Starting phenix.real_space_refine on Tue Aug 26 21:17:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b0t_44055/08_2025/9b0t_44055_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b0t_44055/08_2025/9b0t_44055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b0t_44055/08_2025/9b0t_44055_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b0t_44055/08_2025/9b0t_44055_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b0t_44055/08_2025/9b0t_44055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b0t_44055/08_2025/9b0t_44055.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 112 5.16 5 C 13552 2.51 5 N 3944 2.21 5 O 4072 1.98 5 H 19786 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 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: 41490 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5147 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 Conformer: "B" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 bond proxies already assigned to first conformer: 5155 Chain: "B" Number of atoms: 5147 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 Conformer: "B" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 bond proxies already assigned to first conformer: 5155 Chain: "C" Number of atoms: 5147 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 Conformer: "B" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 bond proxies already assigned to first conformer: 5155 Chain: "D" Number of atoms: 5147 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 Conformer: "B" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 bond proxies already assigned to first conformer: 5155 Chain: "E" Number of atoms: 5147 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 Conformer: "B" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 bond proxies already assigned to first conformer: 5155 Chain: "F" Number of atoms: 5147 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 Conformer: "B" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 bond proxies already assigned to first conformer: 5155 Chain: "G" Number of atoms: 5147 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 Conformer: "B" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 bond proxies already assigned to first conformer: 5155 Chain: "H" Number of atoms: 5133 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 359, 5108 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 Conformer: "B" Number of residues, atoms: 359, 5122 Classifications: {'peptide': 359} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 341} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 255 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 10, 'ASP:plan': 5, 'TYR:plan': 1, 'GLN:plan1': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 139 bond proxies already assigned to first conformer: 5155 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'NO3': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'NO3': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'NO3': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'NO3': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'NO3': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'NO3': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'NO3': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'NO3': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AARG A 151 " occ=0.52 ... (46 atoms not shown) pdb="HH22BARG A 151 " occ=0.48 residue: pdb=" N AARG B 151 " occ=0.55 ... (46 atoms not shown) pdb="HH22BARG B 151 " occ=0.45 residue: pdb=" N AARG C 151 " occ=0.53 ... (46 atoms not shown) pdb="HH22BARG C 151 " occ=0.47 residue: pdb=" N AARG D 151 " occ=0.51 ... (46 atoms not shown) pdb="HH22BARG D 151 " occ=0.49 residue: pdb=" N AARG E 151 " occ=0.53 ... (46 atoms not shown) pdb="HH22BARG E 151 " occ=0.47 residue: pdb=" N AARG F 151 " occ=0.53 ... (46 atoms not shown) pdb="HH22BARG F 151 " occ=0.47 residue: pdb=" N AARG G 151 " occ=0.53 ... (46 atoms not shown) pdb="HH22BARG G 151 " occ=0.47 residue: pdb=" N AARG H 151 " occ=0.39 ... (33 atoms not shown) pdb="HH22BARG H 151 " occ=0.61 Time building chain proxies: 11.57, per 1000 atoms: 0.28 Number of scatterers: 41490 At special positions: 0 Unit cell: (152.152, 152.152, 92.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 112 16.00 P 16 15.00 Mg 8 11.99 O 4072 8.00 N 3944 7.00 C 13552 6.00 H 19786 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: 3.22 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 715.3 nanoseconds 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5296 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 16 sheets defined 41.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.734A pdb=" N GLU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 47 through 58 removed outlier: 4.914A pdb=" N THR A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLY A 55 " --> pdb=" O CYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 92 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.801A pdb=" N LYS A 110 " --> pdb=" O ASP A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.567A pdb=" N LEU A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.899A pdb=" N GLY A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 240 through 261 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.587A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.732A pdb=" N GLU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 47 through 58 removed outlier: 4.915A pdb=" N THR B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLY B 55 " --> pdb=" O CYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 80 through 92 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.802A pdb=" N LYS B 110 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 122 removed outlier: 3.582A pdb=" N LEU B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.899A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 240 through 261 Processing helix chain 'B' and resid 293 through 299 removed outlier: 3.593A pdb=" N LEU B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.731A pdb=" N GLU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 47 through 58 removed outlier: 4.915A pdb=" N THR C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY C 55 " --> pdb=" O CYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 92 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.804A pdb=" N LYS C 110 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 122 removed outlier: 3.586A pdb=" N LEU C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 159 removed outlier: 3.895A pdb=" N GLY C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 240 through 261 Processing helix chain 'C' and resid 293 through 299 removed outlier: 3.604A pdb=" N LEU C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 311 Processing helix chain 'C' and resid 340 through 358 Processing helix chain 'D' and resid 10 through 15 removed outlier: 3.730A pdb=" N GLU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 38 Processing helix chain 'D' and resid 47 through 58 removed outlier: 4.917A pdb=" N THR D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLY D 55 " --> pdb=" O CYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 80 through 92 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.813A pdb=" N LYS D 110 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 122 removed outlier: 3.573A pdb=" N LEU D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 3.898A pdb=" N GLY D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 240 through 261 Processing helix chain 'D' and resid 293 through 299 removed outlier: 3.590A pdb=" N LEU D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS D 299 " --> pdb=" O PRO D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 311 Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'E' and resid 10 through 15 removed outlier: 3.731A pdb=" N GLU E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 38 Processing helix chain 'E' and resid 47 through 58 removed outlier: 4.916A pdb=" N THR E 54 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLY E 55 " --> pdb=" O CYS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 80 Processing helix chain 'E' and resid 80 through 92 Proline residue: E 86 - end of helix Processing helix chain 'E' and resid 107 through 111 removed outlier: 3.833A pdb=" N LYS E 110 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 122 removed outlier: 3.584A pdb=" N LEU E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 159 removed outlier: 3.896A pdb=" N GLY E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 194 through 199 Processing helix chain 'E' and resid 240 through 261 Processing helix chain 'E' and resid 293 through 299 removed outlier: 3.589A pdb=" N LEU E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS E 299 " --> pdb=" O PRO E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 340 through 358 Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.732A pdb=" N GLU F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 38 Processing helix chain 'F' and resid 47 through 58 removed outlier: 4.920A pdb=" N THR F 54 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLY F 55 " --> pdb=" O CYS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 80 through 92 Proline residue: F 86 - end of helix Processing helix chain 'F' and resid 107 through 111 removed outlier: 3.822A pdb=" N LYS F 110 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 122 removed outlier: 3.586A pdb=" N LEU F 122 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 removed outlier: 3.898A pdb=" N GLY F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 194 through 199 Processing helix chain 'F' and resid 240 through 261 Processing helix chain 'F' and resid 293 through 299 removed outlier: 3.602A pdb=" N LEU F 297 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS F 299 " --> pdb=" O PRO F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 340 through 358 Processing helix chain 'G' and resid 10 through 15 removed outlier: 3.731A pdb=" N GLU G 14 " --> pdb=" O PRO G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 47 through 58 removed outlier: 4.920A pdb=" N THR G 54 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLY G 55 " --> pdb=" O CYS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 80 Processing helix chain 'G' and resid 80 through 92 Proline residue: G 86 - end of helix Processing helix chain 'G' and resid 107 through 111 removed outlier: 3.802A pdb=" N LYS G 110 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 122 removed outlier: 3.580A pdb=" N LEU G 122 " --> pdb=" O GLU G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 159 removed outlier: 3.897A pdb=" N GLY G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 185 Processing helix chain 'G' and resid 194 through 199 Processing helix chain 'G' and resid 240 through 261 Processing helix chain 'G' and resid 293 through 299 removed outlier: 3.594A pdb=" N LEU G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS G 299 " --> pdb=" O PRO G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 340 through 358 Processing helix chain 'H' and resid 10 through 15 removed outlier: 3.732A pdb=" N GLU H 14 " --> pdb=" O PRO H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 47 through 58 removed outlier: 4.915A pdb=" N THR H 54 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N GLY H 55 " --> pdb=" O CYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'H' and resid 80 through 92 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.801A pdb=" N LYS H 110 " --> pdb=" O ASP H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 122 removed outlier: 3.580A pdb=" N LEU H 122 " --> pdb=" O GLU H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 159 removed outlier: 3.898A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 194 through 199 Processing helix chain 'H' and resid 240 through 261 Processing helix chain 'H' and resid 293 through 299 removed outlier: 3.697A pdb=" N LEU H 297 " --> pdb=" O LYS H 293 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS H 299 " --> pdb=" O PRO H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 311 Processing helix chain 'H' and resid 340 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 170 removed outlier: 4.026A pdb=" N ARG A 167 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS A 214 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE A 220 " --> pdb=" O ASN A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 Processing sheet with id=AA3, first strand: chain 'B' and resid 166 through 170 removed outlier: 4.027A pdb=" N ARG B 167 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS B 214 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N PHE B 220 " --> pdb=" O ASN B 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 268 through 269 Processing sheet with id=AA5, first strand: chain 'C' and resid 166 through 170 removed outlier: 4.030A pdb=" N ARG C 167 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS C 214 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE C 220 " --> pdb=" O ASN C 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 268 through 269 Processing sheet with id=AA7, first strand: chain 'D' and resid 166 through 170 removed outlier: 4.026A pdb=" N ARG D 167 " --> pdb=" O HIS D 214 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N HIS D 214 " --> pdb=" O ARG D 167 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE D 220 " --> pdb=" O ASN D 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 268 through 269 Processing sheet with id=AA9, first strand: chain 'E' and resid 166 through 170 removed outlier: 4.020A pdb=" N ARG E 167 " --> pdb=" O HIS E 214 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS E 214 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE E 220 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 268 through 269 Processing sheet with id=AB2, first strand: chain 'F' and resid 166 through 170 removed outlier: 4.030A pdb=" N ARG F 167 " --> pdb=" O HIS F 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N HIS F 214 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE F 220 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 268 through 269 Processing sheet with id=AB4, first strand: chain 'G' and resid 166 through 170 removed outlier: 4.025A pdb=" N ARG G 167 " --> pdb=" O HIS G 214 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS G 214 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE G 220 " --> pdb=" O ASN G 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 268 through 269 Processing sheet with id=AB6, first strand: chain 'H' and resid 166 through 170 removed outlier: 4.027A pdb=" N ARG H 167 " --> pdb=" O HIS H 214 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS H 214 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N PHE H 220 " --> pdb=" O ASN H 215 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 268 through 269 871 hydrogen bonds defined for protein. 2501 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: 9.56 Time building geometry restraints manager: 4.65 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: 19730 1.03 - 1.23: 59 1.23 - 1.42: 9429 1.42 - 1.61: 12576 1.61 - 1.80: 168 Bond restraints: 41962 Sorted by residual: bond pdb=" C4 ADP C 402 " pdb=" C5 ADP C 402 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C4 ADP H 402 " pdb=" C5 ADP H 402 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" C4 ADP A 402 " pdb=" C5 ADP A 402 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.55e+00 bond pdb=" C4 ADP B 402 " pdb=" C5 ADP B 402 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.53e+00 bond pdb=" C4 ADP G 402 " pdb=" C5 ADP G 402 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.51e+00 ... (remaining 41957 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 72696 1.34 - 2.68: 2167 2.68 - 4.02: 243 4.02 - 5.37: 55 5.37 - 6.71: 33 Bond angle restraints: 75194 Sorted by residual: angle pdb=" N GLY A 285 " pdb=" CA GLY A 285 " pdb=" C GLY A 285 " ideal model delta sigma weight residual 115.47 111.97 3.50 1.31e+00 5.83e-01 7.14e+00 angle pdb=" C1' ADP B 402 " pdb=" C2' ADP B 402 " pdb=" C3' ADP B 402 " ideal model delta sigma weight residual 111.00 104.29 6.71 3.00e+00 1.11e-01 5.00e+00 angle pdb=" C1' ADP G 402 " pdb=" C2' ADP G 402 " pdb=" C3' ADP G 402 " ideal model delta sigma weight residual 111.00 104.35 6.65 3.00e+00 1.11e-01 4.92e+00 angle pdb=" C1' ADP C 402 " pdb=" C2' ADP C 402 " pdb=" C3' ADP C 402 " ideal model delta sigma weight residual 111.00 104.38 6.62 3.00e+00 1.11e-01 4.87e+00 angle pdb=" C1' ADP E 402 " pdb=" C2' ADP E 402 " pdb=" C3' ADP E 402 " ideal model delta sigma weight residual 111.00 104.40 6.60 3.00e+00 1.11e-01 4.85e+00 ... (remaining 75189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 19076 32.94 - 65.87: 851 65.87 - 98.81: 30 98.81 - 131.74: 7 131.74 - 164.68: 9 Dihedral angle restraints: 19973 sinusoidal: 10413 harmonic: 9560 Sorted by residual: dihedral pdb=" C5' ADP A 402 " pdb=" O5' ADP A 402 " pdb=" PA ADP A 402 " pdb=" O2A ADP A 402 " ideal model delta sinusoidal sigma weight residual -60.00 104.68 -164.68 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" O2A ADP A 402 " pdb=" O3A ADP A 402 " pdb=" PA ADP A 402 " pdb=" PB ADP A 402 " ideal model delta sinusoidal sigma weight residual 300.00 141.19 158.81 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" C5' ADP B 402 " pdb=" O5' ADP B 402 " pdb=" PA ADP B 402 " pdb=" O2A ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 95.01 -155.01 1 2.00e+01 2.50e-03 4.58e+01 ... (remaining 19970 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1993 0.026 - 0.051: 882 0.051 - 0.077: 286 0.077 - 0.102: 152 0.102 - 0.128: 111 Chirality restraints: 3424 Sorted by residual: chirality pdb=" CA ILE H 233 " pdb=" N ILE H 233 " pdb=" C ILE H 233 " pdb=" CB ILE H 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE E 233 " pdb=" N ILE E 233 " pdb=" C ILE E 233 " pdb=" CB ILE E 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 chirality pdb=" CA ILE A 233 " pdb=" N ILE A 233 " pdb=" C ILE A 233 " pdb=" CB ILE A 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 3421 not shown) Planarity restraints: 6710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 137 " -0.017 5.00e-02 4.00e+02 2.55e-02 1.04e+00 pdb=" N PRO C 138 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO C 138 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 138 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 137 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO E 138 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO E 138 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 138 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 137 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO D 138 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO D 138 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO D 138 " 0.014 5.00e-02 4.00e+02 ... (remaining 6707 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 2402 2.17 - 2.78: 81048 2.78 - 3.39: 119190 3.39 - 3.99: 158523 3.99 - 4.60: 243753 Nonbonded interactions: 604916 Sorted by model distance: nonbonded pdb=" OE1 GLU F 341 " pdb=" H GLU F 341 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU G 341 " pdb=" H GLU G 341 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU B 341 " pdb=" H GLU B 341 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU E 341 " pdb=" H GLU E 341 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU H 341 " pdb=" H GLU H 341 " model vdw 1.567 2.450 ... (remaining 604911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 150 or resid 153 through 404)) selection = (chain 'B' and (resid 3 through 150 or resid 153 through 404)) selection = (chain 'C' and (resid 3 through 150 or resid 153 through 404)) selection = (chain 'D' and (resid 3 through 150 or resid 153 through 404)) selection = (chain 'E' and (resid 3 through 150 or resid 153 through 404)) selection = (chain 'F' and (resid 3 through 150 or resid 153 through 404)) selection = (chain 'G' and (resid 3 through 150 or resid 153 through 404)) selection = (chain 'H' and (resid 3 through 150 or resid 153 through 404)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.210 Extract box with map and model: 0.590 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 40.550 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 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 0.027 22176 Z= 0.155 Angle : 0.629 6.707 30304 Z= 0.301 Chirality : 0.039 0.128 3424 Planarity : 0.004 0.037 3968 Dihedral : 17.939 164.678 7704 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.20 % Allowed : 27.01 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2880 helix: 1.15 (0.15), residues: 1088 sheet: -1.98 (0.27), residues: 272 loop : -0.92 (0.18), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 262 TYR 0.006 0.001 TYR G 95 PHE 0.011 0.001 PHE E 303 TRP 0.006 0.001 TRP G 268 HIS 0.004 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00347 (22176) covalent geometry : angle 0.62948 (30304) hydrogen bonds : bond 0.13006 ( 871) hydrogen bonds : angle 6.22733 ( 2501) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 276 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 291 average time/residue: 1.0359 time to fit residues: 351.3289 Evaluate side-chains 296 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 280 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.0980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.158349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.132887 restraints weight = 199812.849| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 4.16 r_work: 0.3884 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22176 Z= 0.204 Angle : 0.651 6.886 30304 Z= 0.316 Chirality : 0.042 0.144 3424 Planarity : 0.004 0.028 3968 Dihedral : 10.651 136.072 3302 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 1.77 % Allowed : 24.71 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.16), residues: 2880 helix: 1.43 (0.16), residues: 1032 sheet: -2.01 (0.26), residues: 272 loop : -0.85 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 315 TYR 0.009 0.002 TYR H 77 PHE 0.011 0.001 PHE B 303 TRP 0.006 0.001 TRP F 46 HIS 0.005 0.001 HIS E 21 Details of bonding type rmsd covalent geometry : bond 0.00460 (22176) covalent geometry : angle 0.65055 (30304) hydrogen bonds : bond 0.04245 ( 871) hydrogen bonds : angle 5.25578 ( 2501) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 327 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 27 residues processed: 316 average time/residue: 1.3466 time to fit residues: 495.4992 Evaluate side-chains 304 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 267 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 172 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 179 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN B 50 GLN C 50 GLN D 50 GLN E 50 GLN F 50 GLN G 50 GLN H 50 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.158523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.133097 restraints weight = 202880.308| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 4.22 r_work: 0.3879 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22176 Z= 0.204 Angle : 0.642 7.035 30304 Z= 0.311 Chirality : 0.042 0.156 3424 Planarity : 0.004 0.038 3968 Dihedral : 9.799 112.072 3288 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.39 % Allowed : 23.80 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.16), residues: 2880 helix: 1.34 (0.15), residues: 1032 sheet: -2.05 (0.25), residues: 272 loop : -0.94 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 127 TYR 0.009 0.001 TYR G 77 PHE 0.008 0.001 PHE F 116 TRP 0.006 0.001 TRP G 46 HIS 0.005 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00460 (22176) covalent geometry : angle 0.64154 (30304) hydrogen bonds : bond 0.04055 ( 871) hydrogen bonds : angle 5.09937 ( 2501) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 335 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 285 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: A 231 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7417 (mmm160) REVERT: B 231 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7463 (mmm160) REVERT: D 227 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: D 231 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7456 (mmm160) REVERT: E 227 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7167 (tt0) REVERT: H 227 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: H 231 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7424 (mmm160) outliers start: 50 outliers final: 27 residues processed: 318 average time/residue: 1.4186 time to fit residues: 519.6310 Evaluate side-chains 308 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 273 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 227 GLN Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 227 GLN Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 227 GLN Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 250 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 165 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.161272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.135027 restraints weight = 190317.705| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 4.46 r_work: 0.3891 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3889 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3889 r_free = 0.3889 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3889 r_free = 0.3889 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3889 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22176 Z= 0.156 Angle : 0.616 6.556 30304 Z= 0.296 Chirality : 0.041 0.138 3424 Planarity : 0.004 0.059 3968 Dihedral : 9.298 109.474 3272 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.30 % Allowed : 24.04 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.16), residues: 2880 helix: 1.50 (0.16), residues: 1032 sheet: -2.03 (0.25), residues: 272 loop : -0.87 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 311 TYR 0.008 0.001 TYR G 77 PHE 0.006 0.001 PHE G 116 TRP 0.005 0.001 TRP F 46 HIS 0.004 0.001 HIS C 21 Details of bonding type rmsd covalent geometry : bond 0.00354 (22176) covalent geometry : angle 0.61620 (30304) hydrogen bonds : bond 0.03578 ( 871) hydrogen bonds : angle 4.92352 ( 2501) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 336 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 288 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7479 (t0) REVERT: B 227 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7278 (tt0) REVERT: B 228 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7425 (t0) REVERT: E 228 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7474 (t0) REVERT: F 227 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7276 (tt0) REVERT: F 228 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7428 (t0) REVERT: G 228 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7416 (t0) REVERT: H 228 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7469 (t0) outliers start: 48 outliers final: 27 residues processed: 316 average time/residue: 1.1516 time to fit residues: 421.4524 Evaluate side-chains 318 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 228 ASP Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 228 ASP Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 230 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 132 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 251 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.160587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.135104 restraints weight = 188152.758| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 4.05 r_work: 0.3893 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3893 r_free = 0.3893 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3893 r_free = 0.3893 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22176 Z= 0.171 Angle : 0.620 6.568 30304 Z= 0.298 Chirality : 0.041 0.152 3424 Planarity : 0.004 0.057 3968 Dihedral : 9.193 111.699 3272 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 2.73 % Allowed : 22.65 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.16), residues: 2880 helix: 1.50 (0.16), residues: 1032 sheet: -2.00 (0.25), residues: 272 loop : -0.87 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 311 TYR 0.009 0.001 TYR G 77 PHE 0.007 0.001 PHE F 116 TRP 0.005 0.001 TRP F 46 HIS 0.004 0.001 HIS F 21 Details of bonding type rmsd covalent geometry : bond 0.00388 (22176) covalent geometry : angle 0.61961 (30304) hydrogen bonds : bond 0.03591 ( 871) hydrogen bonds : angle 4.90972 ( 2501) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 340 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 283 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7403 (mmm160) REVERT: B 227 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: B 231 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7364 (mmm160) REVERT: C 231 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7392 (mmm160) REVERT: D 231 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7446 (mmm160) REVERT: E 231 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.7453 (mmm160) REVERT: F 227 GLN cc_start: 0.7632 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: F 228 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7573 (t0) REVERT: F 231 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7383 (mmm160) REVERT: G 227 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: G 231 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7422 (mmm160) REVERT: H 231 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7423 (mmm160) outliers start: 57 outliers final: 32 residues processed: 319 average time/residue: 1.3579 time to fit residues: 494.1394 Evaluate side-chains 320 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 276 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 227 GLN Chi-restraints excluded: chain F residue 228 ASP Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 227 GLN Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 231 ARG Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 241 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 249 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 148 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.4389 r_free = 0.4389 target = 0.163125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.137039 restraints weight = 192437.515| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 4.06 r_work: 0.3919 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3915 r_free = 0.3915 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22176 Z= 0.160 Angle : 0.615 6.596 30304 Z= 0.294 Chirality : 0.041 0.146 3424 Planarity : 0.005 0.062 3968 Dihedral : 9.038 110.841 3272 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.97 % Allowed : 22.65 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.16), residues: 2880 helix: 1.53 (0.16), residues: 1032 sheet: -1.98 (0.25), residues: 272 loop : -0.85 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 311 TYR 0.008 0.001 TYR H 77 PHE 0.006 0.001 PHE C 116 TRP 0.005 0.001 TRP H 46 HIS 0.003 0.001 HIS G 21 Details of bonding type rmsd covalent geometry : bond 0.00363 (22176) covalent geometry : angle 0.61451 (30304) hydrogen bonds : bond 0.03481 ( 871) hydrogen bonds : angle 4.85322 ( 2501) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 344 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 282 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7406 (mmm160) REVERT: B 231 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7393 (mmm160) REVERT: C 231 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7395 (mmm160) REVERT: E 231 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7467 (mmm160) REVERT: F 231 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7412 (mmm160) REVERT: G 231 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7462 (mmm160) REVERT: H 231 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7409 (mmm160) outliers start: 62 outliers final: 37 residues processed: 324 average time/residue: 1.2869 time to fit residues: 476.0264 Evaluate side-chains 325 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 281 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 231 ARG Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 226 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 244 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 232 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 252 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 254 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.162058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.135906 restraints weight = 200016.591| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 4.10 r_work: 0.3899 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22176 Z= 0.204 Angle : 0.639 6.806 30304 Z= 0.308 Chirality : 0.042 0.159 3424 Planarity : 0.005 0.054 3968 Dihedral : 9.129 114.730 3272 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 2.78 % Allowed : 22.80 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.16), residues: 2880 helix: 1.36 (0.15), residues: 1032 sheet: -1.97 (0.26), residues: 272 loop : -0.91 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 311 TYR 0.010 0.001 TYR C 77 PHE 0.007 0.001 PHE G 116 TRP 0.006 0.001 TRP H 46 HIS 0.005 0.001 HIS A 21 Details of bonding type rmsd covalent geometry : bond 0.00463 (22176) covalent geometry : angle 0.63900 (30304) hydrogen bonds : bond 0.03686 ( 871) hydrogen bonds : angle 4.91492 ( 2501) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 333 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 275 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7450 (mmm160) REVERT: B 231 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7436 (mmm160) REVERT: C 231 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7438 (mmm160) REVERT: D 231 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7496 (mmm160) REVERT: E 231 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7517 (mmm160) REVERT: F 231 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7492 (mmm160) REVERT: G 231 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7505 (mmm160) REVERT: H 231 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7456 (mmm160) outliers start: 58 outliers final: 45 residues processed: 306 average time/residue: 1.4434 time to fit residues: 505.6887 Evaluate side-chains 317 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 170 ARG Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 231 ARG Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 123 SER Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain E residue 231 ARG Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 123 SER Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 231 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain H residue 170 ARG Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 231 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 206 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 268 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 73 optimal weight: 0.9980 chunk 191 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.164124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.137913 restraints weight = 202232.908| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 4.16 r_work: 0.3927 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3925 r_free = 0.3925 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22176 Z= 0.132 Angle : 0.605 6.403 30304 Z= 0.288 Chirality : 0.041 0.132 3424 Planarity : 0.005 0.077 3968 Dihedral : 8.757 107.317 3272 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.63 % Allowed : 24.04 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 2880 helix: 1.59 (0.16), residues: 1032 sheet: -1.95 (0.25), residues: 272 loop : -0.80 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 311 TYR 0.007 0.001 TYR H 77 PHE 0.005 0.001 PHE F 116 TRP 0.005 0.001 TRP F 268 HIS 0.004 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00303 (22176) covalent geometry : angle 0.60527 (30304) hydrogen bonds : bond 0.03284 ( 871) hydrogen bonds : angle 4.76594 ( 2501) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 312 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 231 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7375 (mmm160) outliers start: 34 outliers final: 33 residues processed: 294 average time/residue: 1.2456 time to fit residues: 422.3200 Evaluate side-chains 311 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 170 ARG Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 170 ARG Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 230 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 192 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 264 optimal weight: 0.5980 chunk 185 optimal weight: 7.9990 chunk 253 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.163891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.137678 restraints weight = 196563.732| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 4.11 r_work: 0.3928 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3926 r_free = 0.3926 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22176 Z= 0.141 Angle : 0.609 6.453 30304 Z= 0.290 Chirality : 0.041 0.139 3424 Planarity : 0.004 0.065 3968 Dihedral : 8.672 105.572 3272 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.58 % Allowed : 24.04 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.16), residues: 2880 helix: 1.59 (0.16), residues: 1032 sheet: -1.96 (0.24), residues: 272 loop : -0.81 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 311 TYR 0.008 0.001 TYR H 77 PHE 0.005 0.001 PHE D 116 TRP 0.005 0.001 TRP F 268 HIS 0.003 0.001 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00324 (22176) covalent geometry : angle 0.60887 (30304) hydrogen bonds : bond 0.03280 ( 871) hydrogen bonds : angle 4.74199 ( 2501) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 313 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 280 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 231 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.7396 (mmm160) REVERT: G 231 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7451 (mmm160) outliers start: 33 outliers final: 30 residues processed: 298 average time/residue: 1.2828 time to fit residues: 440.6777 Evaluate side-chains 307 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 231 ARG Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 156 optimal weight: 3.9990 chunk 79 optimal weight: 0.4980 chunk 10 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 237 optimal weight: 0.7980 chunk 129 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4407 r_free = 0.4407 target = 0.164306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.138081 restraints weight = 195949.229| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 4.10 r_work: 0.3932 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3931 r_free = 0.3931 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22176 Z= 0.131 Angle : 0.603 6.388 30304 Z= 0.287 Chirality : 0.040 0.134 3424 Planarity : 0.005 0.068 3968 Dihedral : 8.513 101.764 3272 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.58 % Allowed : 23.85 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.16), residues: 2880 helix: 1.64 (0.16), residues: 1032 sheet: -1.92 (0.24), residues: 272 loop : -0.80 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 311 TYR 0.008 0.001 TYR H 77 PHE 0.005 0.001 PHE A 116 TRP 0.005 0.001 TRP F 268 HIS 0.003 0.001 HIS E 214 Details of bonding type rmsd covalent geometry : bond 0.00301 (22176) covalent geometry : angle 0.60342 (30304) hydrogen bonds : bond 0.03195 ( 871) hydrogen bonds : angle 4.69172 ( 2501) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5760 Ramachandran restraints generated. 2880 Oldfield, 0 Emsley, 2880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 101 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue MET 241 is missing expected H atoms. Skipping. Residue LYS 242 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 278 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 231 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7358 (mmm160) outliers start: 33 outliers final: 30 residues processed: 295 average time/residue: 1.1662 time to fit residues: 396.2273 Evaluate side-chains 304 residues out of total 2473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 273 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 231 ARG Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 170 ARG Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 170 ARG Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 230 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 230 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 135 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.163727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.137702 restraints weight = 189601.469| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 4.02 r_work: 0.3928 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3927 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3927 r_free = 0.3927 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3927 r_free = 0.3927 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3927 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22176 Z= 0.150 Angle : 0.610 6.496 30304 Z= 0.291 Chirality : 0.041 0.140 3424 Planarity : 0.005 0.072 3968 Dihedral : 8.478 104.169 3272 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.68 % Allowed : 23.71 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.16), residues: 2880 helix: 1.60 (0.16), residues: 1032 sheet: -1.88 (0.25), residues: 272 loop : -0.83 (0.17), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 311 TYR 0.008 0.001 TYR D 77 PHE 0.005 0.001 PHE D 116 TRP 0.005 0.001 TRP F 268 HIS 0.003 0.001 HIS F 21 Details of bonding type rmsd covalent geometry : bond 0.00344 (22176) covalent geometry : angle 0.61035 (30304) hydrogen bonds : bond 0.03287 ( 871) hydrogen bonds : angle 4.70329 ( 2501) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19452.50 seconds wall clock time: 328 minutes 36.39 seconds (19716.39 seconds total)