Starting phenix.real_space_refine on Sat Aug 23 15:37:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ex6_50031/08_2025/9ex6_50031.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ex6_50031/08_2025/9ex6_50031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ex6_50031/08_2025/9ex6_50031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ex6_50031/08_2025/9ex6_50031.map" model { file = "/net/cci-nas-00/data/ceres_data/9ex6_50031/08_2025/9ex6_50031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ex6_50031/08_2025/9ex6_50031.cif" } resolution = 2.35 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 25 5.16 5 C 8765 2.51 5 N 2105 2.21 5 O 2220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13115 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2549 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 299} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 70 Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'HEX': 1, 'OCT': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 70 Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'HEX': 1, 'OCT': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 70 Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'HEX': 1, 'OCT': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 70 Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'HEX': 1, 'OCT': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 70 Unusual residues: {'C14': 1, 'D10': 1, 'D12': 2, 'HEX': 1, 'OCT': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.95, per 1000 atoms: 0.22 Number of scatterers: 13115 At special positions: 0 Unit cell: (89.4425, 92.1325, 122.395, 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 25 16.00 O 2220 8.00 N 2105 7.00 C 8765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 647.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 15 sheets defined 42.9% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 43 through 46 Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.703A pdb=" N LYS A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 removed outlier: 4.038A pdb=" N TYR A 198 " --> pdb=" O HIS A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.627A pdb=" N THR A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 221 through 243 removed outlier: 3.650A pdb=" N ASP A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 254 through 283 removed outlier: 3.890A pdb=" N VAL A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 317 removed outlier: 3.627A pdb=" N ILE A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Proline residue: A 301 - end of helix removed outlier: 3.576A pdb=" N TYR A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 46 Processing helix chain 'B' and resid 61 through 72 removed outlier: 3.703A pdb=" N LYS B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 removed outlier: 4.038A pdb=" N TYR B 198 " --> pdb=" O HIS B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.627A pdb=" N THR B 216 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 221 through 243 removed outlier: 3.650A pdb=" N ASP B 227 " --> pdb=" O THR B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 254 through 283 removed outlier: 3.890A pdb=" N VAL B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 317 removed outlier: 3.627A pdb=" N ILE B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.576A pdb=" N TYR B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 46 Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.703A pdb=" N LYS C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 202 removed outlier: 4.038A pdb=" N TYR C 198 " --> pdb=" O HIS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 216 removed outlier: 3.627A pdb=" N THR C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 221 through 243 removed outlier: 3.649A pdb=" N ASP C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 247 Processing helix chain 'C' and resid 254 through 283 removed outlier: 3.890A pdb=" N VAL C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 317 removed outlier: 3.627A pdb=" N ILE C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Proline residue: C 301 - end of helix removed outlier: 3.575A pdb=" N TYR C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 46 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.703A pdb=" N LYS D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 202 removed outlier: 4.037A pdb=" N TYR D 198 " --> pdb=" O HIS D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 216 removed outlier: 3.628A pdb=" N THR D 216 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 221 through 243 removed outlier: 3.650A pdb=" N ASP D 227 " --> pdb=" O THR D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 247 Processing helix chain 'D' and resid 254 through 283 removed outlier: 3.890A pdb=" N VAL D 271 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 272 " --> pdb=" O ALA D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 317 removed outlier: 3.627A pdb=" N ILE D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR D 298 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Proline residue: D 301 - end of helix removed outlier: 3.575A pdb=" N TYR D 304 " --> pdb=" O TYR D 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 46 Processing helix chain 'E' and resid 61 through 72 removed outlier: 3.703A pdb=" N LYS E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 202 removed outlier: 4.038A pdb=" N TYR E 198 " --> pdb=" O HIS E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 216 removed outlier: 3.626A pdb=" N THR E 216 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 221 through 243 removed outlier: 3.650A pdb=" N ASP E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 247 Processing helix chain 'E' and resid 254 through 283 removed outlier: 3.890A pdb=" N VAL E 271 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU E 272 " --> pdb=" O ALA E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 317 removed outlier: 3.627A pdb=" N ILE E 294 " --> pdb=" O ARG E 290 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR E 298 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Proline residue: E 301 - end of helix removed outlier: 3.576A pdb=" N TYR E 304 " --> pdb=" O TYR E 300 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 removed outlier: 10.408A pdb=" N GLY A 85 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N GLN A 113 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET A 87 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR A 111 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE A 89 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR A 109 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 91 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 22 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 33 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE A 20 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N SER A 35 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP A 18 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG A 37 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS A 16 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP A 39 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLY A 14 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ARG A 41 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE A 12 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER A 9 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLN A 145 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL A 11 " --> pdb=" O GLN A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 60 removed outlier: 10.408A pdb=" N GLY A 85 " --> pdb=" O GLN A 113 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N GLN A 113 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET A 87 " --> pdb=" O THR A 111 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR A 111 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE A 89 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR A 109 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 91 " --> pdb=" O ARG A 107 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 22 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 33 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE A 20 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N SER A 35 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP A 18 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG A 37 " --> pdb=" O LYS A 16 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS A 16 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP A 39 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLY A 14 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ARG A 41 " --> pdb=" O PHE A 12 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE A 12 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 80 removed outlier: 5.186A pdb=" N SER A 183 " --> pdb=" O SER A 135 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 166 " --> pdb=" O HIS A 190 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU A 192 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL A 164 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 60 removed outlier: 10.409A pdb=" N GLY B 85 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N GLN B 113 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET B 87 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR B 111 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N PHE B 89 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR B 109 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 91 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 22 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 33 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B 20 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N SER B 35 " --> pdb=" O ASP B 18 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP B 18 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG B 37 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS B 16 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP B 39 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLY B 14 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ARG B 41 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE B 12 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER B 9 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLN B 145 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N VAL B 11 " --> pdb=" O GLN B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 60 removed outlier: 10.409A pdb=" N GLY B 85 " --> pdb=" O GLN B 113 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N GLN B 113 " --> pdb=" O GLY B 85 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET B 87 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR B 111 " --> pdb=" O MET B 87 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N PHE B 89 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR B 109 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN B 91 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 22 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL B 33 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE B 20 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N SER B 35 " --> pdb=" O ASP B 18 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP B 18 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG B 37 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS B 16 " --> pdb=" O ARG B 37 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP B 39 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLY B 14 " --> pdb=" O ASP B 39 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ARG B 41 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE B 12 " --> pdb=" O ARG B 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 80 removed outlier: 5.186A pdb=" N SER B 183 " --> pdb=" O SER B 135 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU B 166 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU B 192 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL B 164 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 60 removed outlier: 10.408A pdb=" N GLY C 85 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N GLN C 113 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET C 87 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR C 111 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE C 89 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR C 109 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN C 91 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 22 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 33 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE C 20 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N SER C 35 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP C 18 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG C 37 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS C 16 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP C 39 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLY C 14 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ARG C 41 " --> pdb=" O PHE C 12 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE C 12 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N SER C 9 " --> pdb=" O ARG C 143 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLN C 145 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL C 11 " --> pdb=" O GLN C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 56 through 60 removed outlier: 10.408A pdb=" N GLY C 85 " --> pdb=" O GLN C 113 " (cutoff:3.500A) removed outlier: 9.392A pdb=" N GLN C 113 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET C 87 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR C 111 " --> pdb=" O MET C 87 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE C 89 " --> pdb=" O THR C 109 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR C 109 " --> pdb=" O PHE C 89 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN C 91 " --> pdb=" O ARG C 107 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 22 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 33 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE C 20 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N SER C 35 " --> pdb=" O ASP C 18 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP C 18 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG C 37 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS C 16 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP C 39 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLY C 14 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ARG C 41 " --> pdb=" O PHE C 12 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE C 12 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 78 through 80 removed outlier: 5.186A pdb=" N SER C 183 " --> pdb=" O SER C 135 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU C 166 " --> pdb=" O HIS C 190 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU C 192 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL C 164 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 60 removed outlier: 10.408A pdb=" N GLY D 85 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N GLN D 113 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET D 87 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR D 111 " --> pdb=" O MET D 87 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE D 89 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR D 109 " --> pdb=" O PHE D 89 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN D 91 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY D 22 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL D 33 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE D 20 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N SER D 35 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP D 18 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG D 37 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LYS D 16 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP D 39 " --> pdb=" O GLY D 14 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLY D 14 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ARG D 41 " --> pdb=" O PHE D 12 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE D 12 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER D 9 " --> pdb=" O ARG D 143 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLN D 145 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL D 11 " --> pdb=" O GLN D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 56 through 60 removed outlier: 10.408A pdb=" N GLY D 85 " --> pdb=" O GLN D 113 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N GLN D 113 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET D 87 " --> pdb=" O THR D 111 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR D 111 " --> pdb=" O MET D 87 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE D 89 " --> pdb=" O THR D 109 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR D 109 " --> pdb=" O PHE D 89 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN D 91 " --> pdb=" O ARG D 107 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR D 101 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY D 22 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL D 33 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE D 20 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 9.065A pdb=" N SER D 35 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP D 18 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ARG D 37 " --> pdb=" O LYS D 16 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LYS D 16 " --> pdb=" O ARG D 37 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP D 39 " --> pdb=" O GLY D 14 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLY D 14 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ARG D 41 " --> pdb=" O PHE D 12 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE D 12 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 78 through 80 removed outlier: 5.187A pdb=" N SER D 183 " --> pdb=" O SER D 135 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 166 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU D 192 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL D 164 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 60 removed outlier: 10.408A pdb=" N GLY E 85 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N GLN E 113 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET E 87 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR E 111 " --> pdb=" O MET E 87 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE E 89 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR E 109 " --> pdb=" O PHE E 89 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN E 91 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR E 101 " --> pdb=" O SER E 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY E 22 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL E 33 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE E 20 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N SER E 35 " --> pdb=" O ASP E 18 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP E 18 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG E 37 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS E 16 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP E 39 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLY E 14 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ARG E 41 " --> pdb=" O PHE E 12 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE E 12 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N SER E 9 " --> pdb=" O ARG E 143 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLN E 145 " --> pdb=" O SER E 9 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL E 11 " --> pdb=" O GLN E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 56 through 60 removed outlier: 10.408A pdb=" N GLY E 85 " --> pdb=" O GLN E 113 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N GLN E 113 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N MET E 87 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR E 111 " --> pdb=" O MET E 87 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE E 89 " --> pdb=" O THR E 109 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR E 109 " --> pdb=" O PHE E 89 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN E 91 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR E 101 " --> pdb=" O SER E 97 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY E 22 " --> pdb=" O SER E 31 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL E 33 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE E 20 " --> pdb=" O VAL E 33 " (cutoff:3.500A) removed outlier: 9.066A pdb=" N SER E 35 " --> pdb=" O ASP E 18 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASP E 18 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ARG E 37 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS E 16 " --> pdb=" O ARG E 37 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASP E 39 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLY E 14 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N ARG E 41 " --> pdb=" O PHE E 12 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N PHE E 12 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 78 through 80 removed outlier: 5.185A pdb=" N SER E 183 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 166 " --> pdb=" O HIS E 190 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU E 192 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL E 164 " --> pdb=" O GLU E 192 " (cutoff:3.500A) 800 hydrogen bonds defined for protein. 2325 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: 2.66 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3339 1.34 - 1.46: 2823 1.46 - 1.58: 7223 1.58 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 13435 Sorted by residual: bond pdb=" CA ILE D 204 " pdb=" C ILE D 204 " ideal model delta sigma weight residual 1.523 1.559 -0.036 9.20e-03 1.18e+04 1.55e+01 bond pdb=" CA ILE B 204 " pdb=" C ILE B 204 " ideal model delta sigma weight residual 1.523 1.559 -0.036 9.20e-03 1.18e+04 1.52e+01 bond pdb=" CA ILE A 204 " pdb=" C ILE A 204 " ideal model delta sigma weight residual 1.523 1.559 -0.036 9.20e-03 1.18e+04 1.50e+01 bond pdb=" CA ILE C 204 " pdb=" C ILE C 204 " ideal model delta sigma weight residual 1.523 1.558 -0.035 9.20e-03 1.18e+04 1.48e+01 bond pdb=" CA ILE E 204 " pdb=" C ILE E 204 " ideal model delta sigma weight residual 1.523 1.558 -0.035 9.20e-03 1.18e+04 1.44e+01 ... (remaining 13430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 16087 1.69 - 3.38: 1505 3.38 - 5.08: 432 5.08 - 6.77: 76 6.77 - 8.46: 15 Bond angle restraints: 18115 Sorted by residual: angle pdb=" N LEU E 203 " pdb=" CA LEU E 203 " pdb=" C LEU E 203 " ideal model delta sigma weight residual 111.07 116.33 -5.26 1.07e+00 8.73e-01 2.41e+01 angle pdb=" N LEU C 203 " pdb=" CA LEU C 203 " pdb=" C LEU C 203 " ideal model delta sigma weight residual 111.07 116.31 -5.24 1.07e+00 8.73e-01 2.40e+01 angle pdb=" N LEU A 203 " pdb=" CA LEU A 203 " pdb=" C LEU A 203 " ideal model delta sigma weight residual 111.07 116.30 -5.23 1.07e+00 8.73e-01 2.39e+01 angle pdb=" N LEU D 203 " pdb=" CA LEU D 203 " pdb=" C LEU D 203 " ideal model delta sigma weight residual 111.07 116.30 -5.23 1.07e+00 8.73e-01 2.39e+01 angle pdb=" N LEU B 203 " pdb=" CA LEU B 203 " pdb=" C LEU B 203 " ideal model delta sigma weight residual 111.07 116.27 -5.20 1.07e+00 8.73e-01 2.36e+01 ... (remaining 18110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7120 17.94 - 35.88: 515 35.88 - 53.82: 75 53.82 - 71.76: 40 71.76 - 89.69: 10 Dihedral angle restraints: 7760 sinusoidal: 3245 harmonic: 4515 Sorted by residual: dihedral pdb=" CA PRO D 138 " pdb=" C PRO D 138 " pdb=" N GLN D 139 " pdb=" CA GLN D 139 " ideal model delta harmonic sigma weight residual 180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PRO A 138 " pdb=" C PRO A 138 " pdb=" N GLN A 139 " pdb=" CA GLN A 139 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PRO C 138 " pdb=" C PRO C 138 " pdb=" N GLN C 139 " pdb=" CA GLN C 139 " ideal model delta harmonic sigma weight residual -180.00 -158.41 -21.59 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 7757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1616 0.089 - 0.179: 248 0.179 - 0.268: 51 0.268 - 0.357: 45 0.357 - 0.447: 10 Chirality restraints: 1970 Sorted by residual: chirality pdb=" CG LEU C 233 " pdb=" CB LEU C 233 " pdb=" CD1 LEU C 233 " pdb=" CD2 LEU C 233 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CG LEU D 233 " pdb=" CB LEU D 233 " pdb=" CD1 LEU D 233 " pdb=" CD2 LEU D 233 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CG LEU A 233 " pdb=" CB LEU A 233 " pdb=" CD1 LEU A 233 " pdb=" CD2 LEU A 233 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 4.95e+00 ... (remaining 1967 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 295 " 0.016 2.00e-02 2.50e+03 3.17e-02 2.00e+01 pdb=" CG TYR D 295 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR D 295 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR D 295 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR D 295 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR D 295 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 295 " -0.059 2.00e-02 2.50e+03 pdb=" OH TYR D 295 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 295 " 0.016 2.00e-02 2.50e+03 3.17e-02 2.00e+01 pdb=" CG TYR C 295 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR C 295 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR C 295 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 TYR C 295 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR C 295 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 295 " -0.059 2.00e-02 2.50e+03 pdb=" OH TYR C 295 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 295 " 0.016 2.00e-02 2.50e+03 3.16e-02 2.00e+01 pdb=" CG TYR B 295 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR B 295 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR B 295 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR B 295 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 295 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR B 295 " -0.059 2.00e-02 2.50e+03 pdb=" OH TYR B 295 " 0.029 2.00e-02 2.50e+03 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4130 2.85 - 3.37: 10488 3.37 - 3.88: 20303 3.88 - 4.39: 23860 4.39 - 4.90: 40860 Nonbonded interactions: 99641 Sorted by model distance: nonbonded pdb=" CA ALA D 238 " pdb=" CE2 PHE D 241 " model vdw 2.343 3.770 nonbonded pdb=" CA ALA B 238 " pdb=" CE2 PHE B 241 " model vdw 2.343 3.770 nonbonded pdb=" CA ALA A 238 " pdb=" CE2 PHE A 241 " model vdw 2.344 3.770 nonbonded pdb=" CA ALA E 238 " pdb=" CE2 PHE E 241 " model vdw 2.344 3.770 nonbonded pdb=" CA ALA C 238 " pdb=" CE2 PHE C 241 " model vdw 2.344 3.770 ... (remaining 99636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 317 or resid 702)) selection = (chain 'B' and (resid 8 through 317 or resid 402)) selection = (chain 'C' and (resid 8 through 317 or resid 402)) selection = (chain 'D' and (resid 8 through 317 or resid 402)) selection = (chain 'E' and (resid 8 through 317 or resid 402)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 7.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.430 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.006 0.039 13435 Z= 0.361 Angle : 1.192 8.460 18115 Z= 0.632 Chirality : 0.087 0.447 1970 Planarity : 0.011 0.068 2250 Dihedral : 13.566 89.694 4840 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.37 % Allowed : 3.35 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.18), residues: 1540 helix: -0.26 (0.17), residues: 605 sheet: 1.09 (0.27), residues: 335 loop : -1.05 (0.21), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.004 ARG D 74 TYR 0.059 0.010 TYR C 295 PHE 0.050 0.008 PHE B 236 TRP 0.054 0.010 TRP C 312 HIS 0.026 0.006 HIS D 190 Details of bonding type rmsd covalent geometry : bond 0.00644 (13435) covalent geometry : angle 1.19197 (18115) hydrogen bonds : bond 0.23832 ( 675) hydrogen bonds : angle 7.41715 ( 2325) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 291 time to evaluate : 0.517 Fit side-chains REVERT: A 26 LYS cc_start: 0.7845 (tttm) cc_final: 0.7546 (tptp) REVERT: A 86 ARG cc_start: 0.7773 (ttt90) cc_final: 0.7523 (tmm160) REVERT: B 26 LYS cc_start: 0.7787 (tttm) cc_final: 0.7418 (tptp) REVERT: B 145 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8069 (mp10) REVERT: B 147 MET cc_start: 0.8579 (ttm) cc_final: 0.8354 (ttm) REVERT: C 26 LYS cc_start: 0.7821 (tttm) cc_final: 0.7433 (tptp) REVERT: C 196 ASN cc_start: 0.8160 (t0) cc_final: 0.7828 (p0) REVERT: D 145 GLN cc_start: 0.8344 (mm-40) cc_final: 0.7987 (mp10) REVERT: D 196 ASN cc_start: 0.8142 (t0) cc_final: 0.7878 (p0) REVERT: E 26 LYS cc_start: 0.7799 (tttm) cc_final: 0.7389 (tptp) REVERT: E 196 ASN cc_start: 0.8183 (t0) cc_final: 0.7879 (p0) REVERT: E 224 LYS cc_start: 0.8218 (mmtt) cc_final: 0.8005 (mmmm) outliers start: 5 outliers final: 2 residues processed: 296 average time/residue: 0.7290 time to fit residues: 232.3643 Evaluate side-chains 212 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 210 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 297 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 175 ASN B 91 ASN B 175 ASN C 84 GLN C 91 ASN C 175 ASN D 84 GLN D 91 ASN D 175 ASN E 91 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.145014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112727 restraints weight = 11916.760| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.27 r_work: 0.3075 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 13435 Z= 0.275 Angle : 0.831 9.227 18115 Z= 0.458 Chirality : 0.054 0.216 1970 Planarity : 0.006 0.039 2250 Dihedral : 9.014 50.061 1929 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.45 % Allowed : 6.69 % Favored : 90.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.20), residues: 1540 helix: 1.82 (0.21), residues: 600 sheet: 0.83 (0.25), residues: 365 loop : -0.84 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 41 TYR 0.017 0.003 TYR C 198 PHE 0.027 0.003 PHE C 129 TRP 0.018 0.002 TRP A 40 HIS 0.010 0.002 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00514 (13435) covalent geometry : angle 0.83080 (18115) hydrogen bonds : bond 0.10996 ( 675) hydrogen bonds : angle 5.18033 ( 2325) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.530 Fit side-chains REVERT: B 26 LYS cc_start: 0.8168 (tttm) cc_final: 0.7954 (tptp) REVERT: B 147 MET cc_start: 0.8788 (ttm) cc_final: 0.8490 (ttm) REVERT: B 224 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8075 (mptp) REVERT: B 241 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6861 (t80) REVERT: B 305 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7916 (tp) REVERT: C 16 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8525 (tttp) REVERT: C 26 LYS cc_start: 0.8102 (tttm) cc_final: 0.7878 (tptp) REVERT: C 305 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7921 (tp) REVERT: E 26 LYS cc_start: 0.8057 (tttm) cc_final: 0.7809 (tptp) outliers start: 33 outliers final: 15 residues processed: 210 average time/residue: 0.7067 time to fit residues: 160.2248 Evaluate side-chains 204 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 241 PHE Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 241 PHE Chi-restraints excluded: chain E residue 294 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 128 optimal weight: 0.0770 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 175 ASN B 91 ASN B 175 ASN C 91 ASN C 175 ASN D 91 ASN D 175 ASN E 91 ASN E 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.147349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115228 restraints weight = 12100.441| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.28 r_work: 0.3114 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13435 Z= 0.195 Angle : 0.646 7.074 18115 Z= 0.360 Chirality : 0.046 0.152 1970 Planarity : 0.004 0.038 2250 Dihedral : 8.280 50.827 1927 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.05 % Allowed : 8.03 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.20), residues: 1540 helix: 2.28 (0.20), residues: 600 sheet: 0.93 (0.25), residues: 365 loop : -0.77 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.012 0.002 TYR E 198 PHE 0.024 0.002 PHE E 241 TRP 0.014 0.002 TRP D 40 HIS 0.008 0.002 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00329 (13435) covalent geometry : angle 0.64585 (18115) hydrogen bonds : bond 0.08834 ( 675) hydrogen bonds : angle 4.75079 ( 2325) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 0.477 Fit side-chains REVERT: A 41 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6571 (tpt90) REVERT: A 86 ARG cc_start: 0.7980 (tmm160) cc_final: 0.7778 (tmm160) REVERT: A 291 LYS cc_start: 0.8124 (ttpp) cc_final: 0.7646 (mtmt) REVERT: B 16 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8573 (tttp) REVERT: B 26 LYS cc_start: 0.8109 (tttm) cc_final: 0.7869 (tptp) REVERT: B 41 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6910 (tpt90) REVERT: B 241 PHE cc_start: 0.7139 (p90) cc_final: 0.6595 (t80) REVERT: B 305 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7896 (tp) REVERT: C 26 LYS cc_start: 0.8058 (tttm) cc_final: 0.7835 (tptp) REVERT: C 41 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6491 (tpt90) REVERT: E 26 LYS cc_start: 0.7981 (tttm) cc_final: 0.7713 (tptp) REVERT: E 172 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8203 (t) outliers start: 41 outliers final: 19 residues processed: 206 average time/residue: 0.7099 time to fit residues: 157.4970 Evaluate side-chains 204 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 240 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 48 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 175 ASN B 91 ASN B 175 ASN C 91 ASN C 175 ASN D 91 ASN D 175 ASN E 91 ASN E 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.147692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.115596 restraints weight = 12060.130| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.27 r_work: 0.3117 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13435 Z= 0.183 Angle : 0.614 6.987 18115 Z= 0.343 Chirality : 0.045 0.151 1970 Planarity : 0.004 0.036 2250 Dihedral : 8.085 58.185 1925 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.68 % Allowed : 9.22 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.20), residues: 1540 helix: 2.43 (0.20), residues: 600 sheet: 1.02 (0.25), residues: 365 loop : -0.79 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 143 TYR 0.012 0.002 TYR C 198 PHE 0.025 0.002 PHE E 241 TRP 0.011 0.002 TRP A 40 HIS 0.007 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00307 (13435) covalent geometry : angle 0.61435 (18115) hydrogen bonds : bond 0.08385 ( 675) hydrogen bonds : angle 4.62062 ( 2325) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 182 time to evaluate : 0.458 Fit side-chains REVERT: A 291 LYS cc_start: 0.8077 (ttpp) cc_final: 0.7639 (mtmt) REVERT: B 16 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8558 (tttp) REVERT: B 26 LYS cc_start: 0.8083 (tttm) cc_final: 0.7837 (tptp) REVERT: B 41 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6970 (tpt90) REVERT: B 224 LYS cc_start: 0.8371 (mmtt) cc_final: 0.8121 (mmmt) REVERT: B 241 PHE cc_start: 0.7035 (p90) cc_final: 0.6455 (t80) REVERT: B 305 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7862 (tp) REVERT: C 26 LYS cc_start: 0.8022 (tttm) cc_final: 0.7813 (tptp) REVERT: C 41 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.6524 (tpt90) REVERT: C 224 LYS cc_start: 0.8408 (mmmm) cc_final: 0.8198 (mmmt) REVERT: D 41 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6393 (tpt90) REVERT: E 26 LYS cc_start: 0.7982 (tttm) cc_final: 0.7730 (tptp) REVERT: E 41 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6986 (tpt90) REVERT: E 172 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8187 (t) outliers start: 36 outliers final: 21 residues processed: 195 average time/residue: 0.7180 time to fit residues: 150.5590 Evaluate side-chains 206 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 240 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 39 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 175 ASN B 91 ASN B 175 ASN C 91 ASN C 175 ASN D 91 ASN D 175 ASN E 91 ASN E 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.146912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.114601 restraints weight = 12123.708| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.28 r_work: 0.3103 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13435 Z= 0.191 Angle : 0.627 7.342 18115 Z= 0.350 Chirality : 0.045 0.162 1970 Planarity : 0.004 0.034 2250 Dihedral : 8.321 58.122 1925 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.90 % Allowed : 9.52 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.20), residues: 1540 helix: 2.48 (0.20), residues: 600 sheet: 1.21 (0.26), residues: 335 loop : -0.91 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 143 TYR 0.013 0.002 TYR E 198 PHE 0.028 0.002 PHE E 241 TRP 0.014 0.002 TRP C 312 HIS 0.008 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00323 (13435) covalent geometry : angle 0.62656 (18115) hydrogen bonds : bond 0.08734 ( 675) hydrogen bonds : angle 4.65208 ( 2325) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.492 Fit side-chains REVERT: A 41 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7162 (tpt90) REVERT: A 291 LYS cc_start: 0.8100 (ttpp) cc_final: 0.7636 (mtmt) REVERT: B 16 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8583 (tttp) REVERT: B 26 LYS cc_start: 0.8088 (tttm) cc_final: 0.7845 (tptp) REVERT: B 41 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6976 (tpt90) REVERT: B 224 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8173 (mmmt) REVERT: B 241 PHE cc_start: 0.7141 (p90) cc_final: 0.6547 (t80) REVERT: B 305 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7886 (tp) REVERT: C 16 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8613 (tttp) REVERT: C 41 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.6532 (tpt90) REVERT: C 224 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8248 (mmmt) REVERT: C 305 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7914 (tp) REVERT: D 41 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6409 (tpt90) REVERT: E 26 LYS cc_start: 0.8006 (tttm) cc_final: 0.7774 (tptp) REVERT: E 41 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7018 (tpt90) REVERT: E 172 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8218 (t) outliers start: 39 outliers final: 23 residues processed: 196 average time/residue: 0.7357 time to fit residues: 154.7841 Evaluate side-chains 209 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 240 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 113 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 175 ASN B 91 ASN B 175 ASN C 91 ASN C 175 ASN D 91 ASN D 175 ASN E 91 ASN E 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.143972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.111563 restraints weight = 12010.770| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.28 r_work: 0.3062 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13435 Z= 0.244 Angle : 0.733 8.902 18115 Z= 0.406 Chirality : 0.050 0.198 1970 Planarity : 0.005 0.037 2250 Dihedral : 9.346 58.089 1925 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.97 % Allowed : 10.04 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.20), residues: 1540 helix: 2.24 (0.20), residues: 600 sheet: 1.42 (0.26), residues: 325 loop : -1.14 (0.21), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 143 TYR 0.016 0.002 TYR E 198 PHE 0.032 0.002 PHE E 241 TRP 0.016 0.002 TRP C 312 HIS 0.010 0.002 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00439 (13435) covalent geometry : angle 0.73305 (18115) hydrogen bonds : bond 0.10455 ( 675) hydrogen bonds : angle 4.96957 ( 2325) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.653 Fit side-chains REVERT: A 41 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7270 (tpt90) REVERT: B 16 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8647 (tttp) REVERT: B 26 LYS cc_start: 0.8110 (tttm) cc_final: 0.7867 (tptp) REVERT: B 41 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7011 (tpt90) REVERT: B 224 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8021 (mptp) REVERT: B 241 PHE cc_start: 0.7407 (p90) cc_final: 0.7109 (t80) REVERT: B 305 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7927 (tp) REVERT: C 41 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6539 (tpt90) REVERT: C 305 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7983 (tp) REVERT: D 41 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6389 (tpt90) REVERT: E 26 LYS cc_start: 0.8071 (tttm) cc_final: 0.7822 (tptp) REVERT: E 41 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7091 (tpt90) REVERT: E 172 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8310 (t) outliers start: 40 outliers final: 24 residues processed: 192 average time/residue: 0.7276 time to fit residues: 150.0107 Evaluate side-chains 207 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 294 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 240 ASN Chi-restraints excluded: chain E residue 241 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 125 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 62 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 35 optimal weight: 0.1980 chunk 96 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 175 ASN B 91 ASN B 175 ASN C 91 ASN C 175 ASN D 91 ASN D 175 ASN E 91 ASN E 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.150215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.118341 restraints weight = 12185.787| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.28 r_work: 0.3157 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13435 Z= 0.157 Angle : 0.557 5.852 18115 Z= 0.313 Chirality : 0.043 0.155 1970 Planarity : 0.004 0.034 2250 Dihedral : 8.059 55.422 1925 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.23 % Allowed : 10.78 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.20), residues: 1540 helix: 2.69 (0.20), residues: 600 sheet: 1.00 (0.25), residues: 365 loop : -0.87 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 143 TYR 0.010 0.001 TYR C 59 PHE 0.028 0.002 PHE E 241 TRP 0.017 0.002 TRP C 312 HIS 0.006 0.001 HIS A 194 Details of bonding type rmsd covalent geometry : bond 0.00261 (13435) covalent geometry : angle 0.55742 (18115) hydrogen bonds : bond 0.07351 ( 675) hydrogen bonds : angle 4.42432 ( 2325) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.568 Fit side-chains REVERT: A 41 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7144 (tpt90) REVERT: A 291 LYS cc_start: 0.8019 (ttpp) cc_final: 0.7631 (mtmt) REVERT: B 16 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8585 (tttp) REVERT: B 26 LYS cc_start: 0.8026 (tttm) cc_final: 0.7786 (tptp) REVERT: B 224 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8035 (mmmt) REVERT: B 241 PHE cc_start: 0.6844 (p90) cc_final: 0.6288 (t80) REVERT: B 305 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7819 (tp) REVERT: C 41 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.6503 (tpt90) REVERT: C 305 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7860 (tp) REVERT: D 41 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6424 (tpt90) REVERT: E 26 LYS cc_start: 0.7929 (tttm) cc_final: 0.7701 (tptp) REVERT: E 41 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7008 (tpt90) outliers start: 30 outliers final: 12 residues processed: 191 average time/residue: 0.6854 time to fit residues: 140.6512 Evaluate side-chains 195 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 240 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 133 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 175 ASN B 91 ASN B 175 ASN C 91 ASN C 175 ASN D 91 ASN D 175 ASN E 91 ASN E 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.144890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112593 restraints weight = 11988.001| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.27 r_work: 0.3074 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13435 Z= 0.231 Angle : 0.704 8.528 18115 Z= 0.390 Chirality : 0.048 0.196 1970 Planarity : 0.005 0.035 2250 Dihedral : 8.919 49.425 1925 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.30 % Allowed : 10.56 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.20), residues: 1540 helix: 2.41 (0.20), residues: 600 sheet: 1.42 (0.26), residues: 325 loop : -1.19 (0.21), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 143 TYR 0.015 0.002 TYR C 198 PHE 0.034 0.002 PHE E 241 TRP 0.020 0.002 TRP C 312 HIS 0.010 0.002 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00414 (13435) covalent geometry : angle 0.70366 (18115) hydrogen bonds : bond 0.09960 ( 675) hydrogen bonds : angle 4.85275 ( 2325) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.551 Fit side-chains REVERT: A 41 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7262 (tpt90) REVERT: B 16 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8640 (tttp) REVERT: B 26 LYS cc_start: 0.8129 (tttm) cc_final: 0.7883 (tptp) REVERT: B 224 LYS cc_start: 0.8474 (mmtt) cc_final: 0.7988 (mptp) REVERT: B 241 PHE cc_start: 0.7324 (p90) cc_final: 0.7062 (t80) REVERT: B 305 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7912 (tp) REVERT: C 41 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6551 (tpt90) REVERT: D 41 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6378 (tpt90) REVERT: E 26 LYS cc_start: 0.8085 (tttm) cc_final: 0.7835 (tptp) REVERT: E 41 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7089 (tpt90) outliers start: 31 outliers final: 19 residues processed: 186 average time/residue: 0.7574 time to fit residues: 151.3545 Evaluate side-chains 199 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 240 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 175 ASN B 91 ASN B 175 ASN C 91 ASN C 175 ASN D 91 ASN D 175 ASN E 91 ASN E 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.145660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.113411 restraints weight = 12127.425| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.28 r_work: 0.3089 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13435 Z= 0.214 Angle : 0.673 7.938 18115 Z= 0.375 Chirality : 0.047 0.183 1970 Planarity : 0.004 0.037 2250 Dihedral : 9.044 52.777 1925 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.08 % Allowed : 10.78 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.20), residues: 1540 helix: 2.44 (0.20), residues: 600 sheet: 1.38 (0.26), residues: 325 loop : -1.25 (0.21), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.015 0.002 TYR C 198 PHE 0.024 0.002 PHE C 241 TRP 0.024 0.002 TRP C 312 HIS 0.009 0.002 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00376 (13435) covalent geometry : angle 0.67277 (18115) hydrogen bonds : bond 0.09445 ( 675) hydrogen bonds : angle 4.78873 ( 2325) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.621 Fit side-chains REVERT: A 41 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7248 (tpt90) REVERT: A 291 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7704 (mtmt) REVERT: B 16 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8628 (tttp) REVERT: B 26 LYS cc_start: 0.8105 (tttm) cc_final: 0.7856 (tptp) REVERT: B 224 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8182 (mmmt) REVERT: B 241 PHE cc_start: 0.7199 (p90) cc_final: 0.6998 (t80) REVERT: B 305 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7910 (tp) REVERT: C 41 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6572 (tpt90) REVERT: D 41 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.6420 (tpt90) REVERT: E 26 LYS cc_start: 0.8062 (tttm) cc_final: 0.7794 (tptp) REVERT: E 41 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7096 (tpt90) outliers start: 28 outliers final: 19 residues processed: 187 average time/residue: 0.7451 time to fit residues: 149.9091 Evaluate side-chains 200 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 SER Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 213 SER Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 213 SER Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 240 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 53 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 102 optimal weight: 8.9990 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 175 ASN B 91 ASN B 175 ASN C 91 ASN C 175 ASN D 91 ASN D 175 ASN E 91 ASN E 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.142856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.110612 restraints weight = 12132.595| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.27 r_work: 0.3049 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13435 Z= 0.287 Angle : 0.814 9.618 18115 Z= 0.449 Chirality : 0.054 0.218 1970 Planarity : 0.005 0.039 2250 Dihedral : 10.322 58.646 1925 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.86 % Allowed : 11.08 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.20), residues: 1540 helix: 2.08 (0.20), residues: 600 sheet: 1.40 (0.26), residues: 325 loop : -1.35 (0.20), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 143 TYR 0.017 0.003 TYR C 198 PHE 0.030 0.003 PHE C 129 TRP 0.029 0.003 TRP C 312 HIS 0.011 0.002 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00547 (13435) covalent geometry : angle 0.81362 (18115) hydrogen bonds : bond 0.11359 ( 675) hydrogen bonds : angle 5.10147 ( 2325) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.340 Fit side-chains REVERT: A 41 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7296 (tpt90) REVERT: B 16 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8669 (tttp) REVERT: B 224 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8035 (mptp) REVERT: B 241 PHE cc_start: 0.7439 (p90) cc_final: 0.7117 (t80) REVERT: B 249 ARG cc_start: 0.7484 (mtt180) cc_final: 0.6924 (tmm160) REVERT: B 305 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7947 (tp) REVERT: C 41 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6640 (tpt90) REVERT: D 41 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6407 (tpt90) REVERT: D 249 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7086 (tmm160) REVERT: E 26 LYS cc_start: 0.8043 (tttm) cc_final: 0.7766 (tptp) REVERT: E 41 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7154 (tpt90) outliers start: 25 outliers final: 14 residues processed: 182 average time/residue: 0.7454 time to fit residues: 145.4295 Evaluate side-chains 196 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain D residue 41 ARG Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain E residue 41 ARG Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 19 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 175 ASN B 91 ASN B 175 ASN C 91 ASN C 175 ASN D 91 ASN D 175 ASN E 91 ASN E 175 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.143793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.111646 restraints weight = 11975.261| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.26 r_work: 0.3043 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13435 Z= 0.256 Angle : 0.757 8.951 18115 Z= 0.420 Chirality : 0.051 0.200 1970 Planarity : 0.005 0.040 2250 Dihedral : 10.401 58.515 1925 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.86 % Allowed : 11.15 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.20), residues: 1540 helix: 2.14 (0.20), residues: 600 sheet: 1.39 (0.27), residues: 325 loop : -1.37 (0.20), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 143 TYR 0.016 0.003 TYR C 198 PHE 0.028 0.003 PHE C 241 TRP 0.032 0.003 TRP C 312 HIS 0.010 0.002 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00471 (13435) covalent geometry : angle 0.75666 (18115) hydrogen bonds : bond 0.10576 ( 675) hydrogen bonds : angle 5.01403 ( 2325) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5947.77 seconds wall clock time: 101 minutes 39.47 seconds (6099.47 seconds total)