Starting phenix.real_space_refine on Thu Aug 6 12:04:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y7p_72665/08_2026/9y7p_72665.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y7p_72665/08_2026/9y7p_72665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y7p_72665/08_2026/9y7p_72665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y7p_72665/08_2026/9y7p_72665.map" model { file = "/net/cci-nas-00/data/ceres_data/9y7p_72665/08_2026/9y7p_72665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y7p_72665/08_2026/9y7p_72665.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 9610 2.51 5 N 2315 2.21 5 O 2650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14665 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "B" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "C" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "D" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "E" Number of atoms: 2812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2812 Classifications: {'peptide': 347} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {'NAG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} 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: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 107 Unusual residues: {'NAG': 1, 'PX4': 6} Inner-chain residues flagged as termini: ['pdbres="GLY A 508 "'] Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PX4:plan-1': 6} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 121 Unusual residues: {'NAG': 2, 'PX4': 6} Inner-chain residues flagged as termini: ['pdbres="GLY B 507 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PX4:plan-1': 6} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 121 Unusual residues: {'NAG': 2, 'PX4': 6} Inner-chain residues flagged as termini: ['pdbres="GLY C 507 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PX4:plan-1': 6} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 121 Unusual residues: {'NAG': 2, 'PX4': 6} Inner-chain residues flagged as termini: ['pdbres="GLY D 507 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PX4:plan-1': 6} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 116 Unusual residues: {'NAG': 2, 'PX4': 6} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PX4:plan-1': 6} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 3.42, per 1000 atoms: 0.23 Number of scatterers: 14665 At special positions: 0 Unit cell: (92.4, 89.04, 130.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2650 8.00 N 2315 7.00 C 9610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 243 " distance=2.04 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 243 " distance=2.04 Simple disulfide: pdb=" SG CYS C 172 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 243 " distance=2.04 Simple disulfide: pdb=" SG CYS D 172 " - pdb=" SG CYS D 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 243 " distance=2.04 Simple disulfide: pdb=" SG CYS E 172 " - pdb=" SG CYS E 186 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS E 243 " distance=2.04 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 72 " " NAG A 503 " - " ASN A 103 " " NAG B 501 " - " ASN B 72 " " NAG B 502 " - " ASN B 103 " " NAG C 501 " - " ASN C 72 " " NAG C 502 " - " ASN C 103 " " NAG D 501 " - " ASN D 72 " " NAG D 502 " - " ASN D 103 " " NAG E 503 " - " ASN E 72 " " NAG E 504 " - " ASN E 103 " Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 737.2 milliseconds 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3330 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 20 sheets defined 42.2% alpha, 40.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.703A pdb=" N PHE A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 48 " --> pdb=" O PRO A 44 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.511A pdb=" N SER A 56 " --> pdb=" O GLY A 53 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY A 57 " --> pdb=" O ARG A 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 53 through 57' Processing helix chain 'A' and resid 105 through 108 Processing helix chain 'A' and resid 120 through 127 removed outlier: 3.784A pdb=" N LEU A 124 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 127 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 261 Processing helix chain 'A' and resid 261 through 275 removed outlier: 4.049A pdb=" N SER A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 282 through 305 Processing helix chain 'A' and resid 315 through 344 Processing helix chain 'A' and resid 410 through 443 removed outlier: 3.909A pdb=" N ALA A 424 " --> pdb=" O THR A 420 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'B' and resid 43 through 52 removed outlier: 3.702A pdb=" N PHE B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 removed outlier: 3.510A pdb=" N SER B 56 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 57 " --> pdb=" O ARG B 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 57' Processing helix chain 'B' and resid 105 through 108 Processing helix chain 'B' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B 125 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 127 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 261 Processing helix chain 'B' and resid 261 through 275 removed outlier: 4.049A pdb=" N SER B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 282 through 305 Processing helix chain 'B' and resid 315 through 344 Processing helix chain 'B' and resid 410 through 443 removed outlier: 3.909A pdb=" N ALA B 424 " --> pdb=" O THR B 420 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.703A pdb=" N PHE C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.510A pdb=" N SER C 56 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY C 57 " --> pdb=" O ARG C 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 53 through 57' Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU C 124 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP C 125 " --> pdb=" O SER C 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE C 127 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 Processing helix chain 'C' and resid 261 through 275 removed outlier: 4.049A pdb=" N SER C 275 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 282 through 305 Processing helix chain 'C' and resid 315 through 344 Processing helix chain 'C' and resid 410 through 443 removed outlier: 3.909A pdb=" N ALA C 424 " --> pdb=" O THR C 420 " (cutoff:3.500A) Proline residue: C 427 - end of helix Processing helix chain 'C' and resid 444 through 449 Processing helix chain 'D' and resid 43 through 52 removed outlier: 3.703A pdb=" N PHE D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.511A pdb=" N SER D 56 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY D 57 " --> pdb=" O ARG D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 57' Processing helix chain 'D' and resid 105 through 108 Processing helix chain 'D' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU D 124 " --> pdb=" O PRO D 121 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D 125 " --> pdb=" O SER D 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE D 127 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 261 Processing helix chain 'D' and resid 261 through 275 removed outlier: 4.049A pdb=" N SER D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 282 through 305 Processing helix chain 'D' and resid 315 through 344 Processing helix chain 'D' and resid 410 through 443 removed outlier: 3.908A pdb=" N ALA D 424 " --> pdb=" O THR D 420 " (cutoff:3.500A) Proline residue: D 427 - end of helix Processing helix chain 'D' and resid 444 through 449 Processing helix chain 'E' and resid 43 through 52 removed outlier: 3.702A pdb=" N PHE E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 48 " --> pdb=" O PRO E 44 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 removed outlier: 3.510A pdb=" N SER E 56 " --> pdb=" O GLY E 53 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY E 57 " --> pdb=" O ARG E 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 57' Processing helix chain 'E' and resid 105 through 108 Processing helix chain 'E' and resid 120 through 127 removed outlier: 3.783A pdb=" N LEU E 124 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP E 125 " --> pdb=" O SER E 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 127 " --> pdb=" O LEU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 261 Processing helix chain 'E' and resid 261 through 275 removed outlier: 4.049A pdb=" N SER E 275 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 278 No H-bonds generated for 'chain 'E' and resid 276 through 278' Processing helix chain 'E' and resid 282 through 305 Processing helix chain 'E' and resid 315 through 344 Processing helix chain 'E' and resid 410 through 443 removed outlier: 3.908A pdb=" N ALA E 424 " --> pdb=" O THR E 420 " (cutoff:3.500A) Proline residue: E 427 - end of helix Processing helix chain 'E' and resid 444 through 449 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 118 removed outlier: 4.273A pdb=" N LYS A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 142 removed outlier: 6.567A pdb=" N THR A 169 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA A 140 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR A 167 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE A 142 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ARG A 165 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP A 91 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER A 84 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG A 93 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE A 82 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN A 95 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN A 103 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN A 72 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 134 removed outlier: 5.266A pdb=" N THR A 242 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU A 245 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 230 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 228 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 223 Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.273A pdb=" N LYS B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 137 through 142 removed outlier: 6.566A pdb=" N THR B 169 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA B 140 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR B 167 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N PHE B 142 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ARG B 165 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 91 " --> pdb=" O SER B 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER B 84 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG B 93 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE B 82 " --> pdb=" O ARG B 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN B 95 " --> pdb=" O ASN B 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN B 103 " --> pdb=" O ASN B 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN B 72 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 134 removed outlier: 5.266A pdb=" N THR B 242 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 245 " --> pdb=" O GLY B 230 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY B 230 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU B 228 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 221 through 223 Processing sheet with id=AA9, first strand: chain 'C' and resid 116 through 118 removed outlier: 4.274A pdb=" N LYS C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 137 through 142 removed outlier: 6.567A pdb=" N THR C 169 " --> pdb=" O LYS C 138 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA C 140 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR C 167 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE C 142 " --> pdb=" O ARG C 165 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ARG C 165 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP C 91 " --> pdb=" O SER C 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER C 84 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG C 93 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE C 82 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN C 95 " --> pdb=" O ASN C 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN C 103 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASN C 72 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 132 through 134 removed outlier: 5.266A pdb=" N THR C 242 " --> pdb=" O SER C 192 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU C 245 " --> pdb=" O GLY C 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 230 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 228 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AB4, first strand: chain 'D' and resid 116 through 118 removed outlier: 4.274A pdb=" N LYS D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 137 through 142 removed outlier: 6.567A pdb=" N THR D 169 " --> pdb=" O LYS D 138 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA D 140 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR D 167 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE D 142 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ARG D 165 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP D 91 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER D 84 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG D 93 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE D 82 " --> pdb=" O ARG D 93 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN D 95 " --> pdb=" O ASN D 80 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN D 103 " --> pdb=" O ASN D 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN D 72 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 132 through 134 removed outlier: 5.267A pdb=" N THR D 242 " --> pdb=" O SER D 192 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU D 245 " --> pdb=" O GLY D 230 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY D 230 " --> pdb=" O GLU D 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU D 228 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 221 through 223 Processing sheet with id=AB8, first strand: chain 'E' and resid 116 through 118 removed outlier: 4.274A pdb=" N LYS E 159 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.568A pdb=" N THR E 169 " --> pdb=" O LYS E 138 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ALA E 140 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR E 167 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N PHE E 142 " --> pdb=" O ARG E 165 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N ARG E 165 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP E 91 " --> pdb=" O SER E 84 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER E 84 " --> pdb=" O ASP E 91 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ARG E 93 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE E 82 " --> pdb=" O ARG E 93 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASN E 95 " --> pdb=" O ASN E 80 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN E 103 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN E 72 " --> pdb=" O ASN E 103 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 132 through 134 removed outlier: 5.266A pdb=" N THR E 242 " --> pdb=" O SER E 192 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU E 245 " --> pdb=" O GLY E 230 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY E 230 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU E 228 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 221 through 223 820 hydrogen bonds defined for protein. 2400 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: 2.83 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2270 1.32 - 1.45: 4152 1.45 - 1.57: 8413 1.57 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 14985 Sorted by residual: bond pdb=" N ASP C 182 " pdb=" CA ASP C 182 " ideal model delta sigma weight residual 1.454 1.485 -0.032 1.23e-02 6.61e+03 6.75e+00 bond pdb=" N TYR E 441 " pdb=" CA TYR E 441 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.75e+00 bond pdb=" N TYR C 441 " pdb=" CA TYR C 441 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.70e+00 bond pdb=" N TYR A 441 " pdb=" CA TYR A 441 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.64e+00 bond pdb=" N TYR D 441 " pdb=" CA TYR D 441 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.32e-02 5.74e+03 6.64e+00 ... (remaining 14980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 18490 1.13 - 2.26: 1265 2.26 - 3.39: 327 3.39 - 4.51: 62 4.51 - 5.64: 31 Bond angle restraints: 20175 Sorted by residual: angle pdb=" CA TRP E 438 " pdb=" C TRP E 438 " pdb=" O TRP E 438 " ideal model delta sigma weight residual 120.55 117.47 3.08 1.06e+00 8.90e-01 8.46e+00 angle pdb=" CA TRP B 438 " pdb=" C TRP B 438 " pdb=" O TRP B 438 " ideal model delta sigma weight residual 120.55 117.48 3.07 1.06e+00 8.90e-01 8.39e+00 angle pdb=" CA TRP D 438 " pdb=" C TRP D 438 " pdb=" O TRP D 438 " ideal model delta sigma weight residual 120.55 117.48 3.07 1.06e+00 8.90e-01 8.38e+00 angle pdb=" CA TRP C 438 " pdb=" C TRP C 438 " pdb=" O TRP C 438 " ideal model delta sigma weight residual 120.55 117.49 3.06 1.06e+00 8.90e-01 8.31e+00 angle pdb=" CA TRP A 438 " pdb=" C TRP A 438 " pdb=" O TRP A 438 " ideal model delta sigma weight residual 120.55 117.50 3.05 1.06e+00 8.90e-01 8.28e+00 ... (remaining 20170 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.15: 7885 13.15 - 26.30: 825 26.30 - 39.45: 295 39.45 - 52.60: 80 52.60 - 65.75: 50 Dihedral angle restraints: 9135 sinusoidal: 4005 harmonic: 5130 Sorted by residual: dihedral pdb=" CA TYR C 231 " pdb=" C TYR C 231 " pdb=" N CYS C 232 " pdb=" CA CYS C 232 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA TYR E 231 " pdb=" C TYR E 231 " pdb=" N CYS E 232 " pdb=" CA CYS E 232 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA TYR D 231 " pdb=" C TYR D 231 " pdb=" N CYS D 232 " pdb=" CA CYS D 232 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 9132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1202 0.027 - 0.053: 581 0.053 - 0.080: 234 0.080 - 0.107: 162 0.107 - 0.134: 71 Chirality restraints: 2250 Sorted by residual: chirality pdb=" CA TYR D 437 " pdb=" N TYR D 437 " pdb=" C TYR D 437 " pdb=" CB TYR D 437 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE B 278 " pdb=" N ILE B 278 " pdb=" C ILE B 278 " pdb=" CB ILE B 278 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA ILE C 278 " pdb=" N ILE C 278 " pdb=" C ILE C 278 " pdb=" CB ILE C 278 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 2247 not shown) Planarity restraints: 2495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 422 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.67e+00 pdb=" C SER C 422 " 0.051 2.00e-02 2.50e+03 pdb=" O SER C 422 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG C 423 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 422 " 0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C SER E 422 " -0.051 2.00e-02 2.50e+03 pdb=" O SER E 422 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG E 423 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 422 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C SER A 422 " 0.051 2.00e-02 2.50e+03 pdb=" O SER A 422 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 423 " -0.017 2.00e-02 2.50e+03 ... (remaining 2492 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4025 2.81 - 3.34: 12897 3.34 - 3.86: 24074 3.86 - 4.38: 29290 4.38 - 4.90: 50179 Nonbonded interactions: 120465 Sorted by model distance: nonbonded pdb=" OE1 GLU E 203 " pdb=" OH TYR E 231 " model vdw 2.293 3.040 nonbonded pdb=" OE1 GLU B 203 " pdb=" OH TYR B 231 " model vdw 2.293 3.040 nonbonded pdb=" OE1 GLU D 203 " pdb=" OH TYR D 231 " model vdw 2.293 3.040 nonbonded pdb=" OE1 GLU A 203 " pdb=" OH TYR A 231 " model vdw 2.293 3.040 nonbonded pdb=" OE1 GLU C 203 " pdb=" OH TYR C 231 " model vdw 2.293 3.040 ... (remaining 120460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 42 through 450 or resid 503 or (resid 505 and (name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name O7 or name O8 )) or resid 506 through 507 or r \ esid 510)) selection = (chain 'B' and (resid 42 through 450 or resid 502 or (resid 504 and (name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name O7 or name O8 )) or resid 505 through 506 or r \ esid 509)) selection = (chain 'C' and (resid 42 through 450 or resid 502 or (resid 504 and (name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name O7 or name O8 )) or resid 505 through 506 or r \ esid 509)) selection = (chain 'D' and (resid 42 through 450 or resid 502 or (resid 504 and (name C23 or \ name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 \ 0 or name C31 or name C32 or name O7 or name O8 )) or resid 505 through 506 or r \ esid 509)) selection = (chain 'E' and (resid 42 through 450 or resid 503 or resid 505 through 507 or (r \ esid 508 and (name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C30 or name C31 or name C32 or name O7 or name O8 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.350 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 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 : 0.004 0.035 15005 Z= 0.245 Angle : 0.712 5.642 20225 Z= 0.425 Chirality : 0.045 0.134 2250 Planarity : 0.009 0.103 2485 Dihedral : 13.608 65.752 5775 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.19), residues: 1715 helix: 0.33 (0.19), residues: 605 sheet: -0.19 (0.24), residues: 405 loop : -0.44 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG B 445 TYR 0.014 0.002 TYR B 257 PHE 0.021 0.001 PHE D 327 TRP 0.009 0.001 TRP C 273 HIS 0.002 0.001 HIS E 446 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.25 (14985) covalent geometry : angle 0.69963 / 0.42 (20175) SS BOND : bond 0.00414 / 0.23 ( 10) SS BOND : angle 2.18329 / 1.23 ( 20) hydrogen bonds : bond 0.16664 / 11.09 ( 725) hydrogen bonds : angle 7.27755 / 4.95 ( 2400) link_NAG-ASN : bond 0.00847 / 0.47 ( 10) link_NAG-ASN : angle 3.13681 / 2.23 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8755 (tmmt) cc_final: 0.8456 (tttm) REVERT: A 111 GLU cc_start: 0.8528 (mp0) cc_final: 0.8261 (mp0) REVERT: A 177 LYS cc_start: 0.9096 (ttmm) cc_final: 0.8630 (ttpt) REVERT: A 207 ASP cc_start: 0.8517 (t70) cc_final: 0.8072 (p0) REVERT: A 251 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8110 (mt-10) REVERT: B 207 ASP cc_start: 0.8532 (t70) cc_final: 0.8075 (p0) REVERT: B 416 LYS cc_start: 0.8746 (mtpt) cc_final: 0.8390 (mttp) REVERT: C 116 SER cc_start: 0.8900 (p) cc_final: 0.8548 (t) REVERT: C 203 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8648 (mm-30) REVERT: C 207 ASP cc_start: 0.8419 (t70) cc_final: 0.8129 (p0) REVERT: C 416 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8424 (mtpp) REVERT: D 116 SER cc_start: 0.8963 (p) cc_final: 0.8569 (t) REVERT: D 207 ASP cc_start: 0.8514 (t70) cc_final: 0.8109 (p0) REVERT: E 101 GLN cc_start: 0.8910 (mt0) cc_final: 0.8695 (mt0) REVERT: E 207 ASP cc_start: 0.8592 (t70) cc_final: 0.8269 (p0) REVERT: E 228 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7988 (mt-10) REVERT: E 416 LYS cc_start: 0.8681 (mtpt) cc_final: 0.8240 (mttm) outliers start: 0 outliers final: 3 residues processed: 295 average time/residue: 0.7334 time to fit residues: 232.4556 Evaluate side-chains 249 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 246 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain E residue 157 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN C 220 GLN C 300 GLN D 220 GLN D 300 GLN E 220 GLN E 300 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.103121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.074833 restraints weight = 20689.970| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.49 r_work: 0.2673 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15005 Z= 0.130 Angle : 0.580 5.408 20225 Z= 0.297 Chirality : 0.042 0.146 2250 Planarity : 0.004 0.033 2485 Dihedral : 9.640 56.912 2421 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.92 % Allowed : 8.43 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.20), residues: 1715 helix: 2.23 (0.20), residues: 605 sheet: 0.35 (0.25), residues: 400 loop : -0.15 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 417 TYR 0.018 0.001 TYR C 335 PHE 0.011 0.001 PHE A 134 TRP 0.011 0.001 TRP A 102 HIS 0.002 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (14985) covalent geometry : angle 0.56441 / 0.29 (20175) SS BOND : bond 0.00121 / 0.07 ( 10) SS BOND : angle 0.90445 / 0.50 ( 20) hydrogen bonds : bond 0.04730 / 3.26 ( 725) hydrogen bonds : angle 5.03576 / 3.44 ( 2400) link_NAG-ASN : bond 0.00749 / 0.42 ( 10) link_NAG-ASN : angle 3.48234 / 2.56 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8745 (tmmt) cc_final: 0.8476 (tttm) REVERT: A 111 GLU cc_start: 0.8631 (mp0) cc_final: 0.8295 (mp0) REVERT: A 116 SER cc_start: 0.8923 (p) cc_final: 0.8528 (t) REVERT: A 177 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8514 (ttpt) REVERT: A 207 ASP cc_start: 0.8691 (t70) cc_final: 0.7995 (p0) REVERT: A 214 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8480 (mm-30) REVERT: A 225 GLU cc_start: 0.7960 (pm20) cc_final: 0.7716 (pm20) REVERT: A 251 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8549 (mt-10) REVERT: B 111 GLU cc_start: 0.8749 (mp0) cc_final: 0.8370 (mp0) REVERT: B 116 SER cc_start: 0.8895 (p) cc_final: 0.8443 (t) REVERT: B 207 ASP cc_start: 0.8749 (t70) cc_final: 0.8047 (p0) REVERT: B 214 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8602 (mm-30) REVERT: B 225 GLU cc_start: 0.8007 (pm20) cc_final: 0.7734 (pm20) REVERT: B 416 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8458 (mtpp) REVERT: C 111 GLU cc_start: 0.8718 (mp0) cc_final: 0.8369 (mp0) REVERT: C 116 SER cc_start: 0.8824 (p) cc_final: 0.8432 (t) REVERT: C 207 ASP cc_start: 0.8691 (t70) cc_final: 0.8110 (p0) REVERT: C 225 GLU cc_start: 0.7969 (pm20) cc_final: 0.7669 (pm20) REVERT: C 416 LYS cc_start: 0.8583 (mtpt) cc_final: 0.8381 (mtpp) REVERT: D 116 SER cc_start: 0.8886 (p) cc_final: 0.8401 (t) REVERT: D 123 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7699 (mpp) REVERT: D 207 ASP cc_start: 0.8684 (t70) cc_final: 0.8033 (p0) REVERT: D 343 ARG cc_start: 0.7394 (mtp-110) cc_final: 0.7057 (mtm-85) REVERT: E 50 LYS cc_start: 0.8707 (tttm) cc_final: 0.8478 (tttm) REVERT: E 101 GLN cc_start: 0.9182 (mt0) cc_final: 0.8973 (mt0) REVERT: E 111 GLU cc_start: 0.8523 (mp0) cc_final: 0.8271 (mp0) REVERT: E 116 SER cc_start: 0.8827 (p) cc_final: 0.8326 (t) REVERT: E 207 ASP cc_start: 0.8817 (t70) cc_final: 0.8209 (p0) REVERT: E 416 LYS cc_start: 0.8556 (mtpt) cc_final: 0.8108 (mttm) outliers start: 30 outliers final: 9 residues processed: 259 average time/residue: 0.6487 time to fit residues: 180.6694 Evaluate side-chains 245 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 254 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 85 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.2896 > 50:) chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 166 optimal weight: 0.4980 chunk 130 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN B 220 GLN C 220 GLN C 300 GLN D 220 GLN D 300 GLN E 220 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.069537 restraints weight = 20939.325| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.50 r_work: 0.2586 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2443 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9078 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15005 Z= 0.178 Angle : 0.578 6.124 20225 Z= 0.300 Chirality : 0.043 0.146 2250 Planarity : 0.004 0.042 2485 Dihedral : 9.337 58.966 2417 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.73 % Allowed : 10.73 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.20), residues: 1715 helix: 2.48 (0.21), residues: 610 sheet: 0.30 (0.25), residues: 405 loop : 0.06 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 417 TYR 0.026 0.002 TYR A 335 PHE 0.015 0.002 PHE D 82 TRP 0.011 0.001 TRP A 102 HIS 0.003 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (14985) covalent geometry : angle 0.56745 / 0.30 (20175) SS BOND : bond 0.00344 / 0.19 ( 10) SS BOND : angle 1.22630 / 0.70 ( 20) hydrogen bonds : bond 0.05257 / 3.61 ( 725) hydrogen bonds : angle 4.71634 / 3.23 ( 2400) link_NAG-ASN : bond 0.00706 / 0.40 ( 10) link_NAG-ASN : angle 2.82992 / 2.11 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 241 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8748 (tmmt) cc_final: 0.8452 (tttm) REVERT: A 111 GLU cc_start: 0.8665 (mp0) cc_final: 0.8214 (mp0) REVERT: A 116 SER cc_start: 0.8917 (p) cc_final: 0.8555 (t) REVERT: A 207 ASP cc_start: 0.8746 (t70) cc_final: 0.8081 (p0) REVERT: A 225 GLU cc_start: 0.8024 (pm20) cc_final: 0.7797 (pm20) REVERT: A 251 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8540 (mt-10) REVERT: B 111 GLU cc_start: 0.8763 (mp0) cc_final: 0.8320 (mp0) REVERT: B 116 SER cc_start: 0.8897 (p) cc_final: 0.8491 (t) REVERT: B 207 ASP cc_start: 0.8771 (t70) cc_final: 0.8075 (p0) REVERT: B 225 GLU cc_start: 0.8048 (pm20) cc_final: 0.7818 (pm20) REVERT: B 416 LYS cc_start: 0.8650 (mtpt) cc_final: 0.8448 (mtpp) REVERT: C 111 GLU cc_start: 0.8714 (mp0) cc_final: 0.8441 (mp0) REVERT: C 116 SER cc_start: 0.8953 (p) cc_final: 0.8552 (t) REVERT: C 181 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8347 (ptt) REVERT: C 207 ASP cc_start: 0.8789 (t70) cc_final: 0.8198 (p0) REVERT: C 225 GLU cc_start: 0.7991 (pm20) cc_final: 0.7743 (pm20) REVERT: D 111 GLU cc_start: 0.8710 (mp0) cc_final: 0.8188 (mp0) REVERT: D 116 SER cc_start: 0.8940 (p) cc_final: 0.8524 (t) REVERT: D 207 ASP cc_start: 0.8758 (t70) cc_final: 0.8121 (p0) REVERT: E 111 GLU cc_start: 0.8548 (mp0) cc_final: 0.8327 (mp0) REVERT: E 116 SER cc_start: 0.8862 (p) cc_final: 0.8383 (t) REVERT: E 207 ASP cc_start: 0.8873 (t70) cc_final: 0.8310 (p0) outliers start: 27 outliers final: 10 residues processed: 243 average time/residue: 0.6707 time to fit residues: 174.9771 Evaluate side-chains 228 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 181 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 254 MET Chi-restraints excluded: chain E residue 326 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 104 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 GLN B 220 GLN C 300 GLN D 300 GLN E 220 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.070761 restraints weight = 20852.484| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.49 r_work: 0.2608 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2466 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15005 Z= 0.139 Angle : 0.542 5.757 20225 Z= 0.278 Chirality : 0.042 0.153 2250 Planarity : 0.004 0.036 2485 Dihedral : 8.973 59.934 2417 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.36 % Allowed : 11.18 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.21), residues: 1715 helix: 2.74 (0.21), residues: 605 sheet: 0.55 (0.25), residues: 405 loop : 0.01 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 417 TYR 0.022 0.002 TYR E 335 PHE 0.012 0.001 PHE A 433 TRP 0.009 0.001 TRP A 102 HIS 0.002 0.001 HIS D 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (14985) covalent geometry : angle 0.53308 / 0.28 (20175) SS BOND : bond 0.00248 / 0.14 ( 10) SS BOND : angle 0.69430 / 0.42 ( 20) hydrogen bonds : bond 0.04622 / 3.19 ( 725) hydrogen bonds : angle 4.45558 / 3.05 ( 2400) link_NAG-ASN : bond 0.00636 / 0.36 ( 10) link_NAG-ASN : angle 2.58055 / 1.93 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 232 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8763 (tmmt) cc_final: 0.8472 (tttm) REVERT: A 111 GLU cc_start: 0.8589 (mp0) cc_final: 0.8173 (mp0) REVERT: A 116 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8595 (t) REVERT: A 123 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7837 (ptp) REVERT: A 207 ASP cc_start: 0.8750 (t70) cc_final: 0.8130 (p0) REVERT: A 225 GLU cc_start: 0.8066 (pm20) cc_final: 0.7467 (pm20) REVERT: A 251 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8574 (mt-10) REVERT: B 111 GLU cc_start: 0.8673 (mp0) cc_final: 0.8153 (mp0) REVERT: B 116 SER cc_start: 0.8919 (p) cc_final: 0.8554 (t) REVERT: B 123 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7615 (ptp) REVERT: B 207 ASP cc_start: 0.8761 (t70) cc_final: 0.8088 (p0) REVERT: B 225 GLU cc_start: 0.8061 (pm20) cc_final: 0.7843 (pm20) REVERT: B 416 LYS cc_start: 0.8633 (mtpt) cc_final: 0.8428 (mtpp) REVERT: C 111 GLU cc_start: 0.8712 (mp0) cc_final: 0.8287 (mp0) REVERT: C 116 SER cc_start: 0.8954 (p) cc_final: 0.8552 (t) REVERT: C 207 ASP cc_start: 0.8793 (t70) cc_final: 0.8189 (p0) REVERT: C 225 GLU cc_start: 0.8027 (pm20) cc_final: 0.7810 (pm20) REVERT: D 111 GLU cc_start: 0.8602 (mp0) cc_final: 0.8118 (mp0) REVERT: D 116 SER cc_start: 0.8896 (p) cc_final: 0.8510 (t) REVERT: D 207 ASP cc_start: 0.8747 (t70) cc_final: 0.8133 (p0) REVERT: D 220 GLN cc_start: 0.8660 (tt0) cc_final: 0.8437 (tt0) REVERT: E 111 GLU cc_start: 0.8610 (mp0) cc_final: 0.8259 (mp0) REVERT: E 116 SER cc_start: 0.8877 (p) cc_final: 0.8419 (t) REVERT: E 207 ASP cc_start: 0.8836 (t70) cc_final: 0.8306 (p0) outliers start: 37 outliers final: 14 residues processed: 239 average time/residue: 0.7079 time to fit residues: 181.9307 Evaluate side-chains 229 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 137 GLU Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 343 ARG Chi-restraints excluded: chain E residue 119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 63 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 144 optimal weight: 0.4980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN C 300 GLN D 300 GLN E 220 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.099858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.071128 restraints weight = 20737.948| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 2.48 r_work: 0.2616 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15005 Z= 0.128 Angle : 0.532 6.149 20225 Z= 0.273 Chirality : 0.041 0.152 2250 Planarity : 0.004 0.041 2485 Dihedral : 8.496 59.244 2415 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.49 % Allowed : 11.37 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.21), residues: 1715 helix: 2.86 (0.21), residues: 605 sheet: 0.61 (0.25), residues: 405 loop : 0.04 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 417 TYR 0.023 0.002 TYR A 335 PHE 0.011 0.001 PHE A 433 TRP 0.009 0.001 TRP A 102 HIS 0.002 0.001 HIS C 450 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (14985) covalent geometry : angle 0.52508 / 0.27 (20175) SS BOND : bond 0.00254 / 0.14 ( 10) SS BOND : angle 0.64596 / 0.39 ( 20) hydrogen bonds : bond 0.04420 / 3.06 ( 725) hydrogen bonds : angle 4.32600 / 2.96 ( 2400) link_NAG-ASN : bond 0.00578 / 0.32 ( 10) link_NAG-ASN : angle 2.32349 / 1.76 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 226 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8750 (tmmt) cc_final: 0.8525 (tttm) REVERT: A 111 GLU cc_start: 0.8580 (mp0) cc_final: 0.8245 (mp0) REVERT: A 116 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8619 (t) REVERT: A 207 ASP cc_start: 0.8727 (t70) cc_final: 0.8112 (p0) REVERT: B 111 GLU cc_start: 0.8686 (mp0) cc_final: 0.8187 (mp0) REVERT: B 116 SER cc_start: 0.8899 (p) cc_final: 0.8564 (t) REVERT: B 123 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7709 (ptp) REVERT: B 207 ASP cc_start: 0.8766 (t70) cc_final: 0.8101 (p0) REVERT: B 225 GLU cc_start: 0.8027 (pm20) cc_final: 0.7820 (pm20) REVERT: B 416 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8431 (mtpp) REVERT: C 111 GLU cc_start: 0.8682 (mp0) cc_final: 0.8394 (mp0) REVERT: C 116 SER cc_start: 0.8899 (p) cc_final: 0.8527 (t) REVERT: C 207 ASP cc_start: 0.8808 (t70) cc_final: 0.8181 (p0) REVERT: C 225 GLU cc_start: 0.8047 (pm20) cc_final: 0.7679 (pm20) REVERT: D 111 GLU cc_start: 0.8592 (mp0) cc_final: 0.8112 (mp0) REVERT: D 116 SER cc_start: 0.8875 (p) cc_final: 0.8498 (t) REVERT: D 207 ASP cc_start: 0.8744 (t70) cc_final: 0.8161 (p0) REVERT: D 220 GLN cc_start: 0.8702 (tt0) cc_final: 0.8490 (tt0) REVERT: E 111 GLU cc_start: 0.8591 (mp0) cc_final: 0.8317 (mp0) REVERT: E 116 SER cc_start: 0.8900 (p) cc_final: 0.8477 (t) REVERT: E 207 ASP cc_start: 0.8837 (t70) cc_final: 0.8285 (p0) outliers start: 39 outliers final: 16 residues processed: 235 average time/residue: 0.6720 time to fit residues: 169.9402 Evaluate side-chains 227 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 343 ARG Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 254 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 69 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 60 optimal weight: 0.3980 chunk 39 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN C 235 HIS C 300 GLN D 300 GLN E 149 ASN E 220 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.099416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.070865 restraints weight = 20827.685| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 2.47 r_work: 0.2611 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2469 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15005 Z= 0.136 Angle : 0.543 6.903 20225 Z= 0.278 Chirality : 0.041 0.154 2250 Planarity : 0.004 0.040 2485 Dihedral : 8.223 56.832 2415 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.49 % Allowed : 12.20 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.21), residues: 1715 helix: 2.86 (0.21), residues: 605 sheet: 0.65 (0.25), residues: 405 loop : 0.07 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 417 TYR 0.024 0.002 TYR A 335 PHE 0.011 0.001 PHE A 433 TRP 0.008 0.001 TRP A 102 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (14985) covalent geometry : angle 0.53575 / 0.28 (20175) SS BOND : bond 0.00413 / 0.21 ( 10) SS BOND : angle 1.23121 / 0.50 ( 20) hydrogen bonds : bond 0.04431 / 3.06 ( 725) hydrogen bonds : angle 4.30710 / 2.95 ( 2400) link_NAG-ASN : bond 0.00552 / 0.31 ( 10) link_NAG-ASN : angle 2.21768 / 1.69 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8582 (mp0) cc_final: 0.8331 (mp0) REVERT: A 116 SER cc_start: 0.8919 (p) cc_final: 0.8607 (t) REVERT: A 207 ASP cc_start: 0.8724 (t70) cc_final: 0.8113 (p0) REVERT: B 111 GLU cc_start: 0.8694 (mp0) cc_final: 0.8170 (mp0) REVERT: B 116 SER cc_start: 0.8896 (p) cc_final: 0.8568 (t) REVERT: B 123 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7703 (ptp) REVERT: B 207 ASP cc_start: 0.8753 (t70) cc_final: 0.8078 (p0) REVERT: B 225 GLU cc_start: 0.8043 (pm20) cc_final: 0.7832 (pm20) REVERT: B 416 LYS cc_start: 0.8617 (mtpt) cc_final: 0.8385 (mtpp) REVERT: C 111 GLU cc_start: 0.8670 (mp0) cc_final: 0.8272 (mp0) REVERT: C 116 SER cc_start: 0.8891 (p) cc_final: 0.8528 (t) REVERT: C 207 ASP cc_start: 0.8790 (t70) cc_final: 0.8178 (p0) REVERT: D 111 GLU cc_start: 0.8586 (mp0) cc_final: 0.8039 (mp0) REVERT: D 116 SER cc_start: 0.8868 (p) cc_final: 0.8493 (t) REVERT: D 123 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8212 (mtt) REVERT: D 207 ASP cc_start: 0.8738 (t70) cc_final: 0.8148 (p0) REVERT: D 220 GLN cc_start: 0.8694 (tt0) cc_final: 0.8477 (tt0) REVERT: E 111 GLU cc_start: 0.8569 (mp0) cc_final: 0.8286 (mp0) REVERT: E 116 SER cc_start: 0.8894 (p) cc_final: 0.8478 (t) REVERT: E 207 ASP cc_start: 0.8822 (t70) cc_final: 0.8267 (p0) outliers start: 39 outliers final: 21 residues processed: 231 average time/residue: 0.6651 time to fit residues: 165.5245 Evaluate side-chains 230 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 207 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 343 ARG Chi-restraints excluded: chain D residue 446 HIS Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 254 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 150 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN B 235 HIS C 300 GLN D 300 GLN E 149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.070085 restraints weight = 20774.694| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.48 r_work: 0.2598 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2456 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15005 Z= 0.149 Angle : 0.554 7.401 20225 Z= 0.283 Chirality : 0.042 0.156 2250 Planarity : 0.004 0.041 2485 Dihedral : 7.983 52.208 2415 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.56 % Allowed : 12.40 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.21), residues: 1715 helix: 2.85 (0.21), residues: 605 sheet: 0.63 (0.25), residues: 405 loop : 0.11 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 417 TYR 0.025 0.002 TYR A 335 PHE 0.011 0.001 PHE A 433 TRP 0.008 0.001 TRP C 102 HIS 0.003 0.001 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (14985) covalent geometry : angle 0.54691 / 0.28 (20175) SS BOND : bond 0.00299 / 0.16 ( 10) SS BOND : angle 1.22744 / 0.52 ( 20) hydrogen bonds : bond 0.04563 / 3.15 ( 725) hydrogen bonds : angle 4.32462 / 2.96 ( 2400) link_NAG-ASN : bond 0.00526 / 0.29 ( 10) link_NAG-ASN : angle 2.15857 / 1.65 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8628 (mp0) cc_final: 0.8230 (mp0) REVERT: A 116 SER cc_start: 0.8922 (p) cc_final: 0.8631 (t) REVERT: A 207 ASP cc_start: 0.8750 (t70) cc_final: 0.8149 (p0) REVERT: B 111 GLU cc_start: 0.8676 (mp0) cc_final: 0.8103 (mp0) REVERT: B 116 SER cc_start: 0.8898 (p) cc_final: 0.8576 (t) REVERT: B 123 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7751 (ptp) REVERT: B 207 ASP cc_start: 0.8761 (t70) cc_final: 0.8136 (p0) REVERT: B 225 GLU cc_start: 0.8059 (pm20) cc_final: 0.7855 (pm20) REVERT: B 416 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8404 (mtpp) REVERT: C 111 GLU cc_start: 0.8654 (mp0) cc_final: 0.8232 (mp0) REVERT: C 116 SER cc_start: 0.8874 (p) cc_final: 0.8491 (t) REVERT: C 207 ASP cc_start: 0.8793 (t70) cc_final: 0.8187 (p0) REVERT: D 111 GLU cc_start: 0.8598 (mp0) cc_final: 0.8261 (mp0) REVERT: D 116 SER cc_start: 0.8867 (p) cc_final: 0.8493 (t) REVERT: D 123 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8214 (mtt) REVERT: D 207 ASP cc_start: 0.8743 (t70) cc_final: 0.8155 (p0) REVERT: D 220 GLN cc_start: 0.8709 (tt0) cc_final: 0.8488 (tt0) REVERT: E 111 GLU cc_start: 0.8556 (mp0) cc_final: 0.8170 (mp0) REVERT: E 116 SER cc_start: 0.8886 (p) cc_final: 0.8467 (t) REVERT: E 207 ASP cc_start: 0.8855 (t70) cc_final: 0.8309 (p0) outliers start: 40 outliers final: 17 residues processed: 231 average time/residue: 0.6146 time to fit residues: 153.3327 Evaluate side-chains 220 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 181 MET Chi-restraints excluded: chain D residue 343 ARG Chi-restraints excluded: chain D residue 446 HIS Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 254 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 128 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 95 optimal weight: 0.0980 chunk 53 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN C 300 GLN D 235 HIS D 300 GLN E 149 ASN E 235 HIS ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.072729 restraints weight = 20827.770| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.48 r_work: 0.2646 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15005 Z= 0.106 Angle : 0.530 8.343 20225 Z= 0.269 Chirality : 0.040 0.148 2250 Planarity : 0.003 0.042 2485 Dihedral : 7.471 47.432 2415 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.11 % Allowed : 13.29 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.21), residues: 1715 helix: 2.99 (0.21), residues: 605 sheet: 0.67 (0.26), residues: 405 loop : 0.16 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 417 TYR 0.022 0.001 TYR B 335 PHE 0.010 0.001 PHE A 433 TRP 0.009 0.001 TRP A 102 HIS 0.007 0.001 HIS B 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (14985) covalent geometry : angle 0.52220 / 0.27 (20175) SS BOND : bond 0.00381 / 0.20 ( 10) SS BOND : angle 1.63318 / 0.62 ( 20) hydrogen bonds : bond 0.03967 / 2.76 ( 725) hydrogen bonds : angle 4.15218 / 2.84 ( 2400) link_NAG-ASN : bond 0.00535 / 0.30 ( 10) link_NAG-ASN : angle 2.06212 / 1.57 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.373 Fit side-chains REVERT: A 111 GLU cc_start: 0.8586 (mp0) cc_final: 0.8230 (mp0) REVERT: A 116 SER cc_start: 0.8934 (p) cc_final: 0.8655 (t) REVERT: A 207 ASP cc_start: 0.8707 (t70) cc_final: 0.8113 (p0) REVERT: B 111 GLU cc_start: 0.8692 (mp0) cc_final: 0.8220 (mp0) REVERT: B 116 SER cc_start: 0.8911 (p) cc_final: 0.8587 (t) REVERT: B 207 ASP cc_start: 0.8769 (t70) cc_final: 0.8111 (p0) REVERT: B 225 GLU cc_start: 0.8149 (pm20) cc_final: 0.7579 (pm20) REVERT: B 416 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8365 (mtpp) REVERT: C 111 GLU cc_start: 0.8648 (mp0) cc_final: 0.8224 (mp0) REVERT: C 116 SER cc_start: 0.8857 (p) cc_final: 0.8506 (t) REVERT: C 181 MET cc_start: 0.8411 (ptp) cc_final: 0.8066 (ptt) REVERT: C 207 ASP cc_start: 0.8790 (t70) cc_final: 0.8138 (p0) REVERT: D 111 GLU cc_start: 0.8627 (mp0) cc_final: 0.8231 (mp0) REVERT: D 116 SER cc_start: 0.8867 (p) cc_final: 0.8497 (t) REVERT: D 123 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8309 (mtp) REVERT: D 207 ASP cc_start: 0.8740 (t70) cc_final: 0.8197 (p0) REVERT: D 220 GLN cc_start: 0.8722 (tt0) cc_final: 0.8512 (tt0) REVERT: D 226 GLU cc_start: 0.7867 (pm20) cc_final: 0.7439 (mp0) REVERT: E 111 GLU cc_start: 0.8536 (mp0) cc_final: 0.8210 (mp0) REVERT: E 116 SER cc_start: 0.8888 (p) cc_final: 0.8514 (t) REVERT: E 207 ASP cc_start: 0.8815 (t70) cc_final: 0.8276 (p0) outliers start: 33 outliers final: 14 residues processed: 231 average time/residue: 0.6083 time to fit residues: 151.7865 Evaluate side-chains 215 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 343 ARG Chi-restraints excluded: chain D residue 446 HIS Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 157 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 138 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 149 ASN B 220 GLN C 220 GLN C 300 GLN D 300 GLN E 149 ASN ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.098864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.070336 restraints weight = 20963.352| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.50 r_work: 0.2602 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15005 Z= 0.158 Angle : 0.574 10.187 20225 Z= 0.292 Chirality : 0.042 0.152 2250 Planarity : 0.004 0.036 2485 Dihedral : 7.491 48.111 2415 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.79 % Allowed : 13.74 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.21), residues: 1715 helix: 2.91 (0.21), residues: 605 sheet: 0.66 (0.25), residues: 405 loop : 0.20 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 417 TYR 0.025 0.002 TYR A 335 PHE 0.011 0.001 PHE A 433 TRP 0.007 0.001 TRP A 102 HIS 0.004 0.001 HIS D 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (14985) covalent geometry : angle 0.56548 / 0.29 (20175) SS BOND : bond 0.00301 / 0.16 ( 10) SS BOND : angle 2.04356 / 1.09 ( 20) hydrogen bonds : bond 0.04469 / 3.09 ( 725) hydrogen bonds : angle 4.27009 / 2.92 ( 2400) link_NAG-ASN : bond 0.00497 / 0.28 ( 10) link_NAG-ASN : angle 2.11199 / 1.61 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.356 Fit side-chains REVERT: A 111 GLU cc_start: 0.8589 (mp0) cc_final: 0.8216 (mp0) REVERT: A 116 SER cc_start: 0.8933 (p) cc_final: 0.8664 (t) REVERT: A 207 ASP cc_start: 0.8732 (t70) cc_final: 0.8136 (p0) REVERT: B 111 GLU cc_start: 0.8653 (mp0) cc_final: 0.8252 (mp0) REVERT: B 116 SER cc_start: 0.8912 (p) cc_final: 0.8577 (t) REVERT: B 207 ASP cc_start: 0.8759 (t70) cc_final: 0.8139 (p0) REVERT: B 416 LYS cc_start: 0.8610 (mtpt) cc_final: 0.8403 (mtpp) REVERT: C 111 GLU cc_start: 0.8655 (mp0) cc_final: 0.8214 (mp0) REVERT: C 116 SER cc_start: 0.8762 (p) cc_final: 0.8396 (t) REVERT: C 181 MET cc_start: 0.8561 (ptp) cc_final: 0.8258 (ptt) REVERT: C 207 ASP cc_start: 0.8802 (t70) cc_final: 0.8189 (p0) REVERT: D 111 GLU cc_start: 0.8574 (mp0) cc_final: 0.8300 (mp0) REVERT: D 116 SER cc_start: 0.8866 (p) cc_final: 0.8494 (t) REVERT: D 207 ASP cc_start: 0.8753 (t70) cc_final: 0.8223 (p0) REVERT: D 220 GLN cc_start: 0.8714 (tt0) cc_final: 0.8498 (tt0) REVERT: D 226 GLU cc_start: 0.7834 (pm20) cc_final: 0.7524 (mp0) REVERT: E 111 GLU cc_start: 0.8544 (mp0) cc_final: 0.8158 (mp0) REVERT: E 116 SER cc_start: 0.8885 (p) cc_final: 0.8512 (t) REVERT: E 123 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7586 (mtm) REVERT: E 207 ASP cc_start: 0.8836 (t70) cc_final: 0.8283 (p0) outliers start: 28 outliers final: 17 residues processed: 218 average time/residue: 0.6020 time to fit residues: 141.5997 Evaluate side-chains 219 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 201 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 232 CYS Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 343 ARG Chi-restraints excluded: chain D residue 137 GLU Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain D residue 343 ARG Chi-restraints excluded: chain D residue 446 HIS Chi-restraints excluded: chain E residue 52 MET Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 446 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 115 optimal weight: 0.1980 chunk 52 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 64 optimal weight: 0.2980 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 300 GLN D 300 GLN E 149 ASN E 300 GLN ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.101703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.073358 restraints weight = 20702.288| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.51 r_work: 0.2657 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15005 Z= 0.102 Angle : 0.543 10.832 20225 Z= 0.273 Chirality : 0.040 0.142 2250 Planarity : 0.003 0.043 2485 Dihedral : 7.037 50.669 2415 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.21 % Allowed : 14.57 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.21), residues: 1715 helix: 3.02 (0.21), residues: 605 sheet: 0.72 (0.26), residues: 405 loop : 0.20 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 417 TYR 0.021 0.001 TYR B 335 PHE 0.010 0.001 PHE A 433 TRP 0.009 0.001 TRP A 102 HIS 0.003 0.000 HIS A 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (14985) covalent geometry : angle 0.53421 / 0.27 (20175) SS BOND : bond 0.00318 / 0.13 ( 10) SS BOND : angle 2.09757 / 1.22 ( 20) hydrogen bonds : bond 0.03785 / 2.63 ( 725) hydrogen bonds : angle 4.07981 / 2.78 ( 2400) link_NAG-ASN : bond 0.00519 / 0.29 ( 10) link_NAG-ASN : angle 2.01249 / 1.53 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3430 Ramachandran restraints generated. 1715 Oldfield, 0 Emsley, 1715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8583 (mp0) cc_final: 0.8218 (mp0) REVERT: A 116 SER cc_start: 0.8951 (p) cc_final: 0.8716 (t) REVERT: A 120 ASP cc_start: 0.8530 (t70) cc_final: 0.8289 (t70) REVERT: A 207 ASP cc_start: 0.8703 (t70) cc_final: 0.8124 (p0) REVERT: B 111 GLU cc_start: 0.8643 (mp0) cc_final: 0.8266 (mp0) REVERT: B 116 SER cc_start: 0.8954 (p) cc_final: 0.8680 (t) REVERT: B 120 ASP cc_start: 0.8557 (t70) cc_final: 0.8336 (t70) REVERT: B 207 ASP cc_start: 0.8763 (t70) cc_final: 0.8095 (p0) REVERT: B 416 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8396 (mtpp) REVERT: C 111 GLU cc_start: 0.8649 (mp0) cc_final: 0.8222 (mp0) REVERT: C 116 SER cc_start: 0.8813 (p) cc_final: 0.8470 (t) REVERT: C 181 MET cc_start: 0.8316 (ptp) cc_final: 0.8025 (ptt) REVERT: C 207 ASP cc_start: 0.8783 (t70) cc_final: 0.8182 (p0) REVERT: D 111 GLU cc_start: 0.8594 (mp0) cc_final: 0.8281 (mp0) REVERT: D 116 SER cc_start: 0.8858 (p) cc_final: 0.8493 (t) REVERT: D 207 ASP cc_start: 0.8748 (t70) cc_final: 0.8218 (p0) REVERT: E 111 GLU cc_start: 0.8528 (mp0) cc_final: 0.8189 (mp0) REVERT: E 116 SER cc_start: 0.8908 (p) cc_final: 0.8556 (t) REVERT: E 207 ASP cc_start: 0.8798 (t70) cc_final: 0.8266 (p0) outliers start: 19 outliers final: 8 residues processed: 216 average time/residue: 0.6381 time to fit residues: 148.9584 Evaluate side-chains 206 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 157 ASN Chi-restraints excluded: chain A residue 446 HIS Chi-restraints excluded: chain B residue 137 GLU Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain D residue 157 ASN Chi-restraints excluded: chain E residue 137 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 70 optimal weight: 0.0370 chunk 61 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 220 GLN C 300 GLN D 220 GLN D 300 GLN E 149 ASN ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.100679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.072417 restraints weight = 20955.502| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.49 r_work: 0.2634 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2494 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9086 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15005 Z= 0.120 Angle : 0.561 11.617 20225 Z= 0.282 Chirality : 0.041 0.147 2250 Planarity : 0.004 0.041 2485 Dihedral : 6.983 53.627 2415 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.21 % Allowed : 14.57 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.21), residues: 1715 helix: 2.99 (0.21), residues: 605 sheet: 0.74 (0.25), residues: 405 loop : 0.20 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 417 TYR 0.023 0.001 TYR A 335 PHE 0.010 0.001 PHE A 433 TRP 0.008 0.001 TRP A 102 HIS 0.006 0.001 HIS E 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14985) covalent geometry : angle 0.55152 / 0.28 (20175) SS BOND : bond 0.00283 / 0.19 ( 10) SS BOND : angle 2.35592 / 1.22 ( 20) hydrogen bonds : bond 0.03974 / 2.75 ( 725) hydrogen bonds : angle 4.11507 / 2.81 ( 2400) link_NAG-ASN : bond 0.00487 / 0.27 ( 10) link_NAG-ASN : angle 2.00867 / 1.53 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4715.07 seconds wall clock time: 80 minutes 53.60 seconds (4853.60 seconds total)