Starting phenix.real_space_refine on Mon Aug 25 10:56:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bhb_16051/08_2025/8bhb_16051_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bhb_16051/08_2025/8bhb_16051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bhb_16051/08_2025/8bhb_16051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bhb_16051/08_2025/8bhb_16051.map" model { file = "/net/cci-nas-00/data/ceres_data/8bhb_16051/08_2025/8bhb_16051_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bhb_16051/08_2025/8bhb_16051_trim.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 85 5.16 5 C 8910 2.51 5 N 2290 2.21 5 O 2550 1.98 5 H 13415 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27250 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5399 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'EIE': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Restraints were copied for chains: B, C, D, E Time building chain proxies: 5.87, per 1000 atoms: 0.22 Number of scatterers: 27250 At special positions: 0 Unit cell: (90.628, 93.888, 123.228, 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 85 16.00 O 2550 8.00 N 2290 7.00 C 8910 6.00 H 13415 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 156 " distance=2.03 Simple disulfide: pdb=" SG CYS E 142 " - pdb=" SG CYS E 156 " 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 205 " " NAG B 501 " - " ASN B 205 " " NAG C 501 " - " ASN C 205 " " NAG D 501 " - " ASN D 205 " " NAG E 501 " - " ASN E 205 " Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 830.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 41.4% alpha, 39.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 removed outlier: 3.573A pdb=" N THR A 19 " --> pdb=" O ILE A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 90 through 94 removed outlier: 3.577A pdb=" N LEU A 93 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 254 through 280 removed outlier: 4.147A pdb=" N SER A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 314 Processing helix chain 'A' and resid 317 through 418 removed outlier: 4.033A pdb=" N ILE A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 15 through 27 removed outlier: 3.573A pdb=" N THR B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 90 through 94 removed outlier: 3.576A pdb=" N LEU B 93 " --> pdb=" O ASN B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 247 through 250 Processing helix chain 'B' and resid 254 through 280 removed outlier: 4.147A pdb=" N SER B 279 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 314 Processing helix chain 'B' and resid 317 through 418 removed outlier: 4.033A pdb=" N ILE B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 15 through 27 removed outlier: 3.574A pdb=" N THR C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.577A pdb=" N LEU C 93 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 181 Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 250 Processing helix chain 'C' and resid 254 through 280 removed outlier: 4.148A pdb=" N SER C 279 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 314 Processing helix chain 'C' and resid 317 through 418 removed outlier: 4.033A pdb=" N ILE C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'D' and resid 15 through 27 removed outlier: 3.573A pdb=" N THR D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 79 Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.577A pdb=" N LEU D 93 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 247 through 250 Processing helix chain 'D' and resid 254 through 280 removed outlier: 4.147A pdb=" N SER D 279 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU D 280 " --> pdb=" O ALA D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 314 Processing helix chain 'D' and resid 317 through 418 removed outlier: 4.034A pdb=" N ILE D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'E' and resid 15 through 27 removed outlier: 3.573A pdb=" N THR E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 79 Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.577A pdb=" N LEU E 93 " --> pdb=" O ASN E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 233 through 246 Processing helix chain 'E' and resid 247 through 250 Processing helix chain 'E' and resid 254 through 280 removed outlier: 4.147A pdb=" N SER E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 314 Processing helix chain 'E' and resid 317 through 418 removed outlier: 4.033A pdb=" N ILE E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) Proline residue: E 403 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88 removed outlier: 3.613A pdb=" N ILE A 124 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 112 removed outlier: 7.067A pdb=" N SER A 139 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N SER A 110 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR A 137 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA A 112 " --> pdb=" O ARG A 135 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG A 135 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU A 62 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A 64 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE A 53 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP A 66 " --> pdb=" O ASN A 51 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 74 " --> pdb=" O GLN A 43 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 43 " --> pdb=" O LYS A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER A 162 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 214 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY A 198 " --> pdb=" O HIS A 221 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS A 223 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU A 196 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.612A pdb=" N ILE B 124 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG B 129 " --> pdb=" O TRP B 125 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 112 removed outlier: 7.067A pdb=" N SER B 139 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER B 110 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR B 137 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA B 112 " --> pdb=" O ARG B 135 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG B 135 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU B 62 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 64 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE B 53 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP B 66 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS B 74 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 43 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER B 162 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR B 214 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY B 198 " --> pdb=" O HIS B 221 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS B 223 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU B 196 " --> pdb=" O LYS B 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 88 removed outlier: 3.612A pdb=" N ILE C 124 " --> pdb=" O LEU C 87 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG C 129 " --> pdb=" O TRP C 125 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 112 removed outlier: 7.068A pdb=" N SER C 139 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER C 110 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C 137 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA C 112 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG C 135 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU C 62 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 64 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE C 53 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP C 66 " --> pdb=" O ASN C 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS C 74 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN C 43 " --> pdb=" O LYS C 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER C 162 " --> pdb=" O THR C 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 214 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY C 198 " --> pdb=" O HIS C 221 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS C 223 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU C 196 " --> pdb=" O LYS C 223 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 88 removed outlier: 3.613A pdb=" N ILE D 124 " --> pdb=" O LEU D 87 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG D 129 " --> pdb=" O TRP D 125 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 112 removed outlier: 7.068A pdb=" N SER D 139 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER D 110 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR D 137 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA D 112 " --> pdb=" O ARG D 135 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG D 135 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU D 62 " --> pdb=" O PRO D 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 64 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N PHE D 53 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP D 66 " --> pdb=" O ASN D 51 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS D 74 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN D 43 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER D 162 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR D 214 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY D 198 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS D 223 " --> pdb=" O LEU D 196 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU D 196 " --> pdb=" O LYS D 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 88 removed outlier: 3.612A pdb=" N ILE E 124 " --> pdb=" O LEU E 87 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG E 129 " --> pdb=" O TRP E 125 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 112 removed outlier: 7.067A pdb=" N SER E 139 " --> pdb=" O LYS E 108 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER E 110 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR E 137 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ALA E 112 " --> pdb=" O ARG E 135 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ARG E 135 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLU E 62 " --> pdb=" O PRO E 55 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR E 64 " --> pdb=" O PHE E 53 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N PHE E 53 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP E 66 " --> pdb=" O ASN E 51 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS E 74 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN E 43 " --> pdb=" O LYS E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 102 through 104 removed outlier: 4.780A pdb=" N SER E 162 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR E 214 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY E 198 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LYS E 223 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU E 196 " --> pdb=" O LYS E 223 " (cutoff:3.500A) 830 hydrogen bonds defined for protein. 2430 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: 5.81 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13415 1.03 - 1.23: 18 1.23 - 1.42: 6102 1.42 - 1.62: 7870 1.62 - 1.81: 150 Bond restraints: 27555 Sorted by residual: bond pdb=" N ASN B 14 " pdb=" H ASN B 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" N ASN D 14 " pdb=" H ASN D 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN E 14 " pdb=" H ASN E 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN C 14 " pdb=" H ASN C 14 " ideal model delta sigma weight residual 0.860 0.960 -0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASN A 14 " pdb=" H ASN A 14 " ideal model delta sigma weight residual 0.860 0.959 -0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 27550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 48531 1.25 - 2.51: 856 2.51 - 3.76: 89 3.76 - 5.02: 34 5.02 - 6.27: 10 Bond angle restraints: 49520 Sorted by residual: angle pdb=" C MET D 115 " pdb=" N THR D 116 " pdb=" CA THR D 116 " ideal model delta sigma weight residual 121.70 126.91 -5.21 1.80e+00 3.09e-01 8.37e+00 angle pdb=" C MET C 115 " pdb=" N THR C 116 " pdb=" CA THR C 116 " ideal model delta sigma weight residual 121.70 126.87 -5.17 1.80e+00 3.09e-01 8.26e+00 angle pdb=" C MET B 115 " pdb=" N THR B 116 " pdb=" CA THR B 116 " ideal model delta sigma weight residual 121.70 126.86 -5.16 1.80e+00 3.09e-01 8.22e+00 angle pdb=" C MET E 115 " pdb=" N THR E 116 " pdb=" CA THR E 116 " ideal model delta sigma weight residual 121.70 126.85 -5.15 1.80e+00 3.09e-01 8.20e+00 angle pdb=" C MET A 115 " pdb=" N THR A 116 " pdb=" CA THR A 116 " ideal model delta sigma weight residual 121.70 126.83 -5.13 1.80e+00 3.09e-01 8.12e+00 ... (remaining 49515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 12603 15.91 - 31.82: 382 31.82 - 47.73: 90 47.73 - 63.63: 95 63.63 - 79.54: 5 Dihedral angle restraints: 13175 sinusoidal: 7045 harmonic: 6130 Sorted by residual: dihedral pdb=" CB MET E 115 " pdb=" CG MET E 115 " pdb=" SD MET E 115 " pdb=" CE MET E 115 " ideal model delta sinusoidal sigma weight residual 60.00 103.42 -43.42 3 1.50e+01 4.44e-03 7.80e+00 dihedral pdb=" CB MET D 115 " pdb=" CG MET D 115 " pdb=" SD MET D 115 " pdb=" CE MET D 115 " ideal model delta sinusoidal sigma weight residual 60.00 103.41 -43.41 3 1.50e+01 4.44e-03 7.80e+00 dihedral pdb=" CB MET A 115 " pdb=" CG MET A 115 " pdb=" SD MET A 115 " pdb=" CE MET A 115 " ideal model delta sinusoidal sigma weight residual 60.00 103.40 -43.40 3 1.50e+01 4.44e-03 7.80e+00 ... (remaining 13172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1225 0.024 - 0.047: 607 0.047 - 0.071: 173 0.071 - 0.095: 71 0.095 - 0.119: 84 Chirality restraints: 2160 Sorted by residual: chirality pdb=" CA ILE D 124 " pdb=" N ILE D 124 " pdb=" C ILE D 124 " pdb=" CB ILE D 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE C 124 " pdb=" N ILE C 124 " pdb=" C ILE C 124 " pdb=" CB ILE C 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 chirality pdb=" CA ILE E 124 " pdb=" N ILE E 124 " pdb=" C ILE E 124 " pdb=" CB ILE E 124 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.45e-01 ... (remaining 2157 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 EIE E 502 " 0.482 2.00e-02 2.50e+03 4.61e-01 5.84e+03 pdb=" C11 EIE E 502 " 0.364 2.00e-02 2.50e+03 pdb=" C12 EIE E 502 " 0.062 2.00e-02 2.50e+03 pdb=" C13 EIE E 502 " -0.130 2.00e-02 2.50e+03 pdb=" C7 EIE E 502 " -0.210 2.00e-02 2.50e+03 pdb=" C8 EIE E 502 " -0.015 2.00e-02 2.50e+03 pdb=" C9 EIE E 502 " 0.294 2.00e-02 2.50e+03 pdb=" N1 EIE E 502 " 0.787 2.00e-02 2.50e+03 pdb=" N2 EIE E 502 " -0.210 2.00e-02 2.50e+03 pdb=" N3 EIE E 502 " -0.978 2.00e-02 2.50e+03 pdb=" N4 EIE E 502 " -0.445 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIE D 502 " -0.482 2.00e-02 2.50e+03 4.61e-01 5.84e+03 pdb=" C11 EIE D 502 " -0.364 2.00e-02 2.50e+03 pdb=" C12 EIE D 502 " -0.062 2.00e-02 2.50e+03 pdb=" C13 EIE D 502 " 0.131 2.00e-02 2.50e+03 pdb=" C7 EIE D 502 " 0.210 2.00e-02 2.50e+03 pdb=" C8 EIE D 502 " 0.014 2.00e-02 2.50e+03 pdb=" C9 EIE D 502 " -0.294 2.00e-02 2.50e+03 pdb=" N1 EIE D 502 " -0.787 2.00e-02 2.50e+03 pdb=" N2 EIE D 502 " 0.211 2.00e-02 2.50e+03 pdb=" N3 EIE D 502 " 0.978 2.00e-02 2.50e+03 pdb=" N4 EIE D 502 " 0.445 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 EIE B 502 " -0.482 2.00e-02 2.50e+03 4.61e-01 5.83e+03 pdb=" C11 EIE B 502 " -0.365 2.00e-02 2.50e+03 pdb=" C12 EIE B 502 " -0.062 2.00e-02 2.50e+03 pdb=" C13 EIE B 502 " 0.130 2.00e-02 2.50e+03 pdb=" C7 EIE B 502 " 0.209 2.00e-02 2.50e+03 pdb=" C8 EIE B 502 " 0.015 2.00e-02 2.50e+03 pdb=" C9 EIE B 502 " -0.294 2.00e-02 2.50e+03 pdb=" N1 EIE B 502 " -0.787 2.00e-02 2.50e+03 pdb=" N2 EIE B 502 " 0.211 2.00e-02 2.50e+03 pdb=" N3 EIE B 502 " 0.978 2.00e-02 2.50e+03 pdb=" N4 EIE B 502 " 0.445 2.00e-02 2.50e+03 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 2393 2.25 - 2.83: 62032 2.83 - 3.42: 69894 3.42 - 4.01: 100558 4.01 - 4.60: 155147 Nonbonded interactions: 390024 Sorted by model distance: nonbonded pdb=" H ASN A 167 " pdb=" O GLU A 212 " model vdw 1.657 2.450 nonbonded pdb=" H ASN E 167 " pdb=" O GLU E 212 " model vdw 1.657 2.450 nonbonded pdb=" H ASN B 167 " pdb=" O GLU B 212 " model vdw 1.658 2.450 nonbonded pdb=" H ASN C 167 " pdb=" O GLU C 212 " model vdw 1.658 2.450 nonbonded pdb=" H ASN D 167 " pdb=" O GLU D 212 " model vdw 1.658 2.450 ... (remaining 390019 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.630 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: 0.180 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 25.400 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14150 Z= 0.119 Angle : 0.418 6.270 19270 Z= 0.194 Chirality : 0.037 0.119 2160 Planarity : 0.021 0.461 2395 Dihedral : 7.198 79.543 5165 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.13 (0.21), residues: 1670 helix: 2.96 (0.22), residues: 585 sheet: 0.65 (0.27), residues: 435 loop : 0.61 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 320 TYR 0.005 0.001 TYR B 285 PHE 0.005 0.001 PHE E 104 TRP 0.004 0.000 TRP B 414 HIS 0.003 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00261 (14140) covalent geometry : angle 0.41514 (19245) SS BOND : bond 0.00064 ( 5) SS BOND : angle 0.15322 ( 10) hydrogen bonds : bond 0.21737 ( 735) hydrogen bonds : angle 7.40739 ( 2430) link_NAG-ASN : bond 0.00061 ( 5) link_NAG-ASN : angle 1.76874 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8597 (tttt) cc_final: 0.8284 (tptp) REVERT: A 193 GLN cc_start: 0.8146 (pt0) cc_final: 0.7829 (pm20) REVERT: B 109 LYS cc_start: 0.8583 (tttt) cc_final: 0.8245 (tptp) REVERT: B 193 GLN cc_start: 0.8164 (pt0) cc_final: 0.7957 (pm20) REVERT: B 253 GLU cc_start: 0.8677 (pm20) cc_final: 0.7852 (pm20) REVERT: C 109 LYS cc_start: 0.8597 (tttt) cc_final: 0.8272 (tptp) REVERT: D 109 LYS cc_start: 0.8619 (tttt) cc_final: 0.8304 (tptp) REVERT: D 193 GLN cc_start: 0.8169 (pt0) cc_final: 0.7950 (pm20) REVERT: E 109 LYS cc_start: 0.8603 (tttt) cc_final: 0.8289 (tptp) REVERT: E 193 GLN cc_start: 0.8149 (pt0) cc_final: 0.7898 (pm20) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 1.5655 time to fit residues: 446.8391 Evaluate side-chains 135 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN B 155 ASN C 155 ASN D 155 ASN E 155 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.080407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.066810 restraints weight = 74554.698| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.34 r_work: 0.2785 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14150 Z= 0.231 Angle : 0.545 6.883 19270 Z= 0.291 Chirality : 0.043 0.136 2160 Planarity : 0.005 0.035 2395 Dihedral : 3.976 18.663 2030 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.28 % Allowed : 6.31 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.21), residues: 1670 helix: 3.14 (0.20), residues: 615 sheet: 0.45 (0.25), residues: 455 loop : 0.29 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 79 TYR 0.010 0.001 TYR E 194 PHE 0.016 0.002 PHE E 68 TRP 0.006 0.001 TRP E 291 HIS 0.004 0.001 HIS C 221 Details of bonding type rmsd covalent geometry : bond 0.00534 (14140) covalent geometry : angle 0.54367 (19245) SS BOND : bond 0.00558 ( 5) SS BOND : angle 0.62717 ( 10) hydrogen bonds : bond 0.04996 ( 735) hydrogen bonds : angle 4.81774 ( 2430) link_NAG-ASN : bond 0.00208 ( 5) link_NAG-ASN : angle 1.56615 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8686 (tttt) cc_final: 0.8142 (tptp) REVERT: A 193 GLN cc_start: 0.8299 (pt0) cc_final: 0.7829 (pm20) REVERT: A 253 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8496 (mp0) REVERT: A 277 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7709 (mmt180) REVERT: B 109 LYS cc_start: 0.8628 (tttt) cc_final: 0.8088 (tptp) REVERT: B 193 GLN cc_start: 0.8310 (pt0) cc_final: 0.7844 (pm20) REVERT: B 251 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7281 (t0) REVERT: B 277 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7767 (mmt180) REVERT: C 39 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: C 60 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8572 (mt-10) REVERT: C 109 LYS cc_start: 0.8635 (tttt) cc_final: 0.8099 (tptp) REVERT: C 253 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8528 (mp0) REVERT: C 277 ARG cc_start: 0.8017 (mtt180) cc_final: 0.7684 (mmt180) REVERT: D 109 LYS cc_start: 0.8653 (tttt) cc_final: 0.8114 (tptp) REVERT: D 193 GLN cc_start: 0.8314 (pt0) cc_final: 0.7847 (pm20) REVERT: D 251 ASN cc_start: 0.8099 (t0) cc_final: 0.7720 (t0) REVERT: D 253 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: E 39 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8080 (tp30) REVERT: E 109 LYS cc_start: 0.8653 (tttt) cc_final: 0.8115 (tptp) REVERT: E 193 GLN cc_start: 0.8250 (pt0) cc_final: 0.7797 (pm20) REVERT: E 253 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8272 (mp0) outliers start: 34 outliers final: 7 residues processed: 164 average time/residue: 1.3529 time to fit residues: 243.3303 Evaluate side-chains 149 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 277 ARG Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 397 MET Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 6 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.079628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.066084 restraints weight = 74858.344| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.33 r_work: 0.2744 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14150 Z= 0.193 Angle : 0.494 6.854 19270 Z= 0.261 Chirality : 0.041 0.146 2160 Planarity : 0.004 0.038 2395 Dihedral : 4.021 18.319 2030 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.55 % Allowed : 6.71 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.21), residues: 1670 helix: 3.23 (0.20), residues: 610 sheet: 0.22 (0.24), residues: 455 loop : 0.13 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 277 TYR 0.011 0.001 TYR A 132 PHE 0.012 0.002 PHE B 69 TRP 0.004 0.001 TRP D 291 HIS 0.004 0.001 HIS C 221 Details of bonding type rmsd covalent geometry : bond 0.00432 (14140) covalent geometry : angle 0.49225 (19245) SS BOND : bond 0.00436 ( 5) SS BOND : angle 0.65229 ( 10) hydrogen bonds : bond 0.04464 ( 735) hydrogen bonds : angle 4.46001 ( 2430) link_NAG-ASN : bond 0.00154 ( 5) link_NAG-ASN : angle 1.68539 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8499 (mt-10) REVERT: A 109 LYS cc_start: 0.8699 (tttt) cc_final: 0.8173 (tptp) REVERT: A 193 GLN cc_start: 0.8325 (pt0) cc_final: 0.7896 (pm20) REVERT: B 109 LYS cc_start: 0.8632 (tttt) cc_final: 0.8112 (tptp) REVERT: B 193 GLN cc_start: 0.8369 (pt0) cc_final: 0.7979 (pm20) REVERT: B 251 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7366 (t0) REVERT: C 39 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: C 60 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8521 (mt-10) REVERT: C 109 LYS cc_start: 0.8626 (tttt) cc_final: 0.8120 (tptp) REVERT: C 245 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8885 (mt0) REVERT: D 60 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8455 (mt-10) REVERT: D 109 LYS cc_start: 0.8667 (tttt) cc_final: 0.8148 (tptp) REVERT: D 193 GLN cc_start: 0.8380 (pt0) cc_final: 0.7926 (pm20) REVERT: D 251 ASN cc_start: 0.8071 (t0) cc_final: 0.7739 (t0) REVERT: E 39 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8094 (tp30) REVERT: E 109 LYS cc_start: 0.8660 (tttt) cc_final: 0.8140 (tptp) REVERT: E 193 GLN cc_start: 0.8307 (pt0) cc_final: 0.7906 (pm20) outliers start: 38 outliers final: 11 residues processed: 160 average time/residue: 1.3448 time to fit residues: 237.9156 Evaluate side-chains 142 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 140 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.077958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.064471 restraints weight = 75194.840| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.29 r_work: 0.2726 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14150 Z= 0.217 Angle : 0.506 8.525 19270 Z= 0.266 Chirality : 0.041 0.163 2160 Planarity : 0.004 0.039 2395 Dihedral : 4.234 20.177 2030 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.95 % Allowed : 7.05 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.21), residues: 1670 helix: 3.22 (0.20), residues: 610 sheet: 0.03 (0.24), residues: 465 loop : 0.06 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 277 TYR 0.010 0.001 TYR A 132 PHE 0.013 0.002 PHE A 104 TRP 0.004 0.001 TRP D 73 HIS 0.004 0.001 HIS C 221 Details of bonding type rmsd covalent geometry : bond 0.00492 (14140) covalent geometry : angle 0.50344 (19245) SS BOND : bond 0.00515 ( 5) SS BOND : angle 0.80671 ( 10) hydrogen bonds : bond 0.04245 ( 735) hydrogen bonds : angle 4.39838 ( 2430) link_NAG-ASN : bond 0.00227 ( 5) link_NAG-ASN : angle 1.77772 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8321 (pt0) cc_final: 0.7826 (pm20) REVERT: B 109 LYS cc_start: 0.8623 (tttt) cc_final: 0.8090 (tptp) REVERT: B 193 GLN cc_start: 0.8352 (pt0) cc_final: 0.7907 (pm20) REVERT: B 251 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7353 (t0) REVERT: C 39 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: C 60 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8520 (mt-10) REVERT: C 109 LYS cc_start: 0.8631 (tttt) cc_final: 0.8091 (tptp) REVERT: C 245 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8873 (mt0) REVERT: C 277 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7705 (mmt180) REVERT: D 109 LYS cc_start: 0.8619 (tttt) cc_final: 0.8107 (tptp) REVERT: D 193 GLN cc_start: 0.8344 (pt0) cc_final: 0.7879 (pm20) REVERT: E 39 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8175 (tp30) REVERT: E 193 GLN cc_start: 0.8304 (pt0) cc_final: 0.7835 (pm20) REVERT: E 251 ASN cc_start: 0.7972 (t0) cc_final: 0.7736 (t0) outliers start: 44 outliers final: 18 residues processed: 152 average time/residue: 1.2792 time to fit residues: 216.0078 Evaluate side-chains 151 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 395 ASP Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 61 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 0.0970 chunk 162 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.065701 restraints weight = 74761.060| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.32 r_work: 0.2807 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14150 Z= 0.134 Angle : 0.458 7.941 19270 Z= 0.238 Chirality : 0.039 0.153 2160 Planarity : 0.004 0.040 2395 Dihedral : 3.919 19.509 2030 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.01 % Allowed : 8.12 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.91 (0.21), residues: 1670 helix: 3.32 (0.20), residues: 610 sheet: 0.13 (0.25), residues: 455 loop : 0.08 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.007 0.001 TYR A 228 PHE 0.008 0.001 PHE B 307 TRP 0.006 0.001 TRP B 73 HIS 0.002 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00294 (14140) covalent geometry : angle 0.45532 (19245) SS BOND : bond 0.00346 ( 5) SS BOND : angle 0.66460 ( 10) hydrogen bonds : bond 0.03644 ( 735) hydrogen bonds : angle 4.18076 ( 2430) link_NAG-ASN : bond 0.00043 ( 5) link_NAG-ASN : angle 1.71557 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8337 (pt0) cc_final: 0.7869 (pm20) REVERT: B 109 LYS cc_start: 0.8646 (tttt) cc_final: 0.8123 (tptp) REVERT: B 134 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8908 (pt) REVERT: B 193 GLN cc_start: 0.8352 (pt0) cc_final: 0.7944 (pm20) REVERT: B 251 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7382 (t0) REVERT: C 60 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8516 (mt-10) REVERT: C 245 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8863 (mt0) REVERT: C 277 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7769 (mmt180) REVERT: D 193 GLN cc_start: 0.8355 (pt0) cc_final: 0.7896 (pm20) REVERT: E 193 GLN cc_start: 0.8295 (pt0) cc_final: 0.7840 (pm20) REVERT: E 251 ASN cc_start: 0.7974 (t0) cc_final: 0.7729 (t0) outliers start: 30 outliers final: 14 residues processed: 141 average time/residue: 1.1996 time to fit residues: 188.8875 Evaluate side-chains 142 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 60 GLU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 102 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.077248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.063789 restraints weight = 75762.501| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.27 r_work: 0.2734 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14150 Z= 0.247 Angle : 0.513 8.923 19270 Z= 0.270 Chirality : 0.042 0.153 2160 Planarity : 0.004 0.039 2395 Dihedral : 4.404 23.525 2030 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.75 % Allowed : 8.32 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.21), residues: 1670 helix: 3.29 (0.20), residues: 610 sheet: -0.09 (0.24), residues: 470 loop : 0.05 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 277 TYR 0.008 0.001 TYR D 413 PHE 0.014 0.002 PHE C 104 TRP 0.006 0.001 TRP E 414 HIS 0.003 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00561 (14140) covalent geometry : angle 0.51006 (19245) SS BOND : bond 0.00537 ( 5) SS BOND : angle 0.90673 ( 10) hydrogen bonds : bond 0.04252 ( 735) hydrogen bonds : angle 4.36105 ( 2430) link_NAG-ASN : bond 0.00314 ( 5) link_NAG-ASN : angle 1.87495 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8202 (p0) REVERT: A 121 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8803 (ttm) REVERT: A 193 GLN cc_start: 0.8327 (pt0) cc_final: 0.7852 (pm20) REVERT: B 134 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8925 (pt) REVERT: B 193 GLN cc_start: 0.8349 (pt0) cc_final: 0.7923 (pm20) REVERT: B 251 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7403 (t0) REVERT: C 60 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8490 (mt-10) REVERT: C 245 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8883 (mt0) REVERT: C 277 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7750 (mmt180) REVERT: D 60 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8468 (mt-10) REVERT: D 193 GLN cc_start: 0.8348 (pt0) cc_final: 0.7892 (pm20) REVERT: E 193 GLN cc_start: 0.8302 (pt0) cc_final: 0.7814 (pm20) outliers start: 41 outliers final: 15 residues processed: 143 average time/residue: 1.0899 time to fit residues: 174.6779 Evaluate side-chains 141 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 277 ARG Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 18 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.078815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.065036 restraints weight = 74618.849| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.36 r_work: 0.2764 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14150 Z= 0.142 Angle : 0.467 7.966 19270 Z= 0.241 Chirality : 0.040 0.169 2160 Planarity : 0.004 0.040 2395 Dihedral : 4.039 19.985 2030 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.95 % Allowed : 8.86 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.21), residues: 1670 helix: 3.38 (0.20), residues: 610 sheet: 0.01 (0.24), residues: 460 loop : 0.06 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 277 TYR 0.007 0.001 TYR A 228 PHE 0.008 0.001 PHE C 307 TRP 0.006 0.001 TRP C 73 HIS 0.002 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00313 (14140) covalent geometry : angle 0.46429 (19245) SS BOND : bond 0.00377 ( 5) SS BOND : angle 0.73007 ( 10) hydrogen bonds : bond 0.03629 ( 735) hydrogen bonds : angle 4.17661 ( 2430) link_NAG-ASN : bond 0.00069 ( 5) link_NAG-ASN : angle 1.81471 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8352 (pt0) cc_final: 0.7853 (pm20) REVERT: B 134 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8950 (pt) REVERT: B 193 GLN cc_start: 0.8336 (pt0) cc_final: 0.7904 (pm20) REVERT: B 251 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7402 (t0) REVERT: C 60 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8510 (mt-10) REVERT: C 245 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8856 (mt0) REVERT: D 60 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8503 (mt-10) REVERT: D 193 GLN cc_start: 0.8364 (pt0) cc_final: 0.7878 (pm20) REVERT: E 193 GLN cc_start: 0.8295 (pt0) cc_final: 0.7833 (pm20) outliers start: 29 outliers final: 16 residues processed: 134 average time/residue: 1.0605 time to fit residues: 159.7712 Evaluate side-chains 136 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 397 MET Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 141 GLU Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 65 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.078423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.065055 restraints weight = 75315.724| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.28 r_work: 0.2762 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14150 Z= 0.160 Angle : 0.476 8.017 19270 Z= 0.246 Chirality : 0.040 0.183 2160 Planarity : 0.004 0.040 2395 Dihedral : 4.082 20.133 2030 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.81 % Allowed : 9.13 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.21), residues: 1670 helix: 3.45 (0.20), residues: 610 sheet: 0.01 (0.24), residues: 460 loop : 0.06 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 277 TYR 0.008 0.001 TYR D 413 PHE 0.010 0.001 PHE A 104 TRP 0.005 0.001 TRP E 73 HIS 0.003 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00359 (14140) covalent geometry : angle 0.47297 (19245) SS BOND : bond 0.00403 ( 5) SS BOND : angle 0.75824 ( 10) hydrogen bonds : bond 0.03668 ( 735) hydrogen bonds : angle 4.16834 ( 2430) link_NAG-ASN : bond 0.00146 ( 5) link_NAG-ASN : angle 1.82440 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8359 (pt0) cc_final: 0.7861 (pm20) REVERT: B 134 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8952 (pt) REVERT: B 193 GLN cc_start: 0.8346 (pt0) cc_final: 0.7945 (pm20) REVERT: B 251 ASN cc_start: 0.7769 (OUTLIER) cc_final: 0.7397 (t0) REVERT: C 60 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8494 (mt-10) REVERT: C 245 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8846 (mt0) REVERT: D 60 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8503 (mt-10) REVERT: D 193 GLN cc_start: 0.8360 (pt0) cc_final: 0.7867 (pm20) REVERT: E 193 GLN cc_start: 0.8305 (pt0) cc_final: 0.7837 (pm20) outliers start: 27 outliers final: 14 residues processed: 130 average time/residue: 1.1606 time to fit residues: 168.7964 Evaluate side-chains 137 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 113 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.080793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.067269 restraints weight = 74428.154| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.32 r_work: 0.2756 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14150 Z= 0.122 Angle : 0.454 7.405 19270 Z= 0.233 Chirality : 0.039 0.172 2160 Planarity : 0.004 0.040 2395 Dihedral : 3.865 19.663 2030 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.61 % Allowed : 9.40 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.21), residues: 1670 helix: 3.48 (0.20), residues: 615 sheet: 0.04 (0.24), residues: 460 loop : 0.11 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 277 TYR 0.007 0.001 TYR B 413 PHE 0.008 0.001 PHE C 307 TRP 0.007 0.001 TRP D 414 HIS 0.002 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00269 (14140) covalent geometry : angle 0.45142 (19245) SS BOND : bond 0.00346 ( 5) SS BOND : angle 0.69383 ( 10) hydrogen bonds : bond 0.03342 ( 735) hydrogen bonds : angle 4.04668 ( 2430) link_NAG-ASN : bond 0.00059 ( 5) link_NAG-ASN : angle 1.74530 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8409 (pt0) cc_final: 0.7931 (pm20) REVERT: B 193 GLN cc_start: 0.8392 (pt0) cc_final: 0.7986 (pm20) REVERT: B 251 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7394 (t0) REVERT: C 60 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8503 (mt-10) REVERT: C 245 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8863 (mt0) REVERT: D 60 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8532 (mt-10) REVERT: D 193 GLN cc_start: 0.8383 (pt0) cc_final: 0.7935 (pm20) REVERT: E 193 GLN cc_start: 0.8362 (pt0) cc_final: 0.7902 (pm20) outliers start: 24 outliers final: 13 residues processed: 127 average time/residue: 1.2247 time to fit residues: 174.0502 Evaluate side-chains 134 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 251 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 397 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 147 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.079245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.065639 restraints weight = 74939.673| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.34 r_work: 0.2757 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14150 Z= 0.128 Angle : 0.457 7.470 19270 Z= 0.235 Chirality : 0.039 0.152 2160 Planarity : 0.004 0.040 2395 Dihedral : 3.873 19.589 2030 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.21 % Allowed : 9.93 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.21), residues: 1670 helix: 3.53 (0.20), residues: 615 sheet: 0.07 (0.25), residues: 460 loop : 0.13 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 277 TYR 0.007 0.001 TYR D 413 PHE 0.009 0.001 PHE C 307 TRP 0.006 0.001 TRP D 414 HIS 0.003 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00283 (14140) covalent geometry : angle 0.45440 (19245) SS BOND : bond 0.00344 ( 5) SS BOND : angle 0.69535 ( 10) hydrogen bonds : bond 0.03377 ( 735) hydrogen bonds : angle 4.03088 ( 2430) link_NAG-ASN : bond 0.00083 ( 5) link_NAG-ASN : angle 1.73704 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLN cc_start: 0.8374 (pt0) cc_final: 0.7875 (pm20) REVERT: B 193 GLN cc_start: 0.8365 (pt0) cc_final: 0.7923 (pm20) REVERT: B 251 ASN cc_start: 0.7737 (t0) cc_final: 0.7385 (t0) REVERT: C 60 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8496 (mt-10) REVERT: C 245 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8833 (mt0) REVERT: D 60 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8498 (mt-10) REVERT: D 193 GLN cc_start: 0.8363 (pt0) cc_final: 0.7879 (pm20) REVERT: E 193 GLN cc_start: 0.8313 (pt0) cc_final: 0.7828 (pm20) outliers start: 18 outliers final: 15 residues processed: 124 average time/residue: 1.1580 time to fit residues: 161.2779 Evaluate side-chains 138 residues out of total 1490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 245 GLN Chi-restraints excluded: chain C residue 395 ASP Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 66 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 0.0050 chunk 73 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.078530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.065150 restraints weight = 74640.983| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.29 r_work: 0.2744 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14150 Z= 0.154 Angle : 0.476 7.801 19270 Z= 0.246 Chirality : 0.040 0.142 2160 Planarity : 0.004 0.040 2395 Dihedral : 3.982 19.964 2030 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.54 % Allowed : 9.73 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.21), residues: 1670 helix: 3.50 (0.20), residues: 615 sheet: 0.06 (0.24), residues: 460 loop : 0.11 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 277 TYR 0.008 0.001 TYR D 413 PHE 0.009 0.001 PHE E 307 TRP 0.006 0.001 TRP D 414 HIS 0.003 0.001 HIS C 195 Details of bonding type rmsd covalent geometry : bond 0.00346 (14140) covalent geometry : angle 0.47299 (19245) SS BOND : bond 0.00380 ( 5) SS BOND : angle 0.73717 ( 10) hydrogen bonds : bond 0.03543 ( 735) hydrogen bonds : angle 4.08822 ( 2430) link_NAG-ASN : bond 0.00132 ( 5) link_NAG-ASN : angle 1.79729 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7950.67 seconds wall clock time: 135 minutes 29.91 seconds (8129.91 seconds total)