Starting phenix.real_space_refine on Tue Dec 31 11:11:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gmq_40230/12_2024/8gmq_40230_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gmq_40230/12_2024/8gmq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gmq_40230/12_2024/8gmq_40230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gmq_40230/12_2024/8gmq_40230.map" model { file = "/net/cci-nas-00/data/ceres_data/8gmq_40230/12_2024/8gmq_40230_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gmq_40230/12_2024/8gmq_40230_trim.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.018 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} 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: C, B, E, D, G, F, H Time building chain proxies: 5.63, per 1000 atoms: 0.39 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 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: 3.94 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.25 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: 3.51 Time building geometry restraints manager: 4.50 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: 8359 24.42 - 48.83: 444 48.83 - 73.25: 96 73.25 - 97.66: 32 97.66 - 122.08: 8 Dihedral angle restraints: 8939 sinusoidal: 3443 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 8936 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: 2.03 - 2.60: 119 2.60 - 3.18: 14402 3.18 - 3.75: 19309 3.75 - 4.33: 26459 4.33 - 4.90: 42746 Nonbonded interactions: 103035 Sorted by model distance: nonbonded pdb=" SG CYS G 41 " pdb=" SG CYS G 126 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS D 41 " pdb=" SG CYS D 126 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS F 41 " pdb=" SG CYS F 126 " model vdw 2.025 3.760 nonbonded pdb=" SG CYS C 41 " pdb=" SG CYS C 126 " model vdw 2.026 3.760 nonbonded pdb=" SG CYS E 41 " pdb=" SG CYS E 126 " model vdw 2.026 3.760 ... (remaining 103030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 5.420 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: 0.000 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 29.850 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- 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 14928 Z= 0.503 Angle : 0.964 11.725 20256 Z= 0.454 Chirality : 0.039 0.210 2328 Planarity : 0.005 0.054 2504 Dihedral : 16.898 122.076 5368 Min Nonbonded Distance : 2.025 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.007 0.001 TRP C 113 HIS 0.003 0.001 HIS D 143 PHE 0.010 0.002 PHE D 207 TYR 0.012 0.002 TYR D 221 ARG 0.002 0.000 ARG H 201 *********************** 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 : 1.568 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: 0.2961 time to fit residues: 159.0567 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 : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 0.9990 chunk 139 optimal weight: 0.0030 chunk 77 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.2980 chunk 144 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14928 Z= 0.227 Angle : 0.706 10.680 20256 Z= 0.364 Chirality : 0.042 0.184 2328 Planarity : 0.006 0.056 2504 Dihedral : 13.025 115.819 2360 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.80 % Allowed : 12.71 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.19), residues: 1856 helix: -1.18 (0.14), residues: 1128 sheet: None (None), residues: 0 loop : -2.56 (0.25), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 218 HIS 0.001 0.000 HIS E 143 PHE 0.006 0.001 PHE B 212 TYR 0.009 0.001 TYR B 221 ARG 0.006 0.001 ARG H 46 *********************** 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 364 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 338 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8904 (tp30) cc_final: 0.8425 (tp30) REVERT: A 146 PRO cc_start: 0.7538 (Cg_exo) cc_final: 0.7258 (Cg_endo) REVERT: A 231 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8103 (tm-30) REVERT: A 235 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7970 (tm-30) REVERT: A 246 GLN cc_start: 0.8426 (mm110) cc_final: 0.7263 (tm-30) REVERT: B 80 GLU cc_start: 0.8593 (tp30) cc_final: 0.8379 (tp30) REVERT: B 246 GLN cc_start: 0.8465 (mm110) cc_final: 0.7354 (tm-30) REVERT: C 80 GLU cc_start: 0.8906 (tp30) cc_final: 0.8420 (tp30) REVERT: C 146 PRO cc_start: 0.7542 (Cg_exo) cc_final: 0.7256 (Cg_endo) REVERT: C 231 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8106 (tm-30) REVERT: C 235 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7973 (tm-30) REVERT: C 246 GLN cc_start: 0.8414 (mm110) cc_final: 0.7254 (tm-30) REVERT: D 80 GLU cc_start: 0.8604 (tp30) cc_final: 0.8383 (tp30) REVERT: D 246 GLN cc_start: 0.8457 (mm110) cc_final: 0.7353 (tm-30) REVERT: E 80 GLU cc_start: 0.8914 (tp30) cc_final: 0.8425 (tp30) REVERT: E 146 PRO cc_start: 0.7524 (Cg_exo) cc_final: 0.7246 (Cg_endo) REVERT: E 231 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8114 (tm-30) REVERT: E 235 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7967 (tm-30) REVERT: E 246 GLN cc_start: 0.8424 (mm110) cc_final: 0.7280 (tm-30) REVERT: F 196 LEU cc_start: 0.8865 (tp) cc_final: 0.8610 (tt) REVERT: F 217 TYR cc_start: 0.9069 (t80) cc_final: 0.8863 (t80) REVERT: F 246 GLN cc_start: 0.8471 (mm110) cc_final: 0.7440 (tm-30) REVERT: G 80 GLU cc_start: 0.8912 (tp30) cc_final: 0.8428 (tp30) REVERT: G 146 PRO cc_start: 0.7547 (Cg_exo) cc_final: 0.7279 (Cg_endo) REVERT: G 231 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8114 (tm-30) REVERT: G 235 GLU cc_start: 0.8390 (tm-30) cc_final: 0.7970 (tm-30) REVERT: G 246 GLN cc_start: 0.8427 (mm110) cc_final: 0.7274 (tm-30) REVERT: H 80 GLU cc_start: 0.8599 (tp30) cc_final: 0.8383 (tp30) REVERT: H 246 GLN cc_start: 0.8439 (mm110) cc_final: 0.7351 (tm-30) outliers start: 26 outliers final: 22 residues processed: 342 average time/residue: 0.2282 time to fit residues: 120.1258 Evaluate side-chains 307 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 285 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 124 ILE 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 124 ILE 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 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 162 ILE 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 92 optimal weight: 10.0000 chunk 51 optimal weight: 0.0570 chunk 139 optimal weight: 0.0470 chunk 113 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 57 optimal weight: 0.0470 chunk 134 optimal weight: 0.9980 overall best weight: 0.6296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 220 HIS B 220 HIS C 40 ASN C 220 HIS D 220 HIS E 40 ASN E 220 HIS F 220 HIS G 40 ASN G 220 HIS H 220 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14928 Z= 0.189 Angle : 0.614 9.967 20256 Z= 0.317 Chirality : 0.039 0.164 2328 Planarity : 0.005 0.055 2504 Dihedral : 11.974 122.134 2360 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 4.21 % Allowed : 15.54 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.20), residues: 1856 helix: 0.08 (0.15), residues: 1168 sheet: None (None), residues: 0 loop : -2.91 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 218 HIS 0.001 0.000 HIS H 236 PHE 0.005 0.001 PHE F 207 TYR 0.010 0.001 TYR D 177 ARG 0.001 0.000 ARG H 216 *********************** 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 372 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 311 time to evaluate : 1.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8946 (tp30) cc_final: 0.8423 (tp30) REVERT: A 231 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 235 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 246 GLN cc_start: 0.8184 (mm110) cc_final: 0.7212 (tm-30) REVERT: B 80 GLU cc_start: 0.8558 (tp30) cc_final: 0.8232 (tp30) REVERT: B 242 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7880 (tmtt) REVERT: C 80 GLU cc_start: 0.8947 (tp30) cc_final: 0.8353 (tp30) REVERT: C 90 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8060 (mmtt) REVERT: C 231 GLU cc_start: 0.8342 (tm-30) cc_final: 0.8131 (tm-30) REVERT: C 235 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8002 (tm-30) REVERT: C 246 GLN cc_start: 0.8172 (mm110) cc_final: 0.7196 (tm-30) REVERT: D 80 GLU cc_start: 0.8560 (tp30) cc_final: 0.8226 (tp30) REVERT: D 242 LYS cc_start: 0.8137 (tmtt) cc_final: 0.7906 (tmtt) REVERT: E 80 GLU cc_start: 0.8952 (tp30) cc_final: 0.8355 (tp30) REVERT: E 90 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8059 (mmtt) REVERT: E 216 ARG cc_start: 0.9394 (tpp80) cc_final: 0.9138 (tpt-90) REVERT: E 231 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8130 (tm-30) REVERT: E 235 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8033 (tm-30) REVERT: E 246 GLN cc_start: 0.8194 (mm110) cc_final: 0.7172 (tm-30) REVERT: F 196 LEU cc_start: 0.8874 (tp) cc_final: 0.8512 (tt) REVERT: G 80 GLU cc_start: 0.8952 (tp30) cc_final: 0.8355 (tp30) REVERT: G 90 LYS cc_start: 0.8658 (mmmm) cc_final: 0.8066 (mmtt) REVERT: G 231 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8111 (tm-30) REVERT: G 235 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7997 (tm-30) REVERT: G 246 GLN cc_start: 0.8193 (mm110) cc_final: 0.7218 (tm-30) REVERT: H 80 GLU cc_start: 0.8564 (tp30) cc_final: 0.8233 (tp30) REVERT: H 242 LYS cc_start: 0.8119 (tmtt) cc_final: 0.7887 (tmtt) outliers start: 61 outliers final: 35 residues processed: 338 average time/residue: 0.2778 time to fit residues: 139.3418 Evaluate side-chains 309 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 274 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 70 LEU 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 70 LEU 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 180 CYS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 102 MET 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 70 LEU Chi-restraints excluded: chain G residue 124 ILE 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 162 ILE 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 165 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 18 optimal weight: 0.0060 chunk 79 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 159 optimal weight: 0.1980 chunk 47 optimal weight: 3.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- 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** E 40 ASN G 40 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14928 Z= 0.196 Angle : 0.626 10.217 20256 Z= 0.318 Chirality : 0.038 0.168 2328 Planarity : 0.005 0.055 2504 Dihedral : 11.373 121.079 2360 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.83 % Allowed : 19.27 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1856 helix: 0.62 (0.15), residues: 1184 sheet: None (None), residues: 0 loop : -2.98 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 218 HIS 0.001 0.000 HIS E 220 PHE 0.004 0.001 PHE F 198 TYR 0.010 0.001 TYR E 177 ARG 0.004 0.000 ARG C 105 *********************** 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 341 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 300 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8953 (tp30) cc_final: 0.8607 (mm-30) REVERT: A 107 MET cc_start: 0.8731 (tpp) cc_final: 0.8424 (ttm) REVERT: A 216 ARG cc_start: 0.9365 (tpp80) cc_final: 0.9038 (tpt-90) REVERT: A 231 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8090 (tm-30) REVERT: A 235 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7990 (tm-30) REVERT: A 246 GLN cc_start: 0.8127 (mm110) cc_final: 0.7264 (tm-30) REVERT: A 250 GLN cc_start: 0.8740 (pp30) cc_final: 0.8478 (pp30) REVERT: B 80 GLU cc_start: 0.8509 (tp30) cc_final: 0.8289 (tp30) REVERT: B 107 MET cc_start: 0.8522 (tpp) cc_final: 0.8285 (ttm) REVERT: B 242 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7868 (tmtt) REVERT: C 80 GLU cc_start: 0.8963 (tp30) cc_final: 0.8590 (mm-30) REVERT: C 107 MET cc_start: 0.8737 (tpp) cc_final: 0.8423 (ttm) REVERT: C 216 ARG cc_start: 0.9370 (tpp80) cc_final: 0.9034 (tpt-90) REVERT: C 231 GLU cc_start: 0.8295 (tm-30) cc_final: 0.8077 (tm-30) REVERT: C 235 GLU cc_start: 0.8292 (tm-30) cc_final: 0.8011 (tm-30) REVERT: C 246 GLN cc_start: 0.8117 (mm110) cc_final: 0.7266 (tm-30) REVERT: C 250 GLN cc_start: 0.8739 (pp30) cc_final: 0.8477 (pp30) REVERT: D 107 MET cc_start: 0.8521 (tpp) cc_final: 0.8277 (ttm) REVERT: D 242 LYS cc_start: 0.8098 (tmtt) cc_final: 0.7878 (tmtt) REVERT: E 80 GLU cc_start: 0.8965 (tp30) cc_final: 0.8591 (mm-30) REVERT: E 107 MET cc_start: 0.8736 (tpp) cc_final: 0.8396 (ttm) REVERT: E 216 ARG cc_start: 0.9364 (tpp80) cc_final: 0.9027 (tpt-90) REVERT: E 231 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8083 (tm-30) REVERT: E 235 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7974 (tm-30) REVERT: E 246 GLN cc_start: 0.8137 (mm110) cc_final: 0.7281 (tm-30) REVERT: E 250 GLN cc_start: 0.8740 (pp30) cc_final: 0.8476 (pp30) REVERT: F 196 LEU cc_start: 0.8887 (tp) cc_final: 0.8456 (tt) REVERT: G 80 GLU cc_start: 0.8970 (tp30) cc_final: 0.8597 (mm-30) REVERT: G 107 MET cc_start: 0.8733 (tpp) cc_final: 0.8419 (ttm) REVERT: G 231 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8093 (tm-30) REVERT: G 235 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8008 (tm-30) REVERT: G 246 GLN cc_start: 0.8152 (mm110) cc_final: 0.7298 (tm-30) REVERT: G 250 GLN cc_start: 0.8725 (pp30) cc_final: 0.8463 (pp30) REVERT: H 80 GLU cc_start: 0.8518 (tp30) cc_final: 0.8290 (tp30) REVERT: H 107 MET cc_start: 0.8522 (tpp) cc_final: 0.8281 (ttm) REVERT: H 242 LYS cc_start: 0.8116 (tmtt) cc_final: 0.7892 (tmtt) outliers start: 41 outliers final: 30 residues processed: 310 average time/residue: 0.2584 time to fit residues: 120.7242 Evaluate side-chains 316 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 286 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN 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 180 CYS Chi-restraints excluded: chain A residue 200 VAL 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 76 MET 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 180 CYS Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 124 ILE 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 76 MET Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain H residue 149 GLU Chi-restraints excluded: chain H residue 180 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 148 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 151 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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** ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14928 Z= 0.214 Angle : 0.620 9.892 20256 Z= 0.316 Chirality : 0.039 0.162 2328 Planarity : 0.005 0.056 2504 Dihedral : 11.178 120.126 2360 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 3.25 % Allowed : 19.27 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.21), residues: 1856 helix: 1.13 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -2.69 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 218 HIS 0.001 0.000 HIS H 143 PHE 0.005 0.001 PHE F 207 TYR 0.012 0.001 TYR B 177 ARG 0.003 0.000 ARG F 105 *********************** 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 337 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8967 (tp30) cc_final: 0.8543 (mm-30) REVERT: A 107 MET cc_start: 0.8687 (tpp) cc_final: 0.8481 (ttm) REVERT: A 216 ARG cc_start: 0.9359 (tpp80) cc_final: 0.8945 (tpt-90) REVERT: A 231 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8128 (tm-30) REVERT: A 235 GLU cc_start: 0.8245 (tm-30) cc_final: 0.8009 (tm-30) REVERT: A 246 GLN cc_start: 0.8140 (mm110) cc_final: 0.7276 (tm-30) REVERT: A 250 GLN cc_start: 0.8752 (pp30) cc_final: 0.8488 (pp30) REVERT: B 80 GLU cc_start: 0.8512 (tp30) cc_final: 0.8266 (tp30) REVERT: C 80 GLU cc_start: 0.8969 (tp30) cc_final: 0.8536 (mm-30) REVERT: C 107 MET cc_start: 0.8689 (tpp) cc_final: 0.8479 (ttm) REVERT: C 216 ARG cc_start: 0.9359 (tpp80) cc_final: 0.8947 (tpt-90) REVERT: C 231 GLU cc_start: 0.8299 (tm-30) cc_final: 0.8084 (tm-30) REVERT: C 235 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7999 (tm-30) REVERT: C 246 GLN cc_start: 0.8121 (mm110) cc_final: 0.7259 (tm-30) REVERT: C 250 GLN cc_start: 0.8750 (pp30) cc_final: 0.8486 (pp30) REVERT: D 80 GLU cc_start: 0.8903 (tp30) cc_final: 0.8472 (tp30) REVERT: D 107 MET cc_start: 0.8565 (tpp) cc_final: 0.8360 (ttm) REVERT: E 80 GLU cc_start: 0.8966 (tp30) cc_final: 0.8538 (mm-30) REVERT: E 107 MET cc_start: 0.8693 (tpp) cc_final: 0.8455 (ttm) REVERT: E 216 ARG cc_start: 0.9356 (tpp80) cc_final: 0.8946 (tpt-90) REVERT: E 231 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8089 (tm-30) REVERT: E 235 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8022 (tm-30) REVERT: E 246 GLN cc_start: 0.8156 (mm110) cc_final: 0.7271 (tm-30) REVERT: E 250 GLN cc_start: 0.8748 (pp30) cc_final: 0.8468 (pp30) REVERT: F 196 LEU cc_start: 0.8863 (tp) cc_final: 0.8379 (tt) REVERT: F 217 TYR cc_start: 0.8894 (t80) cc_final: 0.8673 (t80) REVERT: G 80 GLU cc_start: 0.8973 (tp30) cc_final: 0.8543 (mm-30) REVERT: G 107 MET cc_start: 0.8683 (tpp) cc_final: 0.8472 (ttm) REVERT: G 231 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8095 (tm-30) REVERT: G 235 GLU cc_start: 0.8244 (tm-30) cc_final: 0.8008 (tm-30) REVERT: G 246 GLN cc_start: 0.8144 (mm110) cc_final: 0.7288 (tm-30) REVERT: G 250 GLN cc_start: 0.8745 (pp30) cc_final: 0.8480 (pp30) REVERT: H 80 GLU cc_start: 0.8522 (tp30) cc_final: 0.8271 (tp30) outliers start: 47 outliers final: 37 residues processed: 307 average time/residue: 0.2306 time to fit residues: 109.1514 Evaluate side-chains 319 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 76 MET 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 149 GLU 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 180 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 149 GLU 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 180 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 180 CYS 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 149 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 149 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 ASN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14928 Z= 0.204 Angle : 0.611 10.202 20256 Z= 0.311 Chirality : 0.039 0.165 2328 Planarity : 0.005 0.055 2504 Dihedral : 11.069 120.882 2360 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.25 % Allowed : 21.27 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1856 helix: 1.27 (0.16), residues: 1192 sheet: None (None), residues: 0 loop : -2.84 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 218 HIS 0.001 0.000 HIS C 220 PHE 0.007 0.001 PHE C 189 TYR 0.011 0.001 TYR D 177 ARG 0.002 0.000 ARG F 105 *********************** 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 357 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 310 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8995 (tp30) cc_final: 0.8516 (mm-30) REVERT: A 216 ARG cc_start: 0.9342 (tpp80) cc_final: 0.8851 (tpt-90) REVERT: A 231 GLU cc_start: 0.8303 (tm-30) cc_final: 0.8099 (tm-30) REVERT: A 235 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8031 (tm-30) REVERT: A 246 GLN cc_start: 0.8149 (mm110) cc_final: 0.7276 (tm-30) REVERT: A 250 GLN cc_start: 0.8771 (pp30) cc_final: 0.8508 (pp30) REVERT: B 80 GLU cc_start: 0.8536 (tp30) cc_final: 0.8229 (tp30) REVERT: C 80 GLU cc_start: 0.8993 (tp30) cc_final: 0.8507 (mm-30) REVERT: C 216 ARG cc_start: 0.9343 (tpp80) cc_final: 0.8860 (tpt-90) REVERT: C 231 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8083 (tm-30) REVERT: C 235 GLU cc_start: 0.8280 (tm-30) cc_final: 0.8040 (tm-30) REVERT: C 246 GLN cc_start: 0.8133 (mm110) cc_final: 0.7263 (tm-30) REVERT: C 250 GLN cc_start: 0.8770 (pp30) cc_final: 0.8507 (pp30) REVERT: D 80 GLU cc_start: 0.8876 (tp30) cc_final: 0.8542 (mm-30) REVERT: E 80 GLU cc_start: 0.8981 (tp30) cc_final: 0.8494 (mm-30) REVERT: E 216 ARG cc_start: 0.9341 (tpp80) cc_final: 0.8857 (tpt-90) REVERT: E 231 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8087 (tm-30) REVERT: E 235 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8051 (tm-30) REVERT: E 246 GLN cc_start: 0.8159 (mm110) cc_final: 0.7278 (tm-30) REVERT: E 250 GLN cc_start: 0.8768 (pp30) cc_final: 0.8501 (pp30) REVERT: G 80 GLU cc_start: 0.8998 (tp30) cc_final: 0.8516 (mm-30) REVERT: G 216 ARG cc_start: 0.9338 (tpp80) cc_final: 0.8869 (tpt-90) REVERT: G 231 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8095 (tm-30) REVERT: G 235 GLU cc_start: 0.8278 (tm-30) cc_final: 0.8028 (tm-30) REVERT: G 246 GLN cc_start: 0.8157 (mm110) cc_final: 0.7287 (tm-30) REVERT: G 250 GLN cc_start: 0.8766 (pp30) cc_final: 0.8502 (pp30) REVERT: H 80 GLU cc_start: 0.8536 (tp30) cc_final: 0.8226 (tp30) outliers start: 47 outliers final: 34 residues processed: 319 average time/residue: 0.2215 time to fit residues: 108.7675 Evaluate side-chains 333 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 299 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE 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 A residue 200 VAL 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 B residue 200 VAL Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 149 GLU 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 180 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 76 MET Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 180 CYS 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 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 124 ILE Chi-restraints excluded: chain G residue 149 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 171 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 101 optimal weight: 0.0970 chunk 130 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14928 Z= 0.185 Angle : 0.601 9.767 20256 Z= 0.304 Chirality : 0.038 0.159 2328 Planarity : 0.005 0.055 2504 Dihedral : 11.002 119.031 2360 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.25 % Allowed : 21.69 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1856 helix: 1.44 (0.16), residues: 1192 sheet: None (None), residues: 0 loop : -2.78 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 218 HIS 0.001 0.000 HIS A 220 PHE 0.007 0.001 PHE G 39 TYR 0.009 0.001 TYR B 177 ARG 0.002 0.000 ARG F 105 *********************** 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 371 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 1.757 Fit side-chains REVERT: A 80 GLU cc_start: 0.9007 (tp30) cc_final: 0.8496 (mm-30) REVERT: A 216 ARG cc_start: 0.9326 (tpp80) cc_final: 0.8799 (tpt-90) REVERT: A 235 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 246 GLN cc_start: 0.8119 (mm110) cc_final: 0.7275 (tm-30) REVERT: A 250 GLN cc_start: 0.8759 (pp30) cc_final: 0.8500 (pp30) REVERT: B 80 GLU cc_start: 0.8535 (tp30) cc_final: 0.8216 (tp30) REVERT: B 246 GLN cc_start: 0.8019 (mm110) cc_final: 0.7208 (tm-30) REVERT: C 80 GLU cc_start: 0.9007 (tp30) cc_final: 0.8494 (mm-30) REVERT: C 216 ARG cc_start: 0.9324 (tpp80) cc_final: 0.8799 (tpt-90) REVERT: C 235 GLU cc_start: 0.8283 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 246 GLN cc_start: 0.8072 (mm110) cc_final: 0.7253 (tm-30) REVERT: C 250 GLN cc_start: 0.8760 (pp30) cc_final: 0.8499 (pp30) REVERT: D 80 GLU cc_start: 0.8875 (tp30) cc_final: 0.8520 (mm-30) REVERT: D 216 ARG cc_start: 0.9264 (tpp80) cc_final: 0.8912 (tpt-90) REVERT: D 246 GLN cc_start: 0.8039 (mm110) cc_final: 0.7144 (tm-30) REVERT: E 80 GLU cc_start: 0.9003 (tp30) cc_final: 0.8497 (mm-30) REVERT: E 107 MET cc_start: 0.8573 (ttm) cc_final: 0.8232 (ttm) REVERT: E 216 ARG cc_start: 0.9321 (tpp80) cc_final: 0.8799 (tpt-90) REVERT: E 235 GLU cc_start: 0.8290 (tm-30) cc_final: 0.8066 (tm-30) REVERT: E 246 GLN cc_start: 0.8128 (mm110) cc_final: 0.7290 (tm-30) REVERT: E 250 GLN cc_start: 0.8759 (pp30) cc_final: 0.8492 (pp30) REVERT: F 80 GLU cc_start: 0.8909 (tp30) cc_final: 0.8621 (tp30) REVERT: F 115 SER cc_start: 0.9297 (p) cc_final: 0.9093 (p) REVERT: F 217 TYR cc_start: 0.8847 (t80) cc_final: 0.8622 (t80) REVERT: F 246 GLN cc_start: 0.8099 (mm110) cc_final: 0.7162 (tm-30) REVERT: G 80 GLU cc_start: 0.9014 (tp30) cc_final: 0.8504 (mm-30) REVERT: G 216 ARG cc_start: 0.9322 (tpp80) cc_final: 0.8800 (tpt-90) REVERT: G 235 GLU cc_start: 0.8279 (tm-30) cc_final: 0.8042 (tm-30) REVERT: G 246 GLN cc_start: 0.8140 (mm110) cc_final: 0.7307 (tm-30) REVERT: G 250 GLN cc_start: 0.8755 (pp30) cc_final: 0.8493 (pp30) REVERT: H 80 GLU cc_start: 0.8559 (tp30) cc_final: 0.8242 (tp30) REVERT: H 246 GLN cc_start: 0.8026 (mm110) cc_final: 0.7216 (tm-30) outliers start: 47 outliers final: 39 residues processed: 340 average time/residue: 0.2229 time to fit residues: 117.4162 Evaluate side-chains 350 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 311 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET 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 149 GLU Chi-restraints excluded: chain A residue 180 CYS Chi-restraints excluded: chain B residue 40 ASN 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 76 MET 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 D residue 76 MET 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 134 VAL Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain F residue 124 ILE 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 76 MET Chi-restraints excluded: chain G residue 124 ILE 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 G residue 200 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain H residue 76 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 109 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 0.0040 chunk 53 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 112 optimal weight: 0.3980 chunk 120 optimal weight: 0.6980 chunk 87 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 overall best weight: 1.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14928 Z= 0.233 Angle : 0.622 10.203 20256 Z= 0.316 Chirality : 0.039 0.166 2328 Planarity : 0.005 0.054 2504 Dihedral : 11.089 119.242 2360 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 3.59 % Allowed : 22.03 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1856 helix: 1.49 (0.16), residues: 1176 sheet: None (None), residues: 0 loop : -2.49 (0.27), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 218 HIS 0.001 0.000 HIS E 143 PHE 0.005 0.001 PHE F 198 TYR 0.012 0.001 TYR B 177 ARG 0.002 0.000 ARG F 105 *********************** 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 357 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9009 (tp30) cc_final: 0.8482 (mm-30) REVERT: A 235 GLU cc_start: 0.8326 (tm-30) cc_final: 0.8091 (tm-30) REVERT: A 246 GLN cc_start: 0.8173 (mm110) cc_final: 0.7301 (tm-30) REVERT: A 250 GLN cc_start: 0.8768 (pp30) cc_final: 0.8498 (pp30) REVERT: B 80 GLU cc_start: 0.8486 (tp30) cc_final: 0.8121 (tp30) REVERT: B 246 GLN cc_start: 0.8131 (mm110) cc_final: 0.7235 (tm-30) REVERT: C 80 GLU cc_start: 0.9003 (tp30) cc_final: 0.8479 (mm-30) REVERT: C 235 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8082 (tm-30) REVERT: C 246 GLN cc_start: 0.8151 (mm110) cc_final: 0.7280 (tm-30) REVERT: C 250 GLN cc_start: 0.8767 (pp30) cc_final: 0.8495 (pp30) REVERT: D 80 GLU cc_start: 0.8880 (tp30) cc_final: 0.8493 (mm-30) REVERT: E 80 GLU cc_start: 0.9004 (tp30) cc_final: 0.8478 (mm-30) REVERT: E 107 MET cc_start: 0.8616 (ttm) cc_final: 0.8319 (ttm) REVERT: E 235 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8102 (tm-30) REVERT: E 246 GLN cc_start: 0.8179 (mm110) cc_final: 0.7339 (tm-30) REVERT: E 250 GLN cc_start: 0.8766 (pp30) cc_final: 0.8490 (pp30) REVERT: F 80 GLU cc_start: 0.8852 (tp30) cc_final: 0.8557 (tp30) REVERT: G 80 GLU cc_start: 0.9019 (tp30) cc_final: 0.8499 (mm-30) REVERT: G 235 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8094 (tm-30) REVERT: G 246 GLN cc_start: 0.8187 (mm110) cc_final: 0.7327 (tm-30) REVERT: G 250 GLN cc_start: 0.8763 (pp30) cc_final: 0.8491 (pp30) REVERT: H 80 GLU cc_start: 0.8542 (tp30) cc_final: 0.8180 (tp30) REVERT: H 246 GLN cc_start: 0.8141 (mm110) cc_final: 0.7246 (tm-30) outliers start: 52 outliers final: 41 residues processed: 321 average time/residue: 0.2144 time to fit residues: 108.1707 Evaluate side-chains 342 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 76 MET 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 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 149 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 134 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 149 GLU 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 134 VAL Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain F residue 124 ILE 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 76 MET Chi-restraints excluded: chain G residue 124 ILE 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 G residue 200 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain H residue 76 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 169 optimal weight: 0.8980 chunk 155 optimal weight: 0.4980 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 chunk 156 optimal weight: 5.9990 chunk 164 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14928 Z= 0.183 Angle : 0.599 9.463 20256 Z= 0.304 Chirality : 0.038 0.146 2328 Planarity : 0.005 0.056 2504 Dihedral : 10.533 111.267 2360 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.31 % Allowed : 22.24 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1856 helix: 1.56 (0.16), residues: 1192 sheet: None (None), residues: 0 loop : -2.65 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 218 HIS 0.000 0.000 HIS C 143 PHE 0.010 0.001 PHE E 189 TYR 0.009 0.001 TYR E 177 ARG 0.002 0.000 ARG F 105 *********************** 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 365 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 317 time to evaluate : 1.589 Fit side-chains REVERT: A 80 GLU cc_start: 0.9020 (tp30) cc_final: 0.8468 (mm-30) REVERT: A 216 ARG cc_start: 0.9311 (tpp80) cc_final: 0.8736 (tpt-90) REVERT: A 235 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 246 GLN cc_start: 0.8057 (mm110) cc_final: 0.7249 (tm-30) REVERT: A 250 GLN cc_start: 0.8743 (pp30) cc_final: 0.8492 (pp30) REVERT: B 80 GLU cc_start: 0.8570 (tp30) cc_final: 0.8205 (tp30) REVERT: B 246 GLN cc_start: 0.7971 (mm110) cc_final: 0.7178 (tm-30) REVERT: C 80 GLU cc_start: 0.9015 (tp30) cc_final: 0.8461 (mm-30) REVERT: C 216 ARG cc_start: 0.9311 (tpp80) cc_final: 0.8742 (tpt-90) REVERT: C 235 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8081 (tm-30) REVERT: C 246 GLN cc_start: 0.8054 (mm110) cc_final: 0.7238 (tm-30) REVERT: C 250 GLN cc_start: 0.8741 (pp30) cc_final: 0.8485 (pp30) REVERT: D 80 GLU cc_start: 0.8843 (tp30) cc_final: 0.8460 (mm-30) REVERT: D 246 GLN cc_start: 0.7974 (mm110) cc_final: 0.7183 (tm-30) REVERT: E 80 GLU cc_start: 0.9023 (tp30) cc_final: 0.8474 (mm-30) REVERT: E 107 MET cc_start: 0.8611 (ttm) cc_final: 0.8351 (ttm) REVERT: E 216 ARG cc_start: 0.9306 (tpp80) cc_final: 0.8732 (tpt-90) REVERT: E 235 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8093 (tm-30) REVERT: E 246 GLN cc_start: 0.8058 (mm110) cc_final: 0.7239 (tm-30) REVERT: E 250 GLN cc_start: 0.8744 (pp30) cc_final: 0.8484 (pp30) REVERT: F 80 GLU cc_start: 0.8805 (tp30) cc_final: 0.8547 (tp30) REVERT: F 246 GLN cc_start: 0.8065 (mm110) cc_final: 0.7178 (tm-30) REVERT: G 80 GLU cc_start: 0.9025 (tp30) cc_final: 0.8477 (mm-30) REVERT: G 216 ARG cc_start: 0.9310 (tpp80) cc_final: 0.8744 (tpt-90) REVERT: G 235 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8080 (tm-30) REVERT: G 246 GLN cc_start: 0.8061 (mm110) cc_final: 0.7255 (tm-30) REVERT: G 250 GLN cc_start: 0.8731 (pp30) cc_final: 0.8476 (pp30) REVERT: H 80 GLU cc_start: 0.8572 (tp30) cc_final: 0.8208 (tp30) REVERT: H 246 GLN cc_start: 0.7978 (mm110) cc_final: 0.7188 (tm-30) outliers start: 48 outliers final: 43 residues processed: 333 average time/residue: 0.2208 time to fit residues: 113.8950 Evaluate side-chains 348 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET 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 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 149 GLU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain D residue 76 MET 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 134 VAL Chi-restraints excluded: chain E residue 149 GLU Chi-restraints excluded: chain E residue 180 CYS 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 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 76 MET Chi-restraints excluded: chain G residue 124 ILE 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 G residue 200 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain H residue 76 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 174 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14928 Z= 0.305 Angle : 0.676 10.689 20256 Z= 0.345 Chirality : 0.041 0.177 2328 Planarity : 0.005 0.054 2504 Dihedral : 10.933 112.079 2360 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.73 % Allowed : 22.58 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.21), residues: 1856 helix: 1.25 (0.16), residues: 1192 sheet: None (None), residues: 0 loop : -2.65 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 218 HIS 0.002 0.001 HIS G 143 PHE 0.008 0.001 PHE F 198 TYR 0.017 0.002 TYR D 177 ARG 0.001 0.000 ARG C 216 ********************** 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 321 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 267 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9011 (tp30) cc_final: 0.8433 (mm-30) REVERT: A 196 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8495 (tt) REVERT: A 223 ASP cc_start: 0.8919 (t70) cc_final: 0.8584 (t70) REVERT: A 235 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 246 GLN cc_start: 0.8266 (mm110) cc_final: 0.7330 (tm-30) REVERT: A 250 GLN cc_start: 0.8747 (pp30) cc_final: 0.8454 (pp30) REVERT: B 80 GLU cc_start: 0.8527 (tp30) cc_final: 0.8125 (tp30) REVERT: B 246 GLN cc_start: 0.8281 (mm110) cc_final: 0.7305 (tm-30) REVERT: C 80 GLU cc_start: 0.9011 (tp30) cc_final: 0.8432 (mm-30) REVERT: C 196 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8493 (tt) REVERT: C 223 ASP cc_start: 0.8914 (t70) cc_final: 0.8575 (t70) REVERT: C 235 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8154 (tm-30) REVERT: C 246 GLN cc_start: 0.8262 (mm110) cc_final: 0.7328 (tm-30) REVERT: C 250 GLN cc_start: 0.8745 (pp30) cc_final: 0.8448 (pp30) REVERT: D 62 ILE cc_start: 0.8886 (mt) cc_final: 0.8677 (mt) REVERT: D 80 GLU cc_start: 0.8893 (tp30) cc_final: 0.8484 (mm-30) REVERT: E 80 GLU cc_start: 0.9010 (tp30) cc_final: 0.8431 (mm-30) REVERT: E 107 MET cc_start: 0.8652 (ttm) cc_final: 0.8357 (ttm) REVERT: E 120 ASP cc_start: 0.8734 (m-30) cc_final: 0.8523 (m-30) REVERT: E 223 ASP cc_start: 0.8917 (t70) cc_final: 0.8579 (t70) REVERT: E 235 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8157 (tm-30) REVERT: E 246 GLN cc_start: 0.8258 (mm110) cc_final: 0.7318 (tm-30) REVERT: E 250 GLN cc_start: 0.8747 (pp30) cc_final: 0.8435 (pp30) REVERT: F 62 ILE cc_start: 0.8900 (mt) cc_final: 0.8671 (mt) REVERT: F 80 GLU cc_start: 0.8792 (tp30) cc_final: 0.8457 (tp30) REVERT: G 80 GLU cc_start: 0.9015 (tp30) cc_final: 0.8440 (mm-30) REVERT: G 120 ASP cc_start: 0.8664 (m-30) cc_final: 0.8377 (m-30) REVERT: G 196 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8492 (tt) REVERT: G 223 ASP cc_start: 0.8912 (t70) cc_final: 0.8583 (t70) REVERT: G 235 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8152 (tm-30) REVERT: G 246 GLN cc_start: 0.8253 (mm110) cc_final: 0.7330 (tm-30) REVERT: G 250 GLN cc_start: 0.8741 (pp30) cc_final: 0.8445 (pp30) REVERT: H 80 GLU cc_start: 0.8584 (tp30) cc_final: 0.8185 (tp30) outliers start: 54 outliers final: 37 residues processed: 293 average time/residue: 0.2202 time to fit residues: 100.5970 Evaluate side-chains 304 residues out of total 1592 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 MET 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 A residue 196 LEU Chi-restraints excluded: chain A residue 200 VAL 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 B residue 200 VAL Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain D residue 76 MET 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 76 MET Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 180 CYS 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 149 GLU Chi-restraints excluded: chain F residue 180 CYS Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 124 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain H residue 76 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 0.0970 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.129395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101792 restraints weight = 27510.467| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.61 r_work: 0.2966 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14928 Z= 0.217 Angle : 0.644 10.667 20256 Z= 0.321 Chirality : 0.039 0.160 2328 Planarity : 0.005 0.055 2504 Dihedral : 10.674 108.808 2360 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.80 % Allowed : 22.79 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1856 helix: 1.37 (0.16), residues: 1200 sheet: None (None), residues: 0 loop : -2.50 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 218 HIS 0.001 0.000 HIS H 143 PHE 0.005 0.001 PHE B 37 TYR 0.012 0.001 TYR B 177 ARG 0.002 0.000 ARG C 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3248.84 seconds wall clock time: 60 minutes 38.18 seconds (3638.18 seconds total)