Starting phenix.real_space_refine on Wed Jun 11 17:20:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ex6_50031/06_2025/9ex6_50031.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ex6_50031/06_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_50031/06_2025/9ex6_50031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ex6_50031/06_2025/9ex6_50031.map" model { file = "/net/cci-nas-00/data/ceres_data/9ex6_50031/06_2025/9ex6_50031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ex6_50031/06_2025/9ex6_50031.cif" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2} 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: 7.13, per 1000 atoms: 0.54 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: 2.95 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.41 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: 4.07 Time building geometry restraints manager: 3.52 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: 0.02 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 29.880 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (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 TRP 0.054 0.010 TRP C 312 HIS 0.026 0.006 HIS D 190 PHE 0.050 0.008 PHE B 236 TYR 0.059 0.010 TYR C 295 ARG 0.026 0.004 ARG D 74 Details of bonding type rmsd hydrogen bonds : bond 0.23832 ( 675) hydrogen bonds : angle 7.41715 ( 2325) covalent geometry : bond 0.00644 (13435) covalent geometry : angle 1.19197 (18115) *********************** 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 : 1.352 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: 1.4127 time to fit residues: 451.0690 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 : 1.491 ------------------------------------------------------------------------------- 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 130 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.148186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.116327 restraints weight = 11916.138| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.26 r_work: 0.3123 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13435 Z= 0.224 Angle : 0.727 7.508 18115 Z= 0.401 Chirality : 0.049 0.151 1970 Planarity : 0.005 0.037 2250 Dihedral : 8.231 51.844 1929 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.23 % Allowed : 6.84 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1540 helix: 1.90 (0.20), residues: 600 sheet: 0.84 (0.25), residues: 365 loop : -0.72 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 40 HIS 0.009 0.002 HIS E 194 PHE 0.022 0.002 PHE E 129 TYR 0.014 0.002 TYR C 198 ARG 0.003 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.09358 ( 675) hydrogen bonds : angle 4.98104 ( 2325) covalent geometry : bond 0.00396 (13435) covalent geometry : angle 0.72652 (18115) *********************** 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 232 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 291 LYS cc_start: 0.8076 (ttpp) cc_final: 0.7693 (mtmt) REVERT: B 26 LYS cc_start: 0.8131 (tttm) cc_final: 0.7927 (tptp) REVERT: B 147 MET cc_start: 0.8732 (ttm) cc_final: 0.8433 (ttm) REVERT: B 305 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7892 (tp) REVERT: C 26 LYS cc_start: 0.8075 (tttm) cc_final: 0.7819 (tptp) REVERT: C 305 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7871 (tp) REVERT: E 26 LYS cc_start: 0.8067 (tttm) cc_final: 0.7814 (tptp) outliers start: 30 outliers final: 11 residues processed: 210 average time/residue: 1.3886 time to fit residues: 315.6643 Evaluate side-chains 208 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR 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 33 VAL 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 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 41 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.147543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.115331 restraints weight = 12118.411| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.29 r_work: 0.3112 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13435 Z= 0.192 Angle : 0.640 7.064 18115 Z= 0.357 Chirality : 0.046 0.173 1970 Planarity : 0.004 0.036 2250 Dihedral : 7.936 47.464 1925 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.68 % Allowed : 8.10 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.20), residues: 1540 helix: 2.29 (0.20), residues: 600 sheet: 0.91 (0.25), residues: 365 loop : -0.72 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 40 HIS 0.008 0.001 HIS E 194 PHE 0.028 0.002 PHE C 241 TYR 0.012 0.002 TYR C 198 ARG 0.006 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.08818 ( 675) hydrogen bonds : angle 4.72437 ( 2325) covalent geometry : bond 0.00323 (13435) covalent geometry : angle 0.64008 (18115) *********************** 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 224 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 1.487 Fit side-chains REVERT: A 41 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.6559 (tpt90) REVERT: A 291 LYS cc_start: 0.8048 (ttpp) cc_final: 0.7652 (mtmt) REVERT: B 16 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8563 (tttp) REVERT: B 26 LYS cc_start: 0.8115 (tttm) cc_final: 0.7870 (tptp) REVERT: B 224 LYS cc_start: 0.8383 (mmtt) cc_final: 0.8140 (mmmt) REVERT: B 305 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7894 (tp) REVERT: C 16 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8587 (tttp) REVERT: C 26 LYS cc_start: 0.8089 (tttm) cc_final: 0.7829 (tptp) REVERT: C 41 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6435 (tpt90) REVERT: C 305 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7897 (tp) REVERT: D 41 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6198 (tpt90) REVERT: E 26 LYS cc_start: 0.8034 (tttm) cc_final: 0.7749 (tptp) REVERT: E 172 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8193 (t) outliers start: 36 outliers final: 17 residues processed: 201 average time/residue: 1.6324 time to fit residues: 352.9404 Evaluate side-chains 207 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 1.705 ------------------------------------------------------------------------------- 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 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 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 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 294 ILE Chi-restraints excluded: chain E residue 16 LYS 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 5 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 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 = 0.3598 r_free = 0.3598 target = 0.144425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.112349 restraints weight = 11960.282| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.24 r_work: 0.3068 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13435 Z= 0.237 Angle : 0.729 8.794 18115 Z= 0.405 Chirality : 0.050 0.215 1970 Planarity : 0.005 0.036 2250 Dihedral : 9.149 59.758 1925 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.05 % Allowed : 8.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1540 helix: 2.15 (0.20), residues: 600 sheet: 1.17 (0.26), residues: 335 loop : -0.95 (0.22), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 40 HIS 0.010 0.002 HIS B 194 PHE 0.032 0.002 PHE C 241 TYR 0.015 0.002 TYR C 198 ARG 0.006 0.000 ARG C 143 Details of bonding type rmsd hydrogen bonds : bond 0.10296 ( 675) hydrogen bonds : angle 4.97343 ( 2325) covalent geometry : bond 0.00421 (13435) covalent geometry : angle 0.72916 (18115) *********************** 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 221 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 1.555 Fit side-chains REVERT: A 41 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6914 (tpt90) REVERT: B 16 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8590 (tttp) REVERT: B 26 LYS cc_start: 0.8129 (tttm) cc_final: 0.7899 (tptp) REVERT: B 41 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6993 (tpt90) REVERT: B 224 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8032 (mptp) REVERT: B 305 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7946 (tp) REVERT: C 41 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6542 (tpt90) REVERT: C 305 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7903 (tp) REVERT: D 41 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6309 (tpt90) REVERT: E 26 LYS cc_start: 0.8066 (tttm) cc_final: 0.7839 (tptp) REVERT: E 41 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7018 (tpt90) REVERT: E 172 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8290 (t) outliers start: 41 outliers final: 22 residues processed: 197 average time/residue: 1.4133 time to fit residues: 300.6012 Evaluate side-chains 208 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 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 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 294 ILE Chi-restraints excluded: chain E residue 16 LYS Chi-restraints excluded: chain E residue 33 VAL 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 Chi-restraints excluded: chain E residue 294 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 41 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 75 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 140 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3604 r_free = 0.3604 target = 0.144792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.112440 restraints weight = 12026.387| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.28 r_work: 0.3072 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13435 Z= 0.234 Angle : 0.716 8.513 18115 Z= 0.399 Chirality : 0.049 0.206 1970 Planarity : 0.005 0.038 2250 Dihedral : 9.503 59.285 1925 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.83 % Allowed : 9.67 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1540 helix: 2.22 (0.20), residues: 600 sheet: 1.18 (0.26), residues: 335 loop : -1.04 (0.21), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 312 HIS 0.010 0.002 HIS B 194 PHE 0.026 0.002 PHE E 241 TYR 0.015 0.002 TYR C 198 ARG 0.004 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.10034 ( 675) hydrogen bonds : angle 4.93107 ( 2325) covalent geometry : bond 0.00419 (13435) covalent geometry : angle 0.71614 (18115) *********************** 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 214 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 1.541 Fit side-chains REVERT: A 291 LYS cc_start: 0.8179 (ttpp) cc_final: 0.7696 (mtmt) REVERT: B 16 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8648 (tttp) REVERT: B 26 LYS cc_start: 0.8138 (tttm) cc_final: 0.7884 (tptp) REVERT: B 41 ARG cc_start: 0.7657 (OUTLIER) cc_final: 0.6947 (tpt90) REVERT: B 224 LYS cc_start: 0.8454 (mmtt) cc_final: 0.7982 (mptp) REVERT: B 305 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7922 (tp) REVERT: C 41 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6526 (tpt90) REVERT: C 305 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7942 (tp) REVERT: D 41 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.6365 (tpt90) REVERT: E 26 LYS cc_start: 0.8051 (tttm) cc_final: 0.7793 (tptp) REVERT: E 41 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7034 (tpt90) REVERT: E 172 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8301 (t) outliers start: 38 outliers final: 23 residues processed: 195 average time/residue: 1.4199 time to fit residues: 299.1083 Evaluate side-chains 207 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 294 ILE 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 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 241 PHE 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 E residue 16 LYS Chi-restraints excluded: chain E residue 33 VAL 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 294 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 129 optimal weight: 7.9990 chunk 66 optimal weight: 0.0980 chunk 133 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.148582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.116229 restraints weight = 12263.548| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.30 r_work: 0.3130 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13435 Z= 0.173 Angle : 0.591 6.395 18115 Z= 0.332 Chirality : 0.044 0.173 1970 Planarity : 0.004 0.037 2250 Dihedral : 8.603 59.488 1925 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.23 % Allowed : 10.33 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.20), residues: 1540 helix: 2.55 (0.20), residues: 600 sheet: 0.98 (0.25), residues: 365 loop : -0.90 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 312 HIS 0.007 0.001 HIS E 194 PHE 0.026 0.002 PHE C 241 TYR 0.011 0.002 TYR E 198 ARG 0.004 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.07991 ( 675) hydrogen bonds : angle 4.56116 ( 2325) covalent geometry : bond 0.00289 (13435) covalent geometry : angle 0.59138 (18115) *********************** 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 210 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 180 time to evaluate : 1.532 Fit side-chains REVERT: A 291 LYS cc_start: 0.8078 (ttpp) cc_final: 0.7629 (mtmt) REVERT: B 16 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8578 (tttp) REVERT: B 26 LYS cc_start: 0.8051 (tttm) cc_final: 0.7809 (tptp) REVERT: B 41 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6838 (tpt90) REVERT: B 224 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8097 (mmmt) REVERT: B 305 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7841 (tp) REVERT: C 41 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6495 (tpt90) REVERT: C 305 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7868 (tp) REVERT: D 41 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6394 (tpt90) REVERT: E 26 LYS cc_start: 0.7950 (tttm) cc_final: 0.7709 (tptp) REVERT: E 41 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6998 (tpt90) outliers start: 30 outliers final: 14 residues processed: 191 average time/residue: 1.5309 time to fit residues: 315.4239 Evaluate side-chains 199 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 213 SER Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 213 SER 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 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 16 LYS Chi-restraints excluded: chain E residue 41 ARG 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 41 optimal weight: 6.9990 chunk 24 optimal weight: 0.4980 chunk 106 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.145856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.113566 restraints weight = 12096.346| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.29 r_work: 0.3087 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13435 Z= 0.212 Angle : 0.670 7.949 18115 Z= 0.373 Chirality : 0.047 0.202 1970 Planarity : 0.004 0.038 2250 Dihedral : 8.909 51.162 1925 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.30 % Allowed : 9.96 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 1540 helix: 2.42 (0.20), residues: 600 sheet: 1.16 (0.26), residues: 335 loop : -1.09 (0.21), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 312 HIS 0.009 0.002 HIS B 194 PHE 0.052 0.002 PHE A 241 TYR 0.014 0.002 TYR E 198 ARG 0.005 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.09394 ( 675) hydrogen bonds : angle 4.78674 ( 2325) covalent geometry : bond 0.00372 (13435) covalent geometry : angle 0.66956 (18115) *********************** 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: 31 poor density : 178 time to evaluate : 1.419 Fit side-chains REVERT: A 41 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7297 (tpt90) REVERT: A 291 LYS cc_start: 0.8170 (ttpp) cc_final: 0.7669 (mtmt) REVERT: B 16 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8608 (tttp) REVERT: B 26 LYS cc_start: 0.8103 (tttm) cc_final: 0.7858 (tptp) REVERT: B 41 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6950 (tpt90) REVERT: B 224 LYS cc_start: 0.8429 (mmtt) cc_final: 0.8178 (mmmt) REVERT: B 305 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7913 (tp) REVERT: C 41 ARG cc_start: 0.7589 (OUTLIER) cc_final: 0.6580 (tpt90) REVERT: C 305 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7944 (tp) REVERT: D 41 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6426 (tpt90) REVERT: E 26 LYS cc_start: 0.8069 (tttm) cc_final: 0.7803 (tptp) REVERT: E 41 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.7056 (tpt90) outliers start: 31 outliers final: 20 residues processed: 190 average time/residue: 1.4707 time to fit residues: 300.5642 Evaluate side-chains 204 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 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 294 ILE 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 240 ASN 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 16 LYS Chi-restraints excluded: chain E residue 41 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 B 240 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.147542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.115647 restraints weight = 12102.245| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.26 r_work: 0.3121 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2880 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= 0.188 Angle : 0.623 7.093 18115 Z= 0.349 Chirality : 0.045 0.193 1970 Planarity : 0.004 0.038 2250 Dihedral : 8.565 50.337 1925 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.53 % Allowed : 10.56 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.20), residues: 1540 helix: 2.55 (0.20), residues: 600 sheet: 1.16 (0.26), residues: 335 loop : -1.07 (0.21), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 312 HIS 0.007 0.001 HIS E 194 PHE 0.026 0.002 PHE C 241 TYR 0.012 0.002 TYR C 198 ARG 0.004 0.000 ARG A 143 Details of bonding type rmsd hydrogen bonds : bond 0.08573 ( 675) hydrogen bonds : angle 4.64394 ( 2325) covalent geometry : bond 0.00321 (13435) covalent geometry : angle 0.62279 (18115) *********************** 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 210 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 1.405 Fit side-chains REVERT: A 41 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7273 (tpt90) REVERT: A 291 LYS cc_start: 0.8108 (ttpp) cc_final: 0.7634 (mtmt) REVERT: B 16 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8592 (tttp) REVERT: B 26 LYS cc_start: 0.8043 (tttm) cc_final: 0.7813 (tptp) REVERT: B 41 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6882 (tpt90) REVERT: B 172 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8239 (t) REVERT: B 224 LYS cc_start: 0.8400 (mmtt) cc_final: 0.8143 (mmmt) REVERT: B 305 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7867 (tp) REVERT: C 41 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.6532 (tpt90) REVERT: C 305 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7899 (tp) REVERT: D 41 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6422 (tpt90) REVERT: E 26 LYS cc_start: 0.8006 (tttm) cc_final: 0.7760 (tptp) REVERT: E 41 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7057 (tpt90) outliers start: 34 outliers final: 20 residues processed: 189 average time/residue: 1.5482 time to fit residues: 315.4091 Evaluate side-chains 206 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 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 294 ILE 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 240 ASN 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 16 LYS Chi-restraints excluded: chain E residue 41 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 B 240 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.146175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.114061 restraints weight = 12047.951| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 1.28 r_work: 0.3096 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13435 Z= 0.205 Angle : 0.656 7.770 18115 Z= 0.366 Chirality : 0.046 0.204 1970 Planarity : 0.004 0.039 2250 Dihedral : 8.828 49.864 1925 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.45 % Allowed : 10.63 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 1540 helix: 2.48 (0.20), residues: 600 sheet: 1.14 (0.26), residues: 335 loop : -1.13 (0.21), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 312 HIS 0.008 0.001 HIS B 194 PHE 0.026 0.002 PHE E 241 TYR 0.014 0.002 TYR E 198 ARG 0.005 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.09199 ( 675) hydrogen bonds : angle 4.76077 ( 2325) covalent geometry : bond 0.00354 (13435) covalent geometry : angle 0.65639 (18115) *********************** 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 207 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 1.367 Fit side-chains REVERT: A 41 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7297 (tpt90) REVERT: A 291 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7682 (mtmt) REVERT: B 16 LYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8601 (tttp) REVERT: B 26 LYS cc_start: 0.8086 (tttm) cc_final: 0.7845 (tptp) REVERT: B 41 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.6942 (tpt90) REVERT: B 172 THR cc_start: 0.8484 (OUTLIER) cc_final: 0.8282 (t) REVERT: B 224 LYS cc_start: 0.8431 (mmtt) cc_final: 0.8181 (mmmt) REVERT: B 305 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7901 (tp) REVERT: C 41 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6559 (tpt90) REVERT: C 305 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7932 (tp) REVERT: D 41 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6392 (tpt90) REVERT: E 26 LYS cc_start: 0.8039 (tttm) cc_final: 0.7743 (tptp) REVERT: E 41 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7066 (tpt90) outliers start: 33 outliers final: 22 residues processed: 190 average time/residue: 1.5550 time to fit residues: 318.1915 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 : 1.637 ------------------------------------------------------------------------------- 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 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 294 ILE 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 240 ASN 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 16 LYS Chi-restraints excluded: chain E residue 41 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 125 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.145301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.113061 restraints weight = 12026.585| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.28 r_work: 0.3082 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13435 Z= 0.220 Angle : 0.690 8.214 18115 Z= 0.384 Chirality : 0.048 0.207 1970 Planarity : 0.005 0.039 2250 Dihedral : 9.435 59.492 1925 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.53 % Allowed : 10.63 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1540 helix: 2.38 (0.20), residues: 600 sheet: 1.13 (0.26), residues: 335 loop : -1.17 (0.21), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 312 HIS 0.009 0.002 HIS B 194 PHE 0.065 0.002 PHE A 241 TYR 0.015 0.002 TYR E 198 ARG 0.005 0.000 ARG B 143 Details of bonding type rmsd hydrogen bonds : bond 0.09682 ( 675) hydrogen bonds : angle 4.85814 ( 2325) covalent geometry : bond 0.00388 (13435) covalent geometry : angle 0.68955 (18115) ********************** 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 210 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 1.655 Fit side-chains REVERT: A 41 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7298 (tpt90) REVERT: A 291 LYS cc_start: 0.8224 (ttpp) cc_final: 0.7721 (mtmt) REVERT: B 16 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8604 (tttp) REVERT: B 41 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.6973 (tpt90) REVERT: B 218 PHE cc_start: 0.8704 (m-10) cc_final: 0.8284 (m-80) REVERT: B 224 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8216 (mmmt) REVERT: B 249 ARG cc_start: 0.7475 (mtt180) cc_final: 0.6942 (tmm160) REVERT: B 305 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7915 (tp) REVERT: C 41 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6542 (tpt90) REVERT: C 305 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7964 (tp) REVERT: D 41 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6394 (tpt90) REVERT: E 26 LYS cc_start: 0.8029 (tttm) cc_final: 0.7730 (tptp) REVERT: E 41 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7073 (tpt90) REVERT: E 241 PHE cc_start: 0.7116 (p90) cc_final: 0.6714 (t80) outliers start: 34 outliers final: 23 residues processed: 193 average time/residue: 1.4758 time to fit residues: 306.9210 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 : 1.590 ------------------------------------------------------------------------------- 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 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 294 ILE 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 240 ASN 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 16 LYS Chi-restraints excluded: chain E residue 41 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.6773 > 50: distance: 32 - 175: 3.646 distance: 35 - 172: 6.186 distance: 47 - 158: 3.743 distance: 101 - 102: 3.117 distance: 101 - 107: 4.553 distance: 105 - 106: 3.984 distance: 108 - 109: 3.593 distance: 108 - 111: 3.056 distance: 109 - 110: 11.130 distance: 109 - 115: 8.633 distance: 111 - 112: 3.437 distance: 115 - 116: 9.260 distance: 116 - 117: 17.858 distance: 117 - 118: 17.789 distance: 117 - 126: 15.288 distance: 119 - 120: 4.293 distance: 120 - 121: 4.533 distance: 120 - 122: 4.374 distance: 121 - 123: 5.438 distance: 123 - 125: 4.014 distance: 126 - 127: 23.198 distance: 127 - 128: 6.868 distance: 127 - 130: 29.268 distance: 128 - 129: 7.689 distance: 128 - 131: 10.711 distance: 131 - 132: 3.748 distance: 132 - 135: 4.306 distance: 135 - 136: 4.933 distance: 136 - 137: 6.425 distance: 136 - 138: 4.899 distance: 144 - 145: 3.548 distance: 150 - 220: 3.544 distance: 151 - 154: 3.232 distance: 153 - 217: 5.845 distance: 155 - 157: 3.184 distance: 162 - 164: 3.082 distance: 166 - 203: 3.898 distance: 167 - 168: 3.042 distance: 168 - 169: 4.908 distance: 169 - 200: 3.782 distance: 173 - 174: 4.178 distance: 173 - 176: 4.315 distance: 174 - 175: 3.549 distance: 176 - 177: 3.893 distance: 177 - 178: 6.257