: 83.2414 Evaluate side-chains 254 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 629 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 188 optimal weight: 20.0000 chunk 226 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 243 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 chunk 169 optimal weight: 0.7980 chunk 56 optimal weight: 0.0270 chunk 112 optimal weight: 50.0000 chunk 198 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- 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 = 0.3676 r_free = 0.3676 target = 0.087428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.062888 restraints weight = 197094.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.064473 restraints weight = 71539.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.065321 restraints weight = 38279.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.065768 restraints weight = 27688.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.065919 restraints weight = 23960.942| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17808 Z= 0.126 Angle : 0.453 19.555 24381 Z= 0.248 Chirality : 0.039 0.132 3080 Planarity : 0.003 0.041 3129 Dihedral : 3.261 13.660 2632 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.39 % Allowed : 7.98 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.22 (0.17), residues: 2506 helix: 4.40 (0.12), residues: 1603 sheet: -0.49 (0.30), residues: 322 loop : -0.16 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 712 TYR 0.011 0.001 TYR D 623 PHE 0.042 0.001 PHE B 297 TRP 0.003 0.000 TRP G 664 HIS 0.002 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00269 (17808) covalent geometry : angle 0.45334 (24381) hydrogen bonds : bond 0.03045 ( 1490) hydrogen bonds : angle 3.48735 ( 4446) *********************** 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 264 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 244 time to evaluate : 0.902 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: 0.9192 (OUTLIER) cc_final: 0.8967 (pp) REVERT: A 555 ILE cc_start: 0.9215 (mp) cc_final: 0.8956 (mp) REVERT: A 559 CYS cc_start: 0.8765 (m) cc_final: 0.8383 (m) REVERT: A 629 MET cc_start: 0.8540 (mtt) cc_final: 0.8136 (mtt) REVERT: B 542 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9004 (pp) REVERT: B 588 MET cc_start: 0.8405 (ptp) cc_final: 0.8050 (ptp) REVERT: C 542 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8959 (pp) REVERT: C 555 ILE cc_start: 0.9313 (mp) cc_final: 0.9056 (mp) REVERT: C 559 CYS cc_start: 0.8886 (m) cc_final: 0.8617 (m) REVERT: D 542 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8967 (pp) REVERT: D 727 ASP cc_start: 0.8674 (p0) cc_final: 0.8377 (p0) REVERT: E 542 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9081 (pp) REVERT: G 297 PHE cc_start: 0.9306 (m-80) cc_final: 0.9002 (m-80) REVERT: G 542 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8953 (pp) REVERT: G 555 ILE cc_start: 0.9205 (mp) cc_final: 0.8925 (mp) REVERT: G 559 CYS cc_start: 0.8833 (m) cc_final: 0.8470 (m) outliers start: 20 outliers final: 12 residues processed: 250 average time/residue: 0.1984 time to fit residues: 85.6549 Evaluate side-chains 254 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 236 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 523 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 164 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 245 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 50.0000 chunk 140 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.088163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.062732 restraints weight = 199363.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064268 restraints weight = 71565.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.065080 restraints weight = 38382.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.065496 restraints weight = 28202.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065689 restraints weight = 24731.220| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17808 Z= 0.117 Angle : 0.445 20.158 24381 Z= 0.242 Chirality : 0.039 0.132 3080 Planarity : 0.003 0.040 3129 Dihedral : 3.180 13.299 2632 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.25 % Allowed : 8.39 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.29 (0.17), residues: 2506 helix: 4.43 (0.12), residues: 1603 sheet: -0.45 (0.30), residues: 322 loop : -0.08 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 652 TYR 0.012 0.001 TYR F 623 PHE 0.034 0.001 PHE B 297 TRP 0.003 0.000 TRP F 664 HIS 0.002 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00252 (17808) covalent geometry : angle 0.44479 (24381) hydrogen bonds : bond 0.02945 ( 1490) hydrogen bonds : angle 3.42929 ( 4446) *********************** 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 260 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.930 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: 0.9207 (OUTLIER) cc_final: 0.8993 (pp) REVERT: A 555 ILE cc_start: 0.9229 (mp) cc_final: 0.8981 (mp) REVERT: A 559 CYS cc_start: 0.8841 (m) cc_final: 0.8465 (m) REVERT: A 629 MET cc_start: 0.8551 (mtt) cc_final: 0.8149 (mtt) REVERT: B 542 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9005 (pp) REVERT: C 542 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8965 (pp) REVERT: C 555 ILE cc_start: 0.9322 (mp) cc_final: 0.9109 (mp) REVERT: C 559 CYS cc_start: 0.8889 (m) cc_final: 0.8560 (m) REVERT: D 542 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9037 (pp) REVERT: D 727 ASP cc_start: 0.8680 (p0) cc_final: 0.8382 (p0) REVERT: E 542 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9085 (pp) REVERT: G 297 PHE cc_start: 0.9323 (m-80) cc_final: 0.8974 (m-80) REVERT: G 542 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8975 (pp) REVERT: G 555 ILE cc_start: 0.9195 (mp) cc_final: 0.8896 (mp) REVERT: G 559 CYS cc_start: 0.8834 (m) cc_final: 0.8466 (m) outliers start: 18 outliers final: 8 residues processed: 248 average time/residue: 0.1976 time to fit residues: 84.4864 Evaluate side-chains 248 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 610 TYR 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 542 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 163 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 180 optimal weight: 80.0000 chunk 191 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.086953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.061383 restraints weight = 200252.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.062939 restraints weight = 71724.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.063772 restraints weight = 38384.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.064200 restraints weight = 28048.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064332 restraints weight = 24495.816| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 17808 Z= 0.210 Angle : 0.478 20.031 24381 Z= 0.263 Chirality : 0.039 0.133 3080 Planarity : 0.003 0.039 3129 Dihedral : 3.218 13.397 2632 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.32 % Allowed : 9.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.21 (0.17), residues: 2506 helix: 4.40 (0.12), residues: 1603 sheet: -0.54 (0.30), residues: 322 loop : -0.16 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 712 TYR 0.011 0.001 TYR A 575 PHE 0.036 0.001 PHE C 297 TRP 0.003 0.000 TRP F 664 HIS 0.004 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00452 (17808) covalent geometry : angle 0.47751 (24381) hydrogen bonds : bond 0.03071 ( 1490) hydrogen bonds : angle 3.55314 ( 4446) *********************** 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 254 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.902 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: 0.9218 (OUTLIER) cc_final: 0.8998 (pp) REVERT: A 555 ILE cc_start: 0.9248 (mp) cc_final: 0.8998 (mp) REVERT: A 559 CYS cc_start: 0.8727 (m) cc_final: 0.8357 (m) REVERT: A 629 MET cc_start: 0.8605 (mtt) cc_final: 0.8233 (mtt) REVERT: B 542 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9019 (pp) REVERT: C 542 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8980 (pp) REVERT: C 559 CYS cc_start: 0.8853 (m) cc_final: 0.8538 (m) REVERT: D 542 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9042 (pp) REVERT: D 727 ASP cc_start: 0.8719 (p0) cc_final: 0.8497 (p0) REVERT: E 542 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9093 (pp) REVERT: G 542 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8968 (pp) REVERT: G 555 ILE cc_start: 0.9214 (mp) cc_final: 0.8910 (mp) REVERT: G 559 CYS cc_start: 0.8842 (m) cc_final: 0.8470 (m) outliers start: 19 outliers final: 11 residues processed: 241 average time/residue: 0.1935 time to fit residues: 80.7507 Evaluate side-chains 249 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 551 LEU Chi-restraints excluded: chain D residue 610 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 223 optimal weight: 30.0000 chunk 83 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 40 optimal weight: 50.0000 chunk 110 optimal weight: 40.0000 chunk 145 optimal weight: 7.9990 chunk 246 optimal weight: 0.6980 chunk 196 optimal weight: 10.0000 chunk 231 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.086524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.061825 restraints weight = 199093.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.063370 restraints weight = 72902.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.064197 restraints weight = 39247.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064619 restraints weight = 28694.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.064801 restraints weight = 25057.760| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 17808 Z= 0.176 Angle : 0.466 20.394 24381 Z= 0.255 Chirality : 0.039 0.132 3080 Planarity : 0.003 0.040 3129 Dihedral : 3.220 13.424 2632 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.53 % Allowed : 9.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.23 (0.17), residues: 2506 helix: 4.42 (0.11), residues: 1603 sheet: -0.56 (0.30), residues: 322 loop : -0.18 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 712 TYR 0.011 0.001 TYR G 610 PHE 0.030 0.001 PHE B 297 TRP 0.003 0.000 TRP G 664 HIS 0.003 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00382 (17808) covalent geometry : angle 0.46571 (24381) hydrogen bonds : bond 0.03053 ( 1490) hydrogen bonds : angle 3.48797 ( 4446) *********************** 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 : 0.974 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: 0.9220 (OUTLIER) cc_final: 0.9007 (pp) REVERT: A 555 ILE cc_start: 0.9258 (mp) cc_final: 0.9014 (mp) REVERT: A 559 CYS cc_start: 0.8717 (m) cc_final: 0.8336 (m) REVERT: A 629 MET cc_start: 0.8593 (mtt) cc_final: 0.8225 (mtt) REVERT: B 542 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9015 (pp) REVERT: C 542 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8989 (pp) REVERT: C 555 ILE cc_start: 0.9328 (mp) cc_final: 0.9124 (mp) REVERT: C 559 CYS cc_start: 0.8841 (m) cc_final: 0.8502 (m) REVERT: D 542 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9046 (pp) REVERT: D 727 ASP cc_start: 0.8723 (p0) cc_final: 0.8511 (p0) REVERT: E 542 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9098 (pp) REVERT: G 542 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8972 (pp) REVERT: G 555 ILE cc_start: 0.9220 (mp) cc_final: 0.8929 (mp) REVERT: G 559 CYS cc_start: 0.8846 (m) cc_final: 0.8407 (m) outliers start: 22 outliers final: 13 residues processed: 244 average time/residue: 0.1959 time to fit residues: 82.4933 Evaluate side-chains 254 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 551 LEU Chi-restraints excluded: chain D residue 566 ILE Chi-restraints excluded: chain D residue 610 TYR 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 F residue 678 MET 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 248 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 111 optimal weight: 50.0000 chunk 221 optimal weight: 50.0000 chunk 80 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 chunk 147 optimal weight: 50.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.086487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.060645 restraints weight = 203354.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.062157 restraints weight = 73648.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.062966 restraints weight = 40065.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.063367 restraints weight = 29815.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.063491 restraints weight = 26325.926| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17808 Z= 0.197 Angle : 0.478 20.521 24381 Z= 0.262 Chirality : 0.039 0.135 3080 Planarity : 0.003 0.039 3129 Dihedral : 3.232 13.880 2632 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.32 % Allowed : 9.50 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.22 (0.17), residues: 2506 helix: 4.51 (0.11), residues: 1561 sheet: -0.61 (0.30), residues: 322 loop : -0.06 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 652 TYR 0.011 0.001 TYR G 610 PHE 0.026 0.001 PHE B 297 TRP 0.004 0.000 TRP E 298 HIS 0.003 0.001 HIS A 668 Details of bonding type rmsd covalent geometry : bond 0.00428 (17808) covalent geometry : angle 0.47837 (24381) hydrogen bonds : bond 0.03104 ( 1490) hydrogen bonds : angle 3.52866 ( 4446) ********************** 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 259 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.904 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: 0.9261 (OUTLIER) cc_final: 0.9033 (pp) REVERT: A 555 ILE cc_start: 0.9233 (mp) cc_final: 0.8980 (mp) REVERT: A 559 CYS cc_start: 0.8767 (m) cc_final: 0.8421 (m) REVERT: A 629 MET cc_start: 0.8588 (mtt) cc_final: 0.8250 (mtt) REVERT: B 542 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9024 (pp) REVERT: C 542 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8998 (pp) REVERT: C 555 ILE cc_start: 0.9314 (mp) cc_final: 0.9111 (mp) REVERT: C 559 CYS cc_start: 0.8847 (m) cc_final: 0.8521 (m) REVERT: D 542 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9056 (pp) REVERT: D 727 ASP cc_start: 0.8746 (p0) cc_final: 0.8494 (p0) REVERT: E 542 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9086 (pp) REVERT: G 542 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8967 (pp) REVERT: G 555 ILE cc_start: 0.9200 (mp) cc_final: 0.8900 (mp) REVERT: G 559 CYS cc_start: 0.8871 (m) cc_final: 0.8440 (m) outliers start: 19 outliers final: 13 residues processed: 246 average time/residue: 0.1845 time to fit residues: 78.5123 Evaluate side-chains 256 residues out of total 2345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 237 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 551 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 551 LEU Chi-restraints excluded: chain D residue 610 TYR 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 F residue 678 MET 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 138 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 173 optimal weight: 0.3980 chunk 4 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 251 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.087442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.061855 restraints weight = 202213.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.063403 restraints weight = 72593.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.064241 restraints weight = 39038.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.064648 restraints weight = 28714.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.064774 restraints weight = 25259.230| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 17808 Z= 0.106 Angle : 0.455 20.917 24381 Z= 0.247 Chirality : 0.039 0.134 3080 Planarity : 0.003 0.040 3129 Dihedral : 3.163 13.636 2632 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.29 (0.17), residues: 2506 helix: 4.46 (0.11), residues: 1603 sheet: -0.52 (0.29), residues: 322 loop : -0.14 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 712 TYR 0.012 0.001 TYR G 610 PHE 0.029 0.001 PHE B 297 TRP 0.003 0.000 TRP B 529 HIS 0.002 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00229 (17808) covalent geometry : angle 0.45505 (24381) hydrogen bonds : bond 0.02931 ( 1490) hydrogen bonds : angle 3.35165 ( 4446) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4941.77 seconds wall clock time: 85 minutes 9.48 seconds (5109.48 seconds total)