Starting phenix.real_space_refine on Wed Aug 27 00:14:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b04_44028/08_2025/9b04_44028_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b04_44028/08_2025/9b04_44028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b04_44028/08_2025/9b04_44028.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b04_44028/08_2025/9b04_44028.map" model { file = "/net/cci-nas-00/data/ceres_data/9b04_44028/08_2025/9b04_44028_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b04_44028/08_2025/9b04_44028_trim.cif" } resolution = 2.52 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= 0.027 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 120 5.16 5 C 14248 2.51 5 N 4168 2.21 5 O 4280 1.98 5 H 21200 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s 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: 44040 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5477 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5348 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 368, 5350 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5274 Chain: "B" Number of atoms: 5477 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5348 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 368, 5350 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5274 Chain: "C" Number of atoms: 5477 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5348 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 368, 5350 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5274 Chain: "D" Number of atoms: 5477 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5348 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 368, 5350 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5274 Chain: "E" Number of atoms: 5477 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5348 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 368, 5350 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5274 Chain: "F" Number of atoms: 5477 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5348 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 368, 5350 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5274 Chain: "G" Number of atoms: 5477 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5348 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 368, 5350 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5274 Chain: "H" Number of atoms: 5477 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5348 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 368, 5350 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5274 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 80 residue: pdb=" N AASN A 58 " occ=0.56 ... (26 atoms not shown) pdb="HD22BASN A 58 " occ=0.44 residue: pdb=" N APRO A 59 " occ=0.56 ... (26 atoms not shown) pdb=" HD3BPRO A 59 " occ=0.44 residue: pdb=" N AGLY A 60 " occ=0.56 ... (12 atoms not shown) pdb=" HA3BGLY A 60 " occ=0.44 residue: pdb=" N AHIS A 61 " occ=0.56 ... (12 atoms not shown) pdb=" HA BHIS A 61 " occ=0.44 residue: pdb=" N APRO A 62 " occ=0.56 ... (26 atoms not shown) pdb=" HD3BPRO A 62 " occ=0.44 residue: pdb=" N APHE A 63 " occ=0.56 ... (12 atoms not shown) pdb=" HA BPHE A 63 " occ=0.44 residue: pdb=" N AILE A 64 " occ=0.56 ... (36 atoms not shown) pdb="HD13BILE A 64 " occ=0.44 residue: pdb=" N ALYS A 65 " occ=0.56 ... (12 atoms not shown) pdb=" HA BLYS A 65 " occ=0.44 residue: pdb=" N ATHR A 66 " occ=0.56 ... (26 atoms not shown) pdb="HG23BTHR A 66 " occ=0.44 residue: pdb=" N AARG A 151 " occ=0.45 ... (44 atoms not shown) pdb="HH22BARG A 151 " occ=0.55 residue: pdb=" N AASN B 58 " occ=0.55 ... (26 atoms not shown) pdb="HD22BASN B 58 " occ=0.45 residue: pdb=" N APRO B 59 " occ=0.55 ... (26 atoms not shown) pdb=" HD3BPRO B 59 " occ=0.45 ... (remaining 68 not shown) Time building chain proxies: 13.79, per 1000 atoms: 0.31 Number of scatterers: 44040 At special positions: 0 Unit cell: (130.872, 130.872, 98.952, 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 120 16.00 P 16 15.00 Mg 8 11.99 O 4280 8.00 N 4168 7.00 C 14248 6.00 H 21200 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: 4.07 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5552 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 16 sheets defined 42.1% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 47 through 58 removed outlier: 4.916A pdb=" N THR A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 5.242A 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 142 through 159 removed outlier: 3.823A pdb=" N GLY A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 194 through 200 removed outlier: 3.580A pdb=" N THR A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 262 removed outlier: 3.683A pdb=" N ARG A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 294 through 299 removed outlier: 4.187A 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 Processing helix chain 'B' and resid 23 through 29 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: 5.244A 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 142 through 159 removed outlier: 3.822A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 194 through 200 removed outlier: 3.581A pdb=" N THR B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 262 removed outlier: 3.660A pdb=" N ARG B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 294 through 299 removed outlier: 4.010A pdb=" N LYS B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 23 through 29 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: 5.243A 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 142 through 159 removed outlier: 3.812A pdb=" N GLY C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 194 through 200 removed outlier: 3.611A pdb=" N THR C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 262 removed outlier: 3.653A pdb=" N ARG C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 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 Processing helix chain 'D' and resid 23 through 29 Processing helix chain 'D' and resid 30 through 38 Processing helix chain 'D' and resid 47 through 58 removed outlier: 4.920A pdb=" N THR D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 5.258A 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 142 through 159 removed outlier: 3.810A pdb=" N GLY D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 194 through 200 removed outlier: 3.584A pdb=" N THR D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 262 removed outlier: 3.692A pdb=" N ARG D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 294 through 299 removed outlier: 4.024A 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 Processing helix chain 'E' and resid 23 through 29 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: 5.244A 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 142 through 159 removed outlier: 3.814A pdb=" N GLY E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 194 through 200 removed outlier: 3.576A pdb=" N THR E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 262 removed outlier: 3.676A pdb=" N ARG E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 Processing helix chain 'E' and resid 294 through 299 removed outlier: 4.437A 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 Processing helix chain 'F' and resid 23 through 29 Processing helix chain 'F' and resid 30 through 38 Processing helix chain 'F' and resid 47 through 58 removed outlier: 4.916A pdb=" N THR F 54 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 5.242A 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 142 through 159 removed outlier: 3.820A pdb=" N GLY F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 194 through 200 removed outlier: 3.574A pdb=" N THR F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 262 removed outlier: 3.560A pdb=" N ARG F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 Processing helix chain 'F' and resid 294 through 299 removed outlier: 4.023A 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 Processing helix chain 'G' and resid 23 through 29 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 47 through 58 removed outlier: 4.916A pdb=" N THR G 54 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 5.239A 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 142 through 159 removed outlier: 3.815A pdb=" N GLY G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 164 removed outlier: 7.459A pdb=" N ASP G 163 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU G 164 " --> pdb=" O LYS G 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 160 through 164' Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 175 through 185 Processing helix chain 'G' and resid 194 through 200 removed outlier: 3.587A pdb=" N THR G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 262 removed outlier: 3.661A pdb=" N ARG G 262 " --> pdb=" O LEU G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 282 Processing helix chain 'G' and resid 294 through 299 removed outlier: 4.041A 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 Processing helix chain 'H' and resid 23 through 29 Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 47 through 58 removed outlier: 4.923A pdb=" N THR H 54 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 5.259A 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 142 through 159 removed outlier: 3.813A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 194 through 200 removed outlier: 3.594A pdb=" N THR H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 262 removed outlier: 3.685A pdb=" N ARG H 262 " --> pdb=" O LEU H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 282 Processing helix chain 'H' and resid 294 through 299 removed outlier: 4.049A 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: 5.719A 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: 5.718A 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: 5.721A 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: 5.717A 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: 5.718A 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: 5.718A 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: 5.718A 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: 5.717A 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 269 999 hydrogen bonds defined for protein. 2741 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: 10.08 Time building geometry restraints manager: 5.48 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: 21144 1.03 - 1.23: 69 1.23 - 1.42: 9771 1.42 - 1.62: 13368 1.62 - 1.81: 184 Bond restraints: 44536 Sorted by residual: bond pdb=" C4 ADP F 401 " pdb=" C5 ADP F 401 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C4 ADP D 401 " pdb=" C5 ADP D 401 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C4 ADP G 401 " pdb=" C5 ADP G 401 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.27e+00 ... (remaining 44531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 75269 1.12 - 2.24: 4342 2.24 - 3.36: 208 3.36 - 4.48: 130 4.48 - 5.59: 67 Bond angle restraints: 80016 Sorted by residual: angle pdb=" N LYS C 299 " pdb=" CA LYS C 299 " pdb=" C LYS C 299 " ideal model delta sigma weight residual 110.44 113.35 -2.91 1.20e+00 6.94e-01 5.87e+00 angle pdb=" N LEU A 294 " pdb=" CA LEU A 294 " pdb=" C LEU A 294 " ideal model delta sigma weight residual 109.81 114.72 -4.91 2.21e+00 2.05e-01 4.94e+00 angle pdb=" N LEU F 294 " pdb=" CA LEU F 294 " pdb=" C LEU F 294 " ideal model delta sigma weight residual 109.81 114.71 -4.90 2.21e+00 2.05e-01 4.91e+00 angle pdb=" N LEU D 294 " pdb=" CA LEU D 294 " pdb=" C LEU D 294 " ideal model delta sigma weight residual 109.81 114.70 -4.89 2.21e+00 2.05e-01 4.90e+00 angle pdb=" N LEU H 294 " pdb=" CA LEU H 294 " pdb=" C LEU H 294 " ideal model delta sigma weight residual 109.81 114.69 -4.88 2.21e+00 2.05e-01 4.88e+00 ... (remaining 80011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 18821 17.22 - 34.43: 1547 34.43 - 51.65: 584 51.65 - 68.86: 144 68.86 - 86.08: 48 Dihedral angle restraints: 21144 sinusoidal: 11240 harmonic: 9904 Sorted by residual: dihedral pdb=" CA LEU H 294 " pdb=" C LEU H 294 " pdb=" N PRO H 295 " pdb=" CA PRO H 295 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA LEU F 294 " pdb=" C LEU F 294 " pdb=" N PRO F 295 " pdb=" CA PRO F 295 " ideal model delta harmonic sigma weight residual -180.00 -154.57 -25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA LEU G 294 " pdb=" C LEU G 294 " pdb=" N PRO G 295 " pdb=" CA PRO G 295 " ideal model delta harmonic sigma weight residual 180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 21141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2142 0.027 - 0.054: 982 0.054 - 0.081: 208 0.081 - 0.108: 173 0.108 - 0.135: 87 Chirality restraints: 3592 Sorted by residual: chirality pdb=" CA ILE B 331 " pdb=" N ILE B 331 " pdb=" C ILE B 331 " pdb=" CB ILE B 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE G 331 " pdb=" N ILE G 331 " pdb=" C ILE G 331 " pdb=" CB ILE G 331 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 chirality pdb=" CA ILE D 331 " pdb=" N ILE D 331 " pdb=" C ILE D 331 " pdb=" CB ILE D 331 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 3589 not shown) Planarity restraints: 7064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 294 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO F 295 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 295 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 295 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 294 " 0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO G 295 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO G 295 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 295 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 294 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO D 295 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 295 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 295 " 0.023 5.00e-02 4.00e+02 ... (remaining 7061 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1902 2.15 - 2.76: 81595 2.76 - 3.38: 126266 3.38 - 3.99: 164244 3.99 - 4.60: 258535 Nonbonded interactions: 632542 Sorted by model distance: nonbonded pdb=" OE1 GLU H 359 " pdb=" H GLU H 359 " model vdw 1.538 2.450 nonbonded pdb=" OE1 GLU B 359 " pdb=" H GLU B 359 " model vdw 1.583 2.450 nonbonded pdb=" OE1 GLU C 359 " pdb=" H GLU C 359 " model vdw 1.584 2.450 nonbonded pdb=" OE1 GLU D 359 " pdb=" H GLU D 359 " model vdw 1.595 2.450 nonbonded pdb=" OE1 GLU G 359 " pdb=" H GLU G 359 " model vdw 1.599 2.450 ... (remaining 632537 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 57 or resid 68 through 150 or resid 153 through \ 402)) selection = (chain 'B' and (resid 3 through 57 or resid 68 through 150 or resid 153 through \ 402)) selection = (chain 'C' and (resid 3 through 57 or resid 68 through 150 or resid 153 through \ 402)) selection = (chain 'D' and (resid 3 through 57 or resid 68 through 150 or resid 153 through \ 402)) selection = (chain 'E' and (resid 3 through 57 or resid 68 through 150 or resid 153 through \ 402)) selection = (chain 'F' and (resid 3 through 57 or resid 68 through 150 or resid 153 through \ 402)) selection = (chain 'G' and (resid 3 through 57 or resid 68 through 150 or resid 153 through \ 402)) selection = (chain 'H' and (resid 3 through 57 or resid 68 through 150 or resid 153 through \ 402)) } 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=0.43 max=1.00 mean=0.98 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.300 Extract box with map and model: 0.590 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 47.030 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 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 0.025 23336 Z= 0.110 Angle : 0.572 5.595 31864 Z= 0.267 Chirality : 0.039 0.135 3592 Planarity : 0.004 0.041 4184 Dihedral : 16.376 86.076 8320 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.07 % Allowed : 22.23 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.45 (0.16), residues: 3040 helix: 2.18 (0.17), residues: 1096 sheet: -1.38 (0.22), residues: 448 loop : -0.57 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.013 0.001 TYR D 354 PHE 0.017 0.001 PHE C 303 TRP 0.004 0.001 TRP B 46 HIS 0.004 0.001 HIS E 214 Details of bonding type rmsd covalent geometry : bond 0.00251 (23336) covalent geometry : angle 0.57242 (31864) hydrogen bonds : bond 0.11396 ( 999) hydrogen bonds : angle 4.77789 ( 2741) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 167 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.258 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: E 354 TYR cc_start: 0.7961 (t80) cc_final: 0.7533 (t80) REVERT: F 354 TYR cc_start: 0.8118 (t80) cc_final: 0.7685 (t80) REVERT: G 354 TYR cc_start: 0.8032 (t80) cc_final: 0.7616 (t80) outliers start: 24 outliers final: 21 residues processed: 165 average time/residue: 1.5853 time to fit residues: 297.1162 Evaluate side-chains 160 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 301 SER Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain H residue 301 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.117698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.073982 restraints weight = 368367.931| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 4.97 r_work: 0.2628 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.0488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23336 Z= 0.177 Angle : 0.608 5.604 31864 Z= 0.291 Chirality : 0.041 0.124 3592 Planarity : 0.005 0.046 4184 Dihedral : 6.131 50.606 3490 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.88 % Allowed : 21.38 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.34 (0.16), residues: 3040 helix: 1.94 (0.16), residues: 1112 sheet: -1.25 (0.22), residues: 448 loop : -0.59 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 143 TYR 0.012 0.001 TYR H 354 PHE 0.013 0.001 PHE C 303 TRP 0.007 0.001 TRP E 46 HIS 0.006 0.001 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00405 (23336) covalent geometry : angle 0.60847 (31864) hydrogen bonds : bond 0.03286 ( 999) hydrogen bonds : angle 4.30980 ( 2741) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 181 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 139 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 354 TYR cc_start: 0.7453 (t80) cc_final: 0.7229 (t80) REVERT: E 354 TYR cc_start: 0.8022 (t80) cc_final: 0.7466 (t80) REVERT: F 354 TYR cc_start: 0.8189 (t80) cc_final: 0.7605 (t80) REVERT: G 354 TYR cc_start: 0.8041 (t80) cc_final: 0.7528 (t80) REVERT: H 354 TYR cc_start: 0.7437 (t80) cc_final: 0.7016 (t80) outliers start: 42 outliers final: 3 residues processed: 175 average time/residue: 1.4369 time to fit residues: 288.9199 Evaluate side-chains 149 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 202 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 246 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 221 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 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 = 0.3650 r_free = 0.3650 target = 0.117645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.074103 restraints weight = 348073.042| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.87 r_work: 0.2664 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23336 Z= 0.158 Angle : 0.593 5.518 31864 Z= 0.282 Chirality : 0.040 0.123 3592 Planarity : 0.004 0.040 4184 Dihedral : 5.184 44.999 3444 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.43 % Allowed : 21.25 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 3040 helix: 1.95 (0.16), residues: 1112 sheet: -1.13 (0.23), residues: 448 loop : -0.67 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 143 TYR 0.008 0.001 TYR H 354 PHE 0.010 0.001 PHE H 303 TRP 0.007 0.001 TRP E 46 HIS 0.005 0.001 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00366 (23336) covalent geometry : angle 0.59310 (31864) hydrogen bonds : bond 0.03153 ( 999) hydrogen bonds : angle 4.25869 ( 2741) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 175 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 354 TYR cc_start: 0.8021 (t80) cc_final: 0.7490 (t80) REVERT: F 354 TYR cc_start: 0.8201 (t80) cc_final: 0.7679 (t80) REVERT: G 354 TYR cc_start: 0.8081 (t80) cc_final: 0.7610 (t80) outliers start: 32 outliers final: 3 residues processed: 175 average time/residue: 1.3542 time to fit residues: 271.6565 Evaluate side-chains 140 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 11 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 212 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 220 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.117372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.073723 restraints weight = 340598.948| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 4.83 r_work: 0.2631 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23336 Z= 0.172 Angle : 0.594 5.506 31864 Z= 0.283 Chirality : 0.041 0.123 3592 Planarity : 0.004 0.040 4184 Dihedral : 5.182 44.028 3444 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 1.38 % Allowed : 21.52 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.31 (0.16), residues: 3040 helix: 1.97 (0.16), residues: 1112 sheet: -1.12 (0.23), residues: 448 loop : -0.72 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 143 TYR 0.011 0.001 TYR H 354 PHE 0.011 0.001 PHE F 303 TRP 0.007 0.001 TRP C 46 HIS 0.006 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00399 (23336) covalent geometry : angle 0.59440 (31864) hydrogen bonds : bond 0.03050 ( 999) hydrogen bonds : angle 4.24700 ( 2741) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 171 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 354 TYR cc_start: 0.7986 (t80) cc_final: 0.7477 (t80) REVERT: F 354 TYR cc_start: 0.8162 (t80) cc_final: 0.7655 (t80) REVERT: G 354 TYR cc_start: 0.8074 (t80) cc_final: 0.7612 (t80) REVERT: H 227 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: H 354 TYR cc_start: 0.7441 (t80) cc_final: 0.7114 (t80) outliers start: 31 outliers final: 3 residues processed: 171 average time/residue: 1.2798 time to fit residues: 249.7560 Evaluate side-chains 147 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain H residue 227 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 4 optimal weight: 0.5980 chunk 199 optimal weight: 0.6980 chunk 281 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 284 optimal weight: 9.9990 chunk 261 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 255 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.118356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.074887 restraints weight = 339561.832| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 4.85 r_work: 0.2651 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2698 r_free = 0.2698 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23336 Z= 0.116 Angle : 0.579 5.580 31864 Z= 0.273 Chirality : 0.040 0.126 3592 Planarity : 0.004 0.040 4184 Dihedral : 5.061 43.673 3444 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.34 % Allowed : 21.12 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.42 (0.16), residues: 3040 helix: 2.09 (0.17), residues: 1112 sheet: -1.07 (0.23), residues: 448 loop : -0.68 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 125 TYR 0.009 0.001 TYR D 354 PHE 0.010 0.001 PHE H 303 TRP 0.005 0.001 TRP G 46 HIS 0.005 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00272 (23336) covalent geometry : angle 0.57943 (31864) hydrogen bonds : bond 0.02835 ( 999) hydrogen bonds : angle 4.17356 ( 2741) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 181 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8091 (t80) cc_final: 0.7546 (t80) REVERT: E 354 TYR cc_start: 0.7966 (t80) cc_final: 0.7494 (t80) REVERT: F 354 TYR cc_start: 0.8182 (t80) cc_final: 0.7704 (t80) REVERT: G 354 TYR cc_start: 0.8096 (t80) cc_final: 0.7642 (t80) REVERT: H 354 TYR cc_start: 0.7504 (t80) cc_final: 0.7175 (t80) outliers start: 30 outliers final: 4 residues processed: 181 average time/residue: 1.3079 time to fit residues: 273.8586 Evaluate side-chains 145 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 87 optimal weight: 0.5980 chunk 139 optimal weight: 10.0000 chunk 270 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 265 optimal weight: 0.0570 chunk 108 optimal weight: 1.9990 chunk 193 optimal weight: 0.5980 overall best weight: 1.0502 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.118683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.075143 restraints weight = 343197.913| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 4.89 r_work: 0.2657 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23336 Z= 0.111 Angle : 0.574 5.566 31864 Z= 0.270 Chirality : 0.040 0.125 3592 Planarity : 0.004 0.041 4184 Dihedral : 4.988 43.993 3444 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.98 % Allowed : 21.38 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.45 (0.16), residues: 3040 helix: 2.14 (0.17), residues: 1112 sheet: -1.04 (0.23), residues: 448 loop : -0.70 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 125 TYR 0.010 0.001 TYR D 354 PHE 0.010 0.001 PHE F 187 TRP 0.005 0.001 TRP G 46 HIS 0.005 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00261 (23336) covalent geometry : angle 0.57397 (31864) hydrogen bonds : bond 0.02723 ( 999) hydrogen bonds : angle 4.14993 ( 2741) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 169 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.918 Fit side-chains revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8109 (t80) cc_final: 0.7623 (t80) REVERT: D 354 TYR cc_start: 0.7347 (t80) cc_final: 0.7042 (t80) REVERT: E 354 TYR cc_start: 0.7939 (t80) cc_final: 0.7462 (t80) REVERT: F 354 TYR cc_start: 0.8184 (t80) cc_final: 0.7710 (t80) REVERT: G 354 TYR cc_start: 0.8084 (t80) cc_final: 0.7628 (t80) REVERT: H 354 TYR cc_start: 0.7549 (t80) cc_final: 0.7220 (t80) outliers start: 22 outliers final: 4 residues processed: 168 average time/residue: 1.3402 time to fit residues: 258.5489 Evaluate side-chains 145 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain F residue 292 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 215 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 249 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 262 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.116327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.072656 restraints weight = 335390.081| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 4.81 r_work: 0.2612 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 23336 Z= 0.262 Angle : 0.619 5.627 31864 Z= 0.300 Chirality : 0.042 0.121 3592 Planarity : 0.004 0.043 4184 Dihedral : 5.206 44.382 3444 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.39 % Favored : 93.48 % Rotamer: Outliers : 1.25 % Allowed : 21.34 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.23 (0.16), residues: 3040 helix: 1.88 (0.16), residues: 1112 sheet: -1.16 (0.23), residues: 448 loop : -0.74 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 210 TYR 0.009 0.001 TYR C 34 PHE 0.014 0.002 PHE B 187 TRP 0.007 0.001 TRP H 46 HIS 0.007 0.002 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00603 (23336) covalent geometry : angle 0.61887 (31864) hydrogen bonds : bond 0.03268 ( 999) hydrogen bonds : angle 4.33170 ( 2741) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 168 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 354 TYR cc_start: 0.7415 (t80) cc_final: 0.7094 (t80) REVERT: E 354 TYR cc_start: 0.7996 (t80) cc_final: 0.7523 (t80) REVERT: F 354 TYR cc_start: 0.8177 (t80) cc_final: 0.7682 (t80) REVERT: G 354 TYR cc_start: 0.8103 (t80) cc_final: 0.7680 (t80) REVERT: H 354 TYR cc_start: 0.7586 (t80) cc_final: 0.7248 (t80) outliers start: 28 outliers final: 12 residues processed: 161 average time/residue: 1.3985 time to fit residues: 258.4484 Evaluate side-chains 148 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 355 LEU Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain H residue 39 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 287 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 246 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.117526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.073865 restraints weight = 339895.018| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 4.85 r_work: 0.2632 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23336 Z= 0.159 Angle : 0.592 5.549 31864 Z= 0.282 Chirality : 0.041 0.124 3592 Planarity : 0.004 0.040 4184 Dihedral : 5.155 44.513 3444 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 1.07 % Allowed : 21.74 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.32 (0.16), residues: 3040 helix: 2.00 (0.16), residues: 1112 sheet: -1.11 (0.23), residues: 448 loop : -0.74 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 125 TYR 0.006 0.001 TYR D 354 PHE 0.012 0.001 PHE D 187 TRP 0.006 0.001 TRP E 46 HIS 0.006 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00371 (23336) covalent geometry : angle 0.59244 (31864) hydrogen bonds : bond 0.02964 ( 999) hydrogen bonds : angle 4.23950 ( 2741) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 162 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8140 (t80) cc_final: 0.7641 (t80) REVERT: D 354 TYR cc_start: 0.7421 (t80) cc_final: 0.7120 (t80) REVERT: E 354 TYR cc_start: 0.7977 (t80) cc_final: 0.7536 (t80) REVERT: F 354 TYR cc_start: 0.8205 (t80) cc_final: 0.7750 (t80) REVERT: G 354 TYR cc_start: 0.8095 (t80) cc_final: 0.7677 (t80) REVERT: H 354 TYR cc_start: 0.7621 (t80) cc_final: 0.7250 (t80) outliers start: 24 outliers final: 8 residues processed: 162 average time/residue: 1.4868 time to fit residues: 277.3468 Evaluate side-chains 144 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain H residue 292 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 9 optimal weight: 4.9990 chunk 257 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 256 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 105 optimal weight: 0.0040 chunk 253 optimal weight: 0.6980 chunk 208 optimal weight: 4.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.118957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.075398 restraints weight = 341328.358| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 4.89 r_work: 0.2662 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 23336 Z= 0.100 Angle : 0.576 5.574 31864 Z= 0.270 Chirality : 0.039 0.128 3592 Planarity : 0.004 0.039 4184 Dihedral : 4.968 44.847 3444 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.15 % Rotamer: Outliers : 0.76 % Allowed : 22.14 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.48 (0.16), residues: 3040 helix: 2.19 (0.17), residues: 1112 sheet: -1.01 (0.23), residues: 448 loop : -0.70 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 125 TYR 0.005 0.001 TYR A 34 PHE 0.009 0.001 PHE D 187 TRP 0.004 0.001 TRP C 46 HIS 0.005 0.001 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00233 (23336) covalent geometry : angle 0.57555 (31864) hydrogen bonds : bond 0.02672 ( 999) hydrogen bonds : angle 4.12963 ( 2741) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 161 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8127 (t80) cc_final: 0.7629 (t80) REVERT: D 354 TYR cc_start: 0.7462 (t80) cc_final: 0.7160 (t80) REVERT: E 354 TYR cc_start: 0.7963 (t80) cc_final: 0.7521 (t80) REVERT: F 354 TYR cc_start: 0.8201 (t80) cc_final: 0.7745 (t80) REVERT: G 354 TYR cc_start: 0.8073 (t80) cc_final: 0.7664 (t80) REVERT: H 354 TYR cc_start: 0.7628 (t80) cc_final: 0.7245 (t80) outliers start: 17 outliers final: 9 residues processed: 161 average time/residue: 1.6038 time to fit residues: 293.0642 Evaluate side-chains 151 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain H residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 240 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 269 optimal weight: 0.0270 chunk 83 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.118598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.074800 restraints weight = 344139.612| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 4.92 r_work: 0.2650 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23336 Z= 0.127 Angle : 0.580 5.601 31864 Z= 0.272 Chirality : 0.040 0.125 3592 Planarity : 0.004 0.039 4184 Dihedral : 4.952 45.121 3444 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.99 % Favored : 94.98 % Rotamer: Outliers : 0.80 % Allowed : 22.23 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.46 (0.16), residues: 3040 helix: 2.16 (0.16), residues: 1112 sheet: -1.00 (0.23), residues: 448 loop : -0.71 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 231 TYR 0.006 0.001 TYR C 34 PHE 0.012 0.001 PHE C 187 TRP 0.005 0.001 TRP G 46 HIS 0.009 0.001 HIS E 186 Details of bonding type rmsd covalent geometry : bond 0.00299 (23336) covalent geometry : angle 0.57996 (31864) hydrogen bonds : bond 0.02719 ( 999) hydrogen bonds : angle 4.14612 ( 2741) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 LYS 65 is missing expected H atoms. Skipping. Residue THR 99 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 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 160 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 TYR cc_start: 0.8133 (t80) cc_final: 0.7635 (t80) REVERT: D 354 TYR cc_start: 0.7487 (t80) cc_final: 0.7184 (t80) REVERT: E 354 TYR cc_start: 0.7944 (t80) cc_final: 0.7500 (t80) REVERT: F 354 TYR cc_start: 0.8207 (t80) cc_final: 0.7761 (t80) REVERT: G 354 TYR cc_start: 0.8081 (t80) cc_final: 0.7673 (t80) REVERT: H 354 TYR cc_start: 0.7650 (t80) cc_final: 0.7259 (t80) outliers start: 18 outliers final: 9 residues processed: 160 average time/residue: 1.3555 time to fit residues: 247.3663 Evaluate side-chains 146 residues out of total 2464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain G residue 292 ILE Chi-restraints excluded: chain H residue 292 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 278 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 272 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 154 optimal weight: 0.0070 chunk 180 optimal weight: 0.6980 chunk 256 optimal weight: 0.0070 chunk 6 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.9218 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.119140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.075670 restraints weight = 324840.769| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 4.80 r_work: 0.2667 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23336 Z= 0.104 Angle : 0.574 5.634 31864 Z= 0.268 Chirality : 0.040 0.127 3592 Planarity : 0.004 0.039 4184 Dihedral : 4.868 45.398 3444 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.51 % Favored : 95.42 % Rotamer: Outliers : 0.49 % Allowed : 22.81 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.51 (0.16), residues: 3040 helix: 2.22 (0.16), residues: 1112 sheet: -0.99 (0.23), residues: 448 loop : -0.68 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 204 TYR 0.005 0.001 TYR F 34 PHE 0.011 0.001 PHE E 187 TRP 0.005 0.001 TRP G 46 HIS 0.005 0.001 HIS F 214 Details of bonding type rmsd covalent geometry : bond 0.00246 (23336) covalent geometry : angle 0.57441 (31864) hydrogen bonds : bond 0.02616 ( 999) hydrogen bonds : angle 4.11083 ( 2741) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14411.33 seconds wall clock time: 244 minutes 8.74 seconds (14648.74 seconds total)