Starting phenix.real_space_refine on Sat Aug 23 23:51:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmq_40230/08_2025/8gmq_40230_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmq_40230/08_2025/8gmq_40230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gmq_40230/08_2025/8gmq_40230_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmq_40230/08_2025/8gmq_40230_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gmq_40230/08_2025/8gmq_40230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmq_40230/08_2025/8gmq_40230.map" } resolution = 3.36 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= -0.018 sd= 0.372 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 144 5.16 5 C 9552 2.51 5 N 2408 2.21 5 O 2488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 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: 14600 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1773 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 1.43, per 1000 atoms: 0.10 Number of scatterers: 14600 At special positions: 0 Unit cell: (127.544, 127.544, 101.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 8 15.00 O 2488 8.00 N 2408 7.00 C 9552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.03 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: 1.27 Conformation dependent library (CDL) restraints added in 638.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 69.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.983A pdb=" N ALA A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 70 removed outlier: 3.666A pdb=" N LEU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 3.712A pdb=" N PHE A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 69 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.599A pdb=" N LEU A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 117 removed outlier: 3.746A pdb=" N GLN A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.959A pdb=" N CYS A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 removed outlier: 4.333A pdb=" N LEU A 137 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 155 Processing helix chain 'A' and resid 170 through 201 removed outlier: 3.509A pdb=" N VAL A 175 " --> pdb=" O ASN A 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 176 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A 183 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 249 removed outlier: 3.742A pdb=" N LYS A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS A 244 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE A 248 " --> pdb=" O CYS A 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 37 removed outlier: 4.051A pdb=" N TYR B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 70 removed outlier: 3.666A pdb=" N LEU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 3.711A pdb=" N PHE B 68 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.599A pdb=" N LEU B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 117 removed outlier: 3.746A pdb=" N GLN B 104 " --> pdb=" O CYS B 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE B 108 " --> pdb=" O GLN B 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Proline residue: B 110 - end of helix Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.958A pdb=" N CYS B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 138 removed outlier: 4.333A pdb=" N LEU B 137 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 155 Processing helix chain 'B' and resid 170 through 201 removed outlier: 3.510A pdb=" N VAL B 175 " --> pdb=" O ASN B 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 183 " --> pdb=" O ARG B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 249 removed outlier: 3.741A pdb=" N LYS B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 215 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS B 242 " --> pdb=" O LYS B 238 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS B 244 " --> pdb=" O PHE B 240 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN B 247 " --> pdb=" O VAL B 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE B 248 " --> pdb=" O CYS B 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 removed outlier: 4.051A pdb=" N TYR C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 70 removed outlier: 3.666A pdb=" N LEU C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 3.712A pdb=" N PHE C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 82 removed outlier: 3.599A pdb=" N LEU C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 117 removed outlier: 3.746A pdb=" N GLN C 104 " --> pdb=" O CYS C 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE C 108 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Proline residue: C 110 - end of helix Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.959A pdb=" N CYS C 126 " --> pdb=" O LYS C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 138 removed outlier: 4.333A pdb=" N LEU C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 155 Processing helix chain 'C' and resid 170 through 201 removed outlier: 3.509A pdb=" N VAL C 175 " --> pdb=" O ASN C 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG C 176 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C 183 " --> pdb=" O ARG C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 249 removed outlier: 3.742A pdb=" N LYS C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 215 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 226 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS C 244 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN C 247 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE C 248 " --> pdb=" O CYS C 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE C 249 " --> pdb=" O ILE C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 37 removed outlier: 4.050A pdb=" N TYR D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER D 35 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 70 removed outlier: 3.666A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 3.712A pdb=" N PHE D 68 " --> pdb=" O PHE D 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 69 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 82 removed outlier: 3.599A pdb=" N LEU D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 117 removed outlier: 3.747A pdb=" N GLN D 104 " --> pdb=" O CYS D 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE D 108 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Proline residue: D 110 - end of helix Processing helix chain 'D' and resid 121 through 126 removed outlier: 3.958A pdb=" N CYS D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 138 removed outlier: 4.332A pdb=" N LEU D 137 " --> pdb=" O PRO D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 Processing helix chain 'D' and resid 170 through 201 removed outlier: 3.510A pdb=" N VAL D 175 " --> pdb=" O ASN D 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 176 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 249 removed outlier: 3.741A pdb=" N LYS D 214 " --> pdb=" O ALA D 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER D 215 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS D 242 " --> pdb=" O LYS D 238 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS D 244 " --> pdb=" O PHE D 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN D 247 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE D 248 " --> pdb=" O CYS D 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 37 removed outlier: 4.051A pdb=" N TYR E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER E 35 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 70 removed outlier: 3.666A pdb=" N LEU E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Proline residue: E 59 - end of helix removed outlier: 3.712A pdb=" N PHE E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 70 " --> pdb=" O LEU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 82 removed outlier: 3.599A pdb=" N LEU E 77 " --> pdb=" O ASN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 117 removed outlier: 3.746A pdb=" N GLN E 104 " --> pdb=" O CYS E 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE E 108 " --> pdb=" O GLN E 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Proline residue: E 110 - end of helix Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.959A pdb=" N CYS E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 138 removed outlier: 4.333A pdb=" N LEU E 137 " --> pdb=" O PRO E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 155 Processing helix chain 'E' and resid 170 through 201 removed outlier: 3.509A pdb=" N VAL E 175 " --> pdb=" O ASN E 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG E 176 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN E 183 " --> pdb=" O ARG E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 249 removed outlier: 3.742A pdb=" N LYS E 214 " --> pdb=" O ALA E 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER E 215 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG E 226 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS E 242 " --> pdb=" O LYS E 238 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N CYS E 244 " --> pdb=" O PHE E 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 246 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN E 247 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE E 248 " --> pdb=" O CYS E 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE E 249 " --> pdb=" O ILE E 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 37 removed outlier: 4.051A pdb=" N TYR F 34 " --> pdb=" O SER F 30 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 70 removed outlier: 3.666A pdb=" N LEU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Proline residue: F 59 - end of helix removed outlier: 3.712A pdb=" N PHE F 68 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL F 69 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 70 " --> pdb=" O LEU F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 82 removed outlier: 3.599A pdb=" N LEU F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 117 removed outlier: 3.747A pdb=" N GLN F 104 " --> pdb=" O CYS F 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE F 108 " --> pdb=" O GLN F 104 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Proline residue: F 110 - end of helix Processing helix chain 'F' and resid 121 through 126 removed outlier: 3.958A pdb=" N CYS F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 138 removed outlier: 4.333A pdb=" N LEU F 137 " --> pdb=" O PRO F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 155 Processing helix chain 'F' and resid 170 through 201 removed outlier: 3.510A pdb=" N VAL F 175 " --> pdb=" O ASN F 171 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG F 176 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 249 removed outlier: 3.741A pdb=" N LYS F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER F 215 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 226 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL F 243 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS F 244 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLN F 247 " --> pdb=" O VAL F 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE F 248 " --> pdb=" O CYS F 244 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE F 249 " --> pdb=" O ILE F 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 37 removed outlier: 4.051A pdb=" N TYR G 34 " --> pdb=" O SER G 30 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER G 35 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA G 36 " --> pdb=" O GLN G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 70 removed outlier: 3.666A pdb=" N LEU G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Proline residue: G 59 - end of helix removed outlier: 3.712A pdb=" N PHE G 68 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU G 70 " --> pdb=" O LEU G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 82 removed outlier: 3.600A pdb=" N LEU G 77 " --> pdb=" O ASN G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 117 removed outlier: 3.746A pdb=" N GLN G 104 " --> pdb=" O CYS G 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE G 108 " --> pdb=" O GLN G 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) Proline residue: G 110 - end of helix Processing helix chain 'G' and resid 121 through 126 removed outlier: 3.959A pdb=" N CYS G 126 " --> pdb=" O LYS G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 138 removed outlier: 4.332A pdb=" N LEU G 137 " --> pdb=" O PRO G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 155 Processing helix chain 'G' and resid 170 through 201 removed outlier: 3.509A pdb=" N VAL G 175 " --> pdb=" O ASN G 171 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG G 176 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN G 183 " --> pdb=" O ARG G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 249 removed outlier: 3.742A pdb=" N LYS G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER G 215 " --> pdb=" O VAL G 211 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N HIS G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG G 226 " --> pdb=" O ILE G 222 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR G 232 " --> pdb=" O LEU G 228 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER G 239 " --> pdb=" O GLU G 235 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS G 242 " --> pdb=" O LYS G 238 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL G 243 " --> pdb=" O SER G 239 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS G 244 " --> pdb=" O PHE G 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN G 246 " --> pdb=" O LYS G 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN G 247 " --> pdb=" O VAL G 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE G 248 " --> pdb=" O CYS G 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE G 249 " --> pdb=" O ILE G 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 37 removed outlier: 4.050A pdb=" N TYR H 34 " --> pdb=" O SER H 30 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER H 35 " --> pdb=" O ALA H 31 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA H 36 " --> pdb=" O GLN H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 70 removed outlier: 3.666A pdb=" N LEU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Proline residue: H 59 - end of helix removed outlier: 3.712A pdb=" N PHE H 68 " --> pdb=" O PHE H 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL H 69 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU H 70 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 82 removed outlier: 3.598A pdb=" N LEU H 77 " --> pdb=" O ASN H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 117 removed outlier: 3.747A pdb=" N GLN H 104 " --> pdb=" O CYS H 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ALA H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 121 through 126 removed outlier: 3.959A pdb=" N CYS H 126 " --> pdb=" O LYS H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 138 removed outlier: 4.332A pdb=" N LEU H 137 " --> pdb=" O PRO H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 155 Processing helix chain 'H' and resid 170 through 201 removed outlier: 3.510A pdb=" N VAL H 175 " --> pdb=" O ASN H 171 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG H 176 " --> pdb=" O GLU H 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN H 183 " --> pdb=" O ARG H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 249 removed outlier: 3.742A pdb=" N LYS H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER H 215 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS H 220 " --> pdb=" O ARG H 216 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG H 226 " --> pdb=" O ILE H 222 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER H 239 " --> pdb=" O GLU H 235 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS H 242 " --> pdb=" O LYS H 238 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL H 243 " --> pdb=" O SER H 239 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N CYS H 244 " --> pdb=" O PHE H 240 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN H 246 " --> pdb=" O LYS H 242 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN H 247 " --> pdb=" O VAL H 243 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE H 248 " --> pdb=" O CYS H 244 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE H 249 " --> pdb=" O ILE H 245 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2160 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: 1.85 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2200 1.31 - 1.44: 4032 1.44 - 1.56: 8488 1.56 - 1.69: 16 1.69 - 1.81: 192 Bond restraints: 14928 Sorted by residual: bond pdb=" C21 POV A 401 " pdb=" O21 POV A 401 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 POV C 401 " pdb=" O21 POV C 401 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 POV E 401 " pdb=" O21 POV E 401 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 POV F 401 " pdb=" O21 POV F 401 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C21 POV G 401 " pdb=" O21 POV G 401 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 ... (remaining 14923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 19687 2.35 - 4.69: 435 4.69 - 7.04: 86 7.04 - 9.38: 16 9.38 - 11.73: 32 Bond angle restraints: 20256 Sorted by residual: angle pdb=" N ARG D 204 " pdb=" CA ARG D 204 " pdb=" C ARG D 204 " ideal model delta sigma weight residual 109.81 121.43 -11.62 2.21e+00 2.05e-01 2.77e+01 angle pdb=" N ARG G 204 " pdb=" CA ARG G 204 " pdb=" C ARG G 204 " ideal model delta sigma weight residual 109.81 121.42 -11.61 2.21e+00 2.05e-01 2.76e+01 angle pdb=" N ARG E 204 " pdb=" CA ARG E 204 " pdb=" C ARG E 204 " ideal model delta sigma weight residual 109.81 121.40 -11.59 2.21e+00 2.05e-01 2.75e+01 angle pdb=" N ARG A 204 " pdb=" CA ARG A 204 " pdb=" C ARG A 204 " ideal model delta sigma weight residual 109.81 121.40 -11.59 2.21e+00 2.05e-01 2.75e+01 angle pdb=" N ARG C 204 " pdb=" CA ARG C 204 " pdb=" C ARG C 204 " ideal model delta sigma weight residual 109.81 121.40 -11.59 2.21e+00 2.05e-01 2.75e+01 ... (remaining 20251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.42: 8366 24.42 - 48.83: 458 48.83 - 73.25: 96 73.25 - 97.66: 32 97.66 - 122.08: 8 Dihedral angle restraints: 8960 sinusoidal: 3464 harmonic: 5496 Sorted by residual: dihedral pdb=" CA ARG B 204 " pdb=" C ARG B 204 " pdb=" N PRO B 205 " pdb=" CA PRO B 205 " ideal model delta harmonic sigma weight residual -180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ARG H 204 " pdb=" C ARG H 204 " pdb=" N PRO H 205 " pdb=" CA PRO H 205 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA ARG A 204 " pdb=" C ARG A 204 " pdb=" N PRO A 205 " pdb=" CA PRO A 205 " ideal model delta harmonic sigma weight residual -180.00 -158.64 -21.36 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 8957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1758 0.042 - 0.084: 498 0.084 - 0.126: 64 0.126 - 0.168: 0 0.168 - 0.210: 8 Chirality restraints: 2328 Sorted by residual: chirality pdb=" CA ARG F 204 " pdb=" N ARG F 204 " pdb=" C ARG F 204 " pdb=" CB ARG F 204 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ARG D 204 " pdb=" N ARG D 204 " pdb=" C ARG D 204 " pdb=" CB ARG D 204 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ARG G 204 " pdb=" N ARG G 204 " pdb=" C ARG G 204 " pdb=" CB ARG G 204 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2325 not shown) Planarity restraints: 2504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 59 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO A 60 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 59 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO E 60 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 60 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 60 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 59 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO C 60 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " -0.030 5.00e-02 4.00e+02 ... (remaining 2501 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3351 2.77 - 3.30: 15050 3.30 - 3.83: 20591 3.83 - 4.37: 23767 4.37 - 4.90: 40255 Nonbonded interactions: 103014 Sorted by model distance: nonbonded pdb=" NE2 HIS B 142 " pdb=" O LEU B 145 " model vdw 2.236 3.120 nonbonded pdb=" NE2 HIS D 142 " pdb=" O LEU D 145 " model vdw 2.236 3.120 nonbonded pdb=" NE2 HIS H 142 " pdb=" O LEU H 145 " model vdw 2.236 3.120 nonbonded pdb=" NE2 HIS G 142 " pdb=" O LEU G 145 " model vdw 2.236 3.120 nonbonded pdb=" NE2 HIS F 142 " pdb=" O LEU F 145 " model vdw 2.237 3.120 ... (remaining 103009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.750 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 : 0.008 0.096 14936 Z= 0.357 Angle : 0.965 11.725 20272 Z= 0.454 Chirality : 0.039 0.210 2328 Planarity : 0.005 0.054 2504 Dihedral : 16.898 122.076 5368 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.10 (0.15), residues: 1856 helix: -3.49 (0.09), residues: 1152 sheet: None (None), residues: 0 loop : -2.89 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 201 TYR 0.012 0.002 TYR D 221 PHE 0.010 0.002 PHE D 207 TRP 0.007 0.001 TRP C 113 HIS 0.003 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00774 (14928) covalent geometry : angle 0.96379 (20256) SS BOND : bond 0.00531 ( 8) SS BOND : angle 1.99752 ( 16) hydrogen bonds : bond 0.31735 ( 720) hydrogen bonds : angle 9.29546 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.350 Fit side-chains REVERT: A 96 ARG cc_start: 0.8836 (mtp180) cc_final: 0.8629 (ttp-110) REVERT: A 216 ARG cc_start: 0.9391 (tpp80) cc_final: 0.8793 (tpt-90) REVERT: A 231 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8165 (tm-30) REVERT: A 235 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 244 CYS cc_start: 0.8697 (t) cc_final: 0.8353 (t) REVERT: B 46 ARG cc_start: 0.8636 (mtp180) cc_final: 0.8422 (mtp85) REVERT: B 96 ARG cc_start: 0.8832 (mtp180) cc_final: 0.8602 (ttm110) REVERT: B 216 ARG cc_start: 0.9386 (tpp80) cc_final: 0.9040 (ttt90) REVERT: B 231 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8180 (tm-30) REVERT: B 235 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8288 (tm-30) REVERT: C 96 ARG cc_start: 0.8836 (mtp180) cc_final: 0.8627 (ttp-110) REVERT: C 216 ARG cc_start: 0.9393 (tpp80) cc_final: 0.8813 (tpt-90) REVERT: C 231 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 235 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8232 (tm-30) REVERT: C 244 CYS cc_start: 0.8709 (t) cc_final: 0.8367 (t) REVERT: D 46 ARG cc_start: 0.8639 (mtp180) cc_final: 0.8416 (mtp85) REVERT: D 96 ARG cc_start: 0.8835 (mtp180) cc_final: 0.8598 (ttm110) REVERT: D 216 ARG cc_start: 0.9401 (tpp80) cc_final: 0.9059 (ttt90) REVERT: D 231 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8182 (tm-30) REVERT: D 235 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8297 (tm-30) REVERT: E 96 ARG cc_start: 0.8833 (mtp180) cc_final: 0.8590 (ttm-80) REVERT: E 216 ARG cc_start: 0.9391 (tpp80) cc_final: 0.8811 (tpt-90) REVERT: E 231 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8158 (tm-30) REVERT: E 235 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8236 (tm-30) REVERT: E 244 CYS cc_start: 0.8705 (t) cc_final: 0.8357 (t) REVERT: F 96 ARG cc_start: 0.8837 (mtp180) cc_final: 0.8627 (ttm110) REVERT: F 105 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7745 (ttm-80) REVERT: F 216 ARG cc_start: 0.9412 (tpp80) cc_final: 0.9059 (ttt90) REVERT: F 231 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8166 (tm-30) REVERT: F 235 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8306 (tm-30) REVERT: G 96 ARG cc_start: 0.8824 (mtp180) cc_final: 0.8587 (ttm-80) REVERT: G 216 ARG cc_start: 0.9389 (tpp80) cc_final: 0.8807 (tpt-90) REVERT: G 231 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8171 (tm-30) REVERT: G 235 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8233 (tm-30) REVERT: G 244 CYS cc_start: 0.8710 (t) cc_final: 0.8368 (t) REVERT: H 96 ARG cc_start: 0.8826 (mtp180) cc_final: 0.8599 (ttm110) REVERT: H 216 ARG cc_start: 0.9390 (tpp80) cc_final: 0.9041 (ttt90) REVERT: H 230 ASP cc_start: 0.8457 (m-30) cc_final: 0.8179 (m-30) REVERT: H 231 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8176 (tm-30) REVERT: H 235 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8296 (tm-30) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.1215 time to fit residues: 64.9671 Evaluate side-chains 307 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 ASN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 73 ASN ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.086937 restraints weight = 28737.182| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 3.82 r_work: 0.2910 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14936 Z= 0.164 Angle : 0.698 10.750 20272 Z= 0.364 Chirality : 0.042 0.185 2328 Planarity : 0.006 0.055 2504 Dihedral : 13.187 115.820 2360 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.73 % Allowed : 12.22 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.19), residues: 1856 helix: -1.26 (0.14), residues: 1128 sheet: None (None), residues: 0 loop : -2.58 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 46 TYR 0.009 0.001 TYR G 177 PHE 0.005 0.001 PHE F 240 TRP 0.006 0.001 TRP D 218 HIS 0.001 0.000 HIS G 143 Details of bonding type rmsd covalent geometry : bond 0.00344 (14928) covalent geometry : angle 0.69814 (20256) SS BOND : bond 0.00221 ( 8) SS BOND : angle 1.05220 ( 16) hydrogen bonds : bond 0.08000 ( 720) hydrogen bonds : angle 4.70095 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 353 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8970 (tp30) cc_final: 0.8437 (tp30) REVERT: A 146 PRO cc_start: 0.7240 (Cg_exo) cc_final: 0.6970 (Cg_endo) REVERT: A 231 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8208 (tm-30) REVERT: A 235 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8061 (tm-30) REVERT: A 246 GLN cc_start: 0.8347 (mm110) cc_final: 0.7211 (tm-30) REVERT: B 80 GLU cc_start: 0.8769 (tp30) cc_final: 0.8498 (tp30) REVERT: B 244 CYS cc_start: 0.8869 (t) cc_final: 0.8504 (t) REVERT: B 246 GLN cc_start: 0.8367 (mm110) cc_final: 0.7244 (tm-30) REVERT: C 80 GLU cc_start: 0.8954 (tp30) cc_final: 0.8414 (tp30) REVERT: C 146 PRO cc_start: 0.7220 (Cg_exo) cc_final: 0.6955 (Cg_endo) REVERT: C 231 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8203 (tm-30) REVERT: C 235 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8050 (tm-30) REVERT: C 246 GLN cc_start: 0.8353 (mm110) cc_final: 0.7216 (tm-30) REVERT: D 80 GLU cc_start: 0.8762 (tp30) cc_final: 0.8496 (tp30) REVERT: D 244 CYS cc_start: 0.8847 (t) cc_final: 0.8478 (t) REVERT: D 246 GLN cc_start: 0.8360 (mm110) cc_final: 0.7261 (tm-30) REVERT: E 80 GLU cc_start: 0.8974 (tp30) cc_final: 0.8437 (tp30) REVERT: E 146 PRO cc_start: 0.7223 (Cg_exo) cc_final: 0.6964 (Cg_endo) REVERT: E 231 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8213 (tm-30) REVERT: E 235 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8050 (tm-30) REVERT: E 246 GLN cc_start: 0.8351 (mm110) cc_final: 0.7220 (tm-30) REVERT: F 80 GLU cc_start: 0.8626 (tp30) cc_final: 0.8400 (tp30) REVERT: F 120 ASP cc_start: 0.9192 (m-30) cc_final: 0.8911 (m-30) REVERT: F 196 LEU cc_start: 0.8610 (tp) cc_final: 0.8385 (tt) REVERT: F 244 CYS cc_start: 0.8837 (t) cc_final: 0.8454 (t) REVERT: F 246 GLN cc_start: 0.8426 (mm110) cc_final: 0.7369 (tm-30) REVERT: G 80 GLU cc_start: 0.8957 (tp30) cc_final: 0.8421 (tp30) REVERT: G 146 PRO cc_start: 0.7219 (Cg_exo) cc_final: 0.6961 (Cg_endo) REVERT: G 231 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8196 (tm-30) REVERT: G 235 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8047 (tm-30) REVERT: G 246 GLN cc_start: 0.8370 (mm110) cc_final: 0.7238 (tm-30) REVERT: H 80 GLU cc_start: 0.8761 (tp30) cc_final: 0.8498 (tp30) REVERT: H 244 CYS cc_start: 0.8870 (t) cc_final: 0.8495 (t) REVERT: H 246 GLN cc_start: 0.8375 (mm110) cc_final: 0.7258 (tm-30) outliers start: 25 outliers final: 20 residues processed: 354 average time/residue: 0.0919 time to fit residues: 51.8667 Evaluate side-chains 331 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 311 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 55 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 105 optimal weight: 0.0170 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 172 optimal weight: 40.0000 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 HIS C 40 ASN ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 HIS E 40 ASN ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 HIS G 40 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 220 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.089163 restraints weight = 29097.827| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.86 r_work: 0.2956 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14936 Z= 0.136 Angle : 0.629 10.042 20272 Z= 0.325 Chirality : 0.039 0.163 2328 Planarity : 0.005 0.056 2504 Dihedral : 11.685 123.873 2360 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 4.77 % Allowed : 15.12 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.20), residues: 1856 helix: 0.10 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -2.84 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 46 TYR 0.011 0.001 TYR H 177 PHE 0.006 0.001 PHE F 207 TRP 0.009 0.001 TRP A 218 HIS 0.001 0.000 HIS F 236 Details of bonding type rmsd covalent geometry : bond 0.00305 (14928) covalent geometry : angle 0.62900 (20256) SS BOND : bond 0.00092 ( 8) SS BOND : angle 0.79300 ( 16) hydrogen bonds : bond 0.05921 ( 720) hydrogen bonds : angle 3.91025 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 328 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9004 (tp30) cc_final: 0.8386 (tp30) REVERT: A 90 LYS cc_start: 0.8703 (mmmm) cc_final: 0.8045 (mmtt) REVERT: A 231 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 235 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 246 GLN cc_start: 0.8116 (mm110) cc_final: 0.7105 (tm-30) REVERT: B 80 GLU cc_start: 0.8731 (tp30) cc_final: 0.8333 (tp30) REVERT: B 242 LYS cc_start: 0.7879 (tmtt) cc_final: 0.7655 (tmtt) REVERT: C 80 GLU cc_start: 0.8999 (tp30) cc_final: 0.8377 (tp30) REVERT: C 90 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8026 (mmtt) REVERT: C 231 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 235 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8118 (tm-30) REVERT: C 246 GLN cc_start: 0.8114 (mm110) cc_final: 0.7102 (tm-30) REVERT: D 80 GLU cc_start: 0.8722 (tp30) cc_final: 0.8333 (tp30) REVERT: D 242 LYS cc_start: 0.7893 (tmtt) cc_final: 0.7672 (tmtt) REVERT: E 80 GLU cc_start: 0.9018 (tp30) cc_final: 0.8398 (tp30) REVERT: E 90 LYS cc_start: 0.8710 (mmmm) cc_final: 0.8040 (mmtt) REVERT: E 231 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8227 (tm-30) REVERT: E 235 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8115 (tm-30) REVERT: E 246 GLN cc_start: 0.8127 (mm110) cc_final: 0.7109 (tm-30) REVERT: F 80 GLU cc_start: 0.8629 (tp30) cc_final: 0.8328 (tp30) REVERT: F 196 LEU cc_start: 0.8629 (tp) cc_final: 0.8298 (tt) REVERT: F 244 CYS cc_start: 0.8795 (t) cc_final: 0.8495 (t) REVERT: G 80 GLU cc_start: 0.9001 (tp30) cc_final: 0.8378 (tp30) REVERT: G 90 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8037 (mmtt) REVERT: G 231 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8240 (tm-30) REVERT: G 235 GLU cc_start: 0.8438 (tm-30) cc_final: 0.8105 (tm-30) REVERT: G 246 GLN cc_start: 0.8132 (mm110) cc_final: 0.7127 (tm-30) REVERT: H 80 GLU cc_start: 0.8718 (tp30) cc_final: 0.8324 (tp30) REVERT: H 242 LYS cc_start: 0.7883 (tmtt) cc_final: 0.7659 (tmtt) outliers start: 69 outliers final: 37 residues processed: 356 average time/residue: 0.1011 time to fit residues: 55.6845 Evaluate side-chains 330 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 293 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 chunk 126 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 40 ASN E 40 ASN ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.127211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.100488 restraints weight = 28741.553| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.82 r_work: 0.2953 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14936 Z= 0.198 Angle : 0.688 10.843 20272 Z= 0.351 Chirality : 0.041 0.182 2328 Planarity : 0.005 0.056 2504 Dihedral : 11.462 128.559 2360 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.73 % Favored : 91.27 % Rotamer: Outliers : 4.70 % Allowed : 17.54 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.20), residues: 1856 helix: 0.41 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -2.71 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 105 TYR 0.016 0.002 TYR D 177 PHE 0.008 0.001 PHE F 207 TRP 0.007 0.001 TRP G 218 HIS 0.002 0.001 HIS F 143 Details of bonding type rmsd covalent geometry : bond 0.00477 (14928) covalent geometry : angle 0.68516 (20256) SS BOND : bond 0.00354 ( 8) SS BOND : angle 2.27214 ( 16) hydrogen bonds : bond 0.06117 ( 720) hydrogen bonds : angle 3.95968 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 290 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9008 (tp30) cc_final: 0.8564 (mm-30) REVERT: A 107 MET cc_start: 0.8629 (tpp) cc_final: 0.8397 (ttm) REVERT: A 231 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8181 (tm-30) REVERT: A 235 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8147 (tm-30) REVERT: A 246 GLN cc_start: 0.8247 (mm110) cc_final: 0.7230 (tm-30) REVERT: A 250 GLN cc_start: 0.8830 (pp30) cc_final: 0.8472 (pp30) REVERT: B 80 GLU cc_start: 0.8665 (tp30) cc_final: 0.8419 (tp30) REVERT: B 244 CYS cc_start: 0.8866 (t) cc_final: 0.8600 (t) REVERT: B 246 GLN cc_start: 0.8343 (mm110) cc_final: 0.7267 (tm-30) REVERT: B 250 GLN cc_start: 0.8845 (pp30) cc_final: 0.8578 (pp30) REVERT: C 80 GLU cc_start: 0.9014 (tp30) cc_final: 0.8571 (mm-30) REVERT: C 107 MET cc_start: 0.8625 (tpp) cc_final: 0.8380 (ttm) REVERT: C 231 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8186 (tm-30) REVERT: C 235 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8152 (tm-30) REVERT: C 246 GLN cc_start: 0.8255 (mm110) cc_final: 0.7244 (tm-30) REVERT: C 250 GLN cc_start: 0.8832 (pp30) cc_final: 0.8470 (pp30) REVERT: D 80 GLU cc_start: 0.8666 (tp30) cc_final: 0.8401 (tp30) REVERT: D 244 CYS cc_start: 0.8881 (t) cc_final: 0.8592 (t) REVERT: D 246 GLN cc_start: 0.8332 (mm110) cc_final: 0.7264 (tm-30) REVERT: D 250 GLN cc_start: 0.8841 (pp30) cc_final: 0.8570 (pp30) REVERT: E 80 GLU cc_start: 0.9011 (tp30) cc_final: 0.8571 (mm-30) REVERT: E 107 MET cc_start: 0.8635 (tpp) cc_final: 0.8396 (ttm) REVERT: E 231 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8173 (tm-30) REVERT: E 235 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8144 (tm-30) REVERT: E 246 GLN cc_start: 0.8258 (mm110) cc_final: 0.7208 (tm-30) REVERT: E 250 GLN cc_start: 0.8836 (pp30) cc_final: 0.8482 (pp30) REVERT: F 244 CYS cc_start: 0.8881 (t) cc_final: 0.8585 (t) REVERT: G 80 GLU cc_start: 0.9016 (tp30) cc_final: 0.8572 (mm-30) REVERT: G 107 MET cc_start: 0.8638 (tpp) cc_final: 0.8402 (ttm) REVERT: G 231 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8174 (tm-30) REVERT: G 235 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8149 (tm-30) REVERT: G 246 GLN cc_start: 0.8246 (mm110) cc_final: 0.7243 (tm-30) REVERT: G 250 GLN cc_start: 0.8816 (pp30) cc_final: 0.8457 (pp30) REVERT: H 80 GLU cc_start: 0.8677 (tp30) cc_final: 0.8428 (tp30) REVERT: H 244 CYS cc_start: 0.8882 (t) cc_final: 0.8605 (t) REVERT: H 246 GLN cc_start: 0.8318 (mm110) cc_final: 0.7235 (tm-30) REVERT: H 250 GLN cc_start: 0.8842 (pp30) cc_final: 0.8575 (pp30) outliers start: 68 outliers final: 52 residues processed: 326 average time/residue: 0.0975 time to fit residues: 49.7855 Evaluate side-chains 333 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 281 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 143 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 40 ASN E 40 ASN ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.119481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.092851 restraints weight = 28473.364| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.64 r_work: 0.2945 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14936 Z= 0.200 Angle : 0.678 10.271 20272 Z= 0.347 Chirality : 0.041 0.174 2328 Planarity : 0.005 0.057 2504 Dihedral : 11.589 128.205 2360 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.42 % Allowed : 20.03 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.21), residues: 1856 helix: 0.72 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -2.71 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 105 TYR 0.016 0.002 TYR D 177 PHE 0.007 0.001 PHE F 198 TRP 0.008 0.001 TRP A 218 HIS 0.002 0.001 HIS G 143 Details of bonding type rmsd covalent geometry : bond 0.00483 (14928) covalent geometry : angle 0.67567 (20256) SS BOND : bond 0.00287 ( 8) SS BOND : angle 1.95581 ( 16) hydrogen bonds : bond 0.06159 ( 720) hydrogen bonds : angle 3.92144 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 281 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8993 (tp30) cc_final: 0.8503 (mm-30) REVERT: A 231 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8184 (tm-30) REVERT: A 235 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 246 GLN cc_start: 0.8318 (mm110) cc_final: 0.7266 (tm-30) REVERT: A 250 GLN cc_start: 0.8846 (pp30) cc_final: 0.8477 (pp30) REVERT: B 80 GLU cc_start: 0.8679 (tp30) cc_final: 0.8404 (tp30) REVERT: B 244 CYS cc_start: 0.8888 (t) cc_final: 0.8619 (t) REVERT: B 246 GLN cc_start: 0.8329 (mm110) cc_final: 0.7246 (tm-30) REVERT: B 250 GLN cc_start: 0.8844 (pp30) cc_final: 0.8571 (pp30) REVERT: C 80 GLU cc_start: 0.9015 (tp30) cc_final: 0.8546 (mm-30) REVERT: C 107 MET cc_start: 0.8616 (tpp) cc_final: 0.8400 (ttm) REVERT: C 231 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8182 (tm-30) REVERT: C 235 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8126 (tm-30) REVERT: C 246 GLN cc_start: 0.8291 (mm110) cc_final: 0.7248 (tm-30) REVERT: C 250 GLN cc_start: 0.8827 (pp30) cc_final: 0.8451 (pp30) REVERT: D 80 GLU cc_start: 0.8678 (tp30) cc_final: 0.8405 (tp30) REVERT: D 244 CYS cc_start: 0.8891 (t) cc_final: 0.8602 (t) REVERT: D 246 GLN cc_start: 0.8333 (mm110) cc_final: 0.7248 (tm-30) REVERT: D 250 GLN cc_start: 0.8832 (pp30) cc_final: 0.8546 (pp30) REVERT: E 80 GLU cc_start: 0.9016 (tp30) cc_final: 0.8560 (mm-30) REVERT: E 231 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8166 (tm-30) REVERT: E 235 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8144 (tm-30) REVERT: E 246 GLN cc_start: 0.8296 (mm110) cc_final: 0.7217 (tm-30) REVERT: E 250 GLN cc_start: 0.8836 (pp30) cc_final: 0.8464 (pp30) REVERT: F 80 GLU cc_start: 0.8947 (tp30) cc_final: 0.8461 (tp30) REVERT: F 244 CYS cc_start: 0.8865 (t) cc_final: 0.8579 (t) REVERT: G 80 GLU cc_start: 0.9019 (tp30) cc_final: 0.8535 (mm-30) REVERT: G 107 MET cc_start: 0.8626 (tpp) cc_final: 0.8425 (ttm) REVERT: G 231 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8174 (tm-30) REVERT: G 235 GLU cc_start: 0.8415 (tm-30) cc_final: 0.8154 (tm-30) REVERT: G 246 GLN cc_start: 0.8320 (mm110) cc_final: 0.7274 (tm-30) REVERT: G 250 GLN cc_start: 0.8835 (pp30) cc_final: 0.8463 (pp30) REVERT: H 80 GLU cc_start: 0.8697 (tp30) cc_final: 0.8424 (tp30) REVERT: H 244 CYS cc_start: 0.8886 (t) cc_final: 0.8615 (t) REVERT: H 246 GLN cc_start: 0.8334 (mm110) cc_final: 0.7249 (tm-30) REVERT: H 250 GLN cc_start: 0.8842 (pp30) cc_final: 0.8568 (pp30) outliers start: 64 outliers final: 53 residues processed: 314 average time/residue: 0.0872 time to fit residues: 43.7866 Evaluate side-chains 332 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 279 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 180 CYS Chi-restraints excluded: chain H residue 200 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 159 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 21 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 142 optimal weight: 0.0870 chunk 20 optimal weight: 0.8980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS C 220 HIS E 220 HIS ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 220 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.131367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.104849 restraints weight = 28468.223| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.99 r_work: 0.3040 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14936 Z= 0.128 Angle : 0.615 10.249 20272 Z= 0.312 Chirality : 0.039 0.172 2328 Planarity : 0.005 0.057 2504 Dihedral : 11.121 115.965 2360 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.25 % Allowed : 22.24 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.21), residues: 1856 helix: 1.22 (0.16), residues: 1200 sheet: None (None), residues: 0 loop : -2.80 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 105 TYR 0.011 0.001 TYR A 51 PHE 0.006 0.001 PHE F 189 TRP 0.006 0.001 TRP F 218 HIS 0.001 0.000 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00275 (14928) covalent geometry : angle 0.61468 (20256) SS BOND : bond 0.00215 ( 8) SS BOND : angle 0.97768 ( 16) hydrogen bonds : bond 0.05184 ( 720) hydrogen bonds : angle 3.47799 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 303 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9057 (tp30) cc_final: 0.8545 (mm-30) REVERT: A 105 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7537 (tpp80) REVERT: A 107 MET cc_start: 0.8669 (ttm) cc_final: 0.8420 (ttm) REVERT: A 235 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8070 (tm-30) REVERT: A 246 GLN cc_start: 0.8145 (mm110) cc_final: 0.7249 (tm-30) REVERT: A 250 GLN cc_start: 0.8858 (pp30) cc_final: 0.8533 (pp30) REVERT: B 107 MET cc_start: 0.8805 (tpp) cc_final: 0.8590 (ttm) REVERT: C 80 GLU cc_start: 0.9062 (tp30) cc_final: 0.8556 (mm-30) REVERT: C 235 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8061 (tm-30) REVERT: C 246 GLN cc_start: 0.8139 (mm110) cc_final: 0.7246 (tm-30) REVERT: C 250 GLN cc_start: 0.8855 (pp30) cc_final: 0.8535 (pp30) REVERT: E 80 GLU cc_start: 0.9078 (tp30) cc_final: 0.8580 (mm-30) REVERT: E 105 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7533 (tpp80) REVERT: E 107 MET cc_start: 0.8662 (ttm) cc_final: 0.8414 (ttm) REVERT: E 235 GLU cc_start: 0.8316 (tm-30) cc_final: 0.8085 (tm-30) REVERT: E 246 GLN cc_start: 0.8167 (mm110) cc_final: 0.7249 (tm-30) REVERT: E 250 GLN cc_start: 0.8859 (pp30) cc_final: 0.8539 (pp30) REVERT: F 80 GLU cc_start: 0.8913 (tp30) cc_final: 0.8521 (mm-30) REVERT: F 105 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7413 (tpp80) REVERT: G 80 GLU cc_start: 0.9073 (tp30) cc_final: 0.8570 (mm-30) REVERT: G 105 ARG cc_start: 0.7774 (mtp85) cc_final: 0.7520 (tpp80) REVERT: G 231 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8220 (tm-30) REVERT: G 235 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8069 (tm-30) REVERT: G 246 GLN cc_start: 0.8145 (mm110) cc_final: 0.7256 (tm-30) REVERT: G 250 GLN cc_start: 0.8863 (pp30) cc_final: 0.8545 (pp30) REVERT: H 107 MET cc_start: 0.8797 (tpp) cc_final: 0.8585 (ttm) outliers start: 47 outliers final: 32 residues processed: 327 average time/residue: 0.0921 time to fit residues: 47.4924 Evaluate side-chains 318 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 154 optimal weight: 5.9990 chunk 158 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.0040 chunk 21 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 183 optimal weight: 0.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN C 40 ASN E 40 ASN G 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.128933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100927 restraints weight = 27484.551| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.84 r_work: 0.3046 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14936 Z= 0.131 Angle : 0.622 10.016 20272 Z= 0.316 Chirality : 0.039 0.163 2328 Planarity : 0.005 0.056 2504 Dihedral : 10.963 111.090 2360 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 4.14 % Allowed : 22.38 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.22), residues: 1856 helix: 1.35 (0.16), residues: 1200 sheet: None (None), residues: 0 loop : -2.71 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 46 TYR 0.011 0.001 TYR D 177 PHE 0.005 0.001 PHE E 189 TRP 0.006 0.001 TRP D 218 HIS 0.001 0.000 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00310 (14928) covalent geometry : angle 0.62136 (20256) SS BOND : bond 0.00304 ( 8) SS BOND : angle 1.29096 ( 16) hydrogen bonds : bond 0.05097 ( 720) hydrogen bonds : angle 3.43080 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 297 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9072 (tp30) cc_final: 0.8528 (mm-30) REVERT: A 235 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8122 (tm-30) REVERT: A 246 GLN cc_start: 0.8166 (mm110) cc_final: 0.7286 (tm-30) REVERT: A 250 GLN cc_start: 0.8887 (pp30) cc_final: 0.8560 (pp30) REVERT: B 80 GLU cc_start: 0.8999 (tp30) cc_final: 0.8588 (mm-30) REVERT: C 80 GLU cc_start: 0.9067 (tp30) cc_final: 0.8526 (mm-30) REVERT: C 235 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8106 (tm-30) REVERT: C 246 GLN cc_start: 0.8134 (mm110) cc_final: 0.7243 (tm-30) REVERT: C 250 GLN cc_start: 0.8865 (pp30) cc_final: 0.8539 (pp30) REVERT: D 80 GLU cc_start: 0.8977 (tp30) cc_final: 0.8582 (mm-30) REVERT: E 80 GLU cc_start: 0.9072 (tp30) cc_final: 0.8536 (mm-30) REVERT: E 235 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8123 (tm-30) REVERT: E 246 GLN cc_start: 0.8178 (mm110) cc_final: 0.7264 (tm-30) REVERT: E 250 GLN cc_start: 0.8877 (pp30) cc_final: 0.8542 (pp30) REVERT: F 80 GLU cc_start: 0.8921 (tp30) cc_final: 0.8501 (mm-30) REVERT: G 80 GLU cc_start: 0.9079 (tp30) cc_final: 0.8543 (mm-30) REVERT: G 235 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8186 (tm-30) REVERT: G 246 GLN cc_start: 0.8163 (mm110) cc_final: 0.7294 (tm-30) REVERT: G 250 GLN cc_start: 0.8880 (pp30) cc_final: 0.8556 (pp30) REVERT: H 80 GLU cc_start: 0.8981 (tp30) cc_final: 0.8569 (mm-30) outliers start: 60 outliers final: 40 residues processed: 327 average time/residue: 0.0846 time to fit residues: 44.5616 Evaluate side-chains 330 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 290 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 123 CYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 49 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 72 optimal weight: 0.2980 chunk 107 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 11 optimal weight: 20.0000 chunk 3 optimal weight: 0.0970 chunk 109 optimal weight: 0.5980 chunk 70 optimal weight: 0.0370 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN E 40 ASN ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.125098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098095 restraints weight = 28140.666| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.80 r_work: 0.3081 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14936 Z= 0.121 Angle : 0.598 10.003 20272 Z= 0.302 Chirality : 0.038 0.161 2328 Planarity : 0.005 0.056 2504 Dihedral : 10.320 108.761 2360 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.25 % Allowed : 23.14 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.22), residues: 1856 helix: 1.61 (0.16), residues: 1200 sheet: None (None), residues: 0 loop : -2.79 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 152 TYR 0.007 0.001 TYR C 177 PHE 0.009 0.001 PHE E 189 TRP 0.005 0.001 TRP G 187 HIS 0.001 0.000 HIS G 236 Details of bonding type rmsd covalent geometry : bond 0.00265 (14928) covalent geometry : angle 0.59783 (20256) SS BOND : bond 0.00043 ( 8) SS BOND : angle 0.64035 ( 16) hydrogen bonds : bond 0.04213 ( 720) hydrogen bonds : angle 3.22188 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 359 time to evaluate : 0.570 Fit side-chains REVERT: A 80 GLU cc_start: 0.9100 (tp30) cc_final: 0.8511 (mm-30) REVERT: A 105 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7495 (tpp80) REVERT: A 216 ARG cc_start: 0.9350 (tpp80) cc_final: 0.8886 (tpt-90) REVERT: A 235 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8114 (tm-30) REVERT: A 246 GLN cc_start: 0.7935 (mm110) cc_final: 0.7116 (tm-30) REVERT: A 250 GLN cc_start: 0.8866 (pp30) cc_final: 0.8557 (pp30) REVERT: B 80 GLU cc_start: 0.8898 (tp30) cc_final: 0.8445 (mm-30) REVERT: B 105 ARG cc_start: 0.7790 (mtp85) cc_final: 0.7565 (tpp80) REVERT: B 246 GLN cc_start: 0.7852 (mm110) cc_final: 0.6997 (tm-30) REVERT: C 80 GLU cc_start: 0.9103 (tp30) cc_final: 0.8524 (mm-30) REVERT: C 216 ARG cc_start: 0.9352 (tpp80) cc_final: 0.8899 (tpt-90) REVERT: C 235 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8138 (tm-30) REVERT: C 246 GLN cc_start: 0.7962 (mm110) cc_final: 0.7135 (tm-30) REVERT: C 250 GLN cc_start: 0.8843 (pp30) cc_final: 0.8533 (pp30) REVERT: D 80 GLU cc_start: 0.8874 (tp30) cc_final: 0.8423 (mm-30) REVERT: D 246 GLN cc_start: 0.7885 (mm110) cc_final: 0.7020 (tm-30) REVERT: E 80 GLU cc_start: 0.9117 (tp30) cc_final: 0.8550 (mm-30) REVERT: E 105 ARG cc_start: 0.7783 (mtp85) cc_final: 0.7489 (tpp80) REVERT: E 107 MET cc_start: 0.8657 (ttm) cc_final: 0.8438 (ttm) REVERT: E 216 ARG cc_start: 0.9345 (tpp80) cc_final: 0.8905 (tpt-90) REVERT: E 235 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8135 (tm-30) REVERT: E 246 GLN cc_start: 0.7946 (mm110) cc_final: 0.7098 (tm-30) REVERT: E 250 GLN cc_start: 0.8856 (pp30) cc_final: 0.8553 (pp30) REVERT: F 80 GLU cc_start: 0.8883 (tp30) cc_final: 0.8423 (mm-30) REVERT: F 246 GLN cc_start: 0.7871 (mm110) cc_final: 0.7037 (tm-30) REVERT: G 80 GLU cc_start: 0.9118 (tp30) cc_final: 0.8541 (mm-30) REVERT: G 105 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7513 (tpp80) REVERT: G 182 SER cc_start: 0.9508 (t) cc_final: 0.9242 (p) REVERT: G 216 ARG cc_start: 0.9364 (tpp80) cc_final: 0.8933 (tpt-90) REVERT: G 230 ASP cc_start: 0.8793 (m-30) cc_final: 0.8539 (m-30) REVERT: G 235 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8145 (tm-30) REVERT: G 246 GLN cc_start: 0.7993 (mm110) cc_final: 0.7162 (tm-30) REVERT: G 250 GLN cc_start: 0.8856 (pp30) cc_final: 0.8544 (pp30) REVERT: H 80 GLU cc_start: 0.8886 (tp30) cc_final: 0.8431 (mm-30) REVERT: H 105 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7586 (tpp80) REVERT: H 216 ARG cc_start: 0.9290 (tpp80) cc_final: 0.8847 (tpt-90) REVERT: H 246 GLN cc_start: 0.7895 (mm110) cc_final: 0.7036 (tm-30) outliers start: 47 outliers final: 35 residues processed: 380 average time/residue: 0.0999 time to fit residues: 58.1611 Evaluate side-chains 379 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 344 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 40 ASN Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 123 CYS Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 40 ASN Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 96 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 139 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 ASN D 40 ASN E 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.102004 restraints weight = 28743.087| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.82 r_work: 0.2959 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14936 Z= 0.197 Angle : 0.678 9.904 20272 Z= 0.345 Chirality : 0.042 0.159 2328 Planarity : 0.005 0.053 2504 Dihedral : 10.530 113.205 2360 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.52 % Allowed : 23.76 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.21), residues: 1856 helix: 1.39 (0.16), residues: 1184 sheet: None (None), residues: 0 loop : -2.50 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 105 TYR 0.017 0.002 TYR H 177 PHE 0.012 0.001 PHE C 39 TRP 0.008 0.001 TRP H 218 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00475 (14928) covalent geometry : angle 0.67457 (20256) SS BOND : bond 0.00821 ( 8) SS BOND : angle 2.54218 ( 16) hydrogen bonds : bond 0.05456 ( 720) hydrogen bonds : angle 3.58367 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9083 (tp30) cc_final: 0.8488 (mm-30) REVERT: A 235 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8153 (tm-30) REVERT: A 246 GLN cc_start: 0.8156 (mm110) cc_final: 0.7214 (tm-30) REVERT: A 250 GLN cc_start: 0.8857 (pp30) cc_final: 0.8488 (pp30) REVERT: B 80 GLU cc_start: 0.8998 (tp30) cc_final: 0.8532 (mm-30) REVERT: C 80 GLU cc_start: 0.9085 (tp30) cc_final: 0.8486 (mm-30) REVERT: C 235 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8147 (tm-30) REVERT: C 246 GLN cc_start: 0.8127 (mm110) cc_final: 0.7203 (tm-30) REVERT: C 250 GLN cc_start: 0.8859 (pp30) cc_final: 0.8478 (pp30) REVERT: D 80 GLU cc_start: 0.8989 (tp30) cc_final: 0.8524 (mm-30) REVERT: E 80 GLU cc_start: 0.9094 (tp30) cc_final: 0.8495 (mm-30) REVERT: E 107 MET cc_start: 0.8595 (ttm) cc_final: 0.8388 (ttm) REVERT: E 235 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8156 (tm-30) REVERT: E 246 GLN cc_start: 0.8135 (mm110) cc_final: 0.7203 (tm-30) REVERT: E 250 GLN cc_start: 0.8868 (pp30) cc_final: 0.8500 (pp30) REVERT: F 80 GLU cc_start: 0.8946 (tp30) cc_final: 0.8440 (mm-30) REVERT: G 80 GLU cc_start: 0.9093 (tp30) cc_final: 0.8501 (mm-30) REVERT: G 223 ASP cc_start: 0.8991 (t70) cc_final: 0.8724 (t70) REVERT: G 235 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8155 (tm-30) REVERT: G 246 GLN cc_start: 0.8183 (mm110) cc_final: 0.7252 (tm-30) REVERT: G 250 GLN cc_start: 0.8864 (pp30) cc_final: 0.8495 (pp30) REVERT: H 80 GLU cc_start: 0.8975 (tp30) cc_final: 0.8508 (mm-30) outliers start: 51 outliers final: 40 residues processed: 317 average time/residue: 0.0931 time to fit residues: 46.9920 Evaluate side-chains 321 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 281 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 123 CYS Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN G 40 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.110255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.082546 restraints weight = 29724.922| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.70 r_work: 0.2839 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 14936 Z= 0.361 Angle : 0.836 11.585 20272 Z= 0.426 Chirality : 0.048 0.198 2328 Planarity : 0.005 0.055 2504 Dihedral : 11.534 120.507 2360 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.35 % Allowed : 23.41 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.20), residues: 1856 helix: 0.51 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -2.81 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 105 TYR 0.024 0.003 TYR D 177 PHE 0.011 0.002 PHE F 198 TRP 0.017 0.002 TRP B 218 HIS 0.003 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00856 (14928) covalent geometry : angle 0.83243 (20256) SS BOND : bond 0.00457 ( 8) SS BOND : angle 2.96767 ( 16) hydrogen bonds : bond 0.07207 ( 720) hydrogen bonds : angle 4.32860 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3712 Ramachandran restraints generated. 1856 Oldfield, 0 Emsley, 1856 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 267 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9060 (tp30) cc_final: 0.8494 (mm-30) REVERT: A 235 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8202 (tm-30) REVERT: A 246 GLN cc_start: 0.8479 (mm110) cc_final: 0.7361 (tm-30) REVERT: A 250 GLN cc_start: 0.8861 (pp30) cc_final: 0.8479 (pp30) REVERT: A 252 MET cc_start: 0.5108 (OUTLIER) cc_final: 0.4897 (ptt) REVERT: B 80 GLU cc_start: 0.9004 (tp30) cc_final: 0.8517 (mm-30) REVERT: B 246 GLN cc_start: 0.8532 (mm110) cc_final: 0.7352 (tm-30) REVERT: C 80 GLU cc_start: 0.9057 (tp30) cc_final: 0.8485 (mm-30) REVERT: C 235 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8209 (tm-30) REVERT: C 246 GLN cc_start: 0.8473 (mm110) cc_final: 0.7340 (tm-30) REVERT: C 250 GLN cc_start: 0.8851 (pp30) cc_final: 0.8450 (pp30) REVERT: D 80 GLU cc_start: 0.9004 (tp30) cc_final: 0.8530 (mm-30) REVERT: D 231 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8206 (tm-30) REVERT: E 80 GLU cc_start: 0.9063 (tp30) cc_final: 0.8493 (mm-30) REVERT: E 235 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8247 (tm-30) REVERT: E 246 GLN cc_start: 0.8476 (mm110) cc_final: 0.7358 (tm-30) REVERT: E 250 GLN cc_start: 0.8860 (pp30) cc_final: 0.8487 (pp30) REVERT: F 80 GLU cc_start: 0.9004 (tp30) cc_final: 0.8431 (mm-30) REVERT: F 120 ASP cc_start: 0.9291 (m-30) cc_final: 0.8982 (m-30) REVERT: F 231 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8187 (tm-30) REVERT: F 244 CYS cc_start: 0.8885 (t) cc_final: 0.8617 (t) REVERT: F 252 MET cc_start: 0.5215 (OUTLIER) cc_final: 0.4830 (ptt) REVERT: G 80 GLU cc_start: 0.9064 (tp30) cc_final: 0.8494 (mm-30) REVERT: G 223 ASP cc_start: 0.9094 (t70) cc_final: 0.8811 (t70) REVERT: G 235 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8204 (tm-30) REVERT: G 246 GLN cc_start: 0.8482 (mm110) cc_final: 0.7364 (tm-30) REVERT: G 250 GLN cc_start: 0.8857 (pp30) cc_final: 0.8474 (pp30) REVERT: H 80 GLU cc_start: 0.9015 (tp30) cc_final: 0.8526 (mm-30) REVERT: H 231 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8200 (tm-30) outliers start: 63 outliers final: 49 residues processed: 299 average time/residue: 0.0951 time to fit residues: 45.1843 Evaluate side-chains 314 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 123 CYS Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain B residue 76 MET Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 123 CYS Chi-restraints excluded: chain C residue 126 CYS Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 76 MET Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 149 GLU Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 180 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 123 CYS Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 149 GLU Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 123 CYS Chi-restraints excluded: chain G residue 126 CYS Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 150 VAL Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 38 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 160 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 132 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 73 ASN C 73 ASN G 40 ASN G 73 ASN H 72 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.082804 restraints weight = 29485.945| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.69 r_work: 0.2844 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.175 14936 Z= 0.312 Angle : 1.003 59.146 20272 Z= 0.545 Chirality : 0.051 1.062 2328 Planarity : 0.006 0.055 2504 Dihedral : 11.551 120.415 2360 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 4.14 % Allowed : 23.69 % Favored : 72.17 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.93 (0.20), residues: 1856 helix: 0.51 (0.15), residues: 1200 sheet: None (None), residues: 0 loop : -2.83 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 105 TYR 0.023 0.003 TYR D 177 PHE 0.010 0.002 PHE F 198 TRP 0.017 0.002 TRP B 218 HIS 0.003 0.001 HIS D 143 Details of bonding type rmsd covalent geometry : bond 0.00725 (14928) covalent geometry : angle 0.99990 (20256) SS BOND : bond 0.00462 ( 8) SS BOND : angle 2.96304 ( 16) hydrogen bonds : bond 0.06983 ( 720) hydrogen bonds : angle 4.29831 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2940.62 seconds wall clock time: 51 minutes 8.31 seconds (3068.31 seconds total)