Starting phenix.real_space_refine on Fri Jul 3 19:33:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p0n_71088/07_2026/9p0n_71088.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p0n_71088/07_2026/9p0n_71088.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9p0n_71088/07_2026/9p0n_71088.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p0n_71088/07_2026/9p0n_71088.map" model { file = "/net/cci-nas-00/data/ceres_data/9p0n_71088/07_2026/9p0n_71088.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p0n_71088/07_2026/9p0n_71088.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 28 5.49 5 S 42 5.16 5 C 10031 2.51 5 N 2450 2.21 5 O 2842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15393 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2002 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 259} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 184 Unusual residues: {'D21': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 184 Unusual residues: {'D21': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 230 Unusual residues: {'D21': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'D21': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 230 Unusual residues: {'D21': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'D21': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 184 Unusual residues: {'D21': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 67 residue: pdb=" C01 D21 A 301 " occ=0.46 ... (44 atoms not shown) pdb=" P23 D21 A 301 " occ=0.46 residue: pdb=" C01 D21 A 302 " occ=0.45 ... (44 atoms not shown) pdb=" P23 D21 A 302 " occ=0.45 residue: pdb=" C01 D21 A 303 " occ=0.50 ... (44 atoms not shown) pdb=" P23 D21 A 303 " occ=0.50 residue: pdb=" C01 D21 B 301 " occ=0.76 ... (44 atoms not shown) pdb=" P23 D21 B 301 " occ=0.76 residue: pdb=" O HOH A 401 " occ=0.65 residue: pdb=" O HOH A 402 " occ=0.93 residue: pdb=" O HOH A 403 " occ=0.85 residue: pdb=" O HOH A 404 " occ=0.91 residue: pdb=" O HOH A 406 " occ=0.93 residue: pdb=" O HOH A 408 " occ=0.76 residue: pdb=" O HOH A 411 " occ=0.62 residue: pdb=" O HOH A 412 " occ=0.86 ... (remaining 55 not shown) Time building chain proxies: 3.75, per 1000 atoms: 0.24 Number of scatterers: 15393 At special positions: 0 Unit cell: (102.475, 102.475, 146.514, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 28 15.00 O 2842 8.00 N 2450 7.00 C 10031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 676.6 milliseconds 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 53.6% alpha, 20.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 20 through 60 Processing helix chain 'A' and resid 67 through 90 removed outlier: 3.856A pdb=" N ALA A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 110 Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.981A pdb=" N ASN A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 171 removed outlier: 3.681A pdb=" N ILE A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 171' Processing helix chain 'A' and resid 197 through 212 removed outlier: 3.542A pdb=" N SER A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 265 removed outlier: 3.634A pdb=" N TYR A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 60 Processing helix chain 'B' and resid 67 through 90 removed outlier: 3.855A pdb=" N ALA B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE B 77 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 78 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA B 85 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 110 Processing helix chain 'B' and resid 111 through 127 removed outlier: 3.982A pdb=" N ASN B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 171 removed outlier: 3.683A pdb=" N ILE B 171 " --> pdb=" O ASN B 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 167 through 171' Processing helix chain 'B' and resid 197 through 212 removed outlier: 3.542A pdb=" N SER B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.635A pdb=" N TYR B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP B 262 " --> pdb=" O LYS B 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 60 Processing helix chain 'C' and resid 67 through 90 removed outlier: 3.855A pdb=" N ALA C 71 " --> pdb=" O ASP C 67 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE C 77 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE C 78 " --> pdb=" O ARG C 74 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 110 Processing helix chain 'C' and resid 111 through 127 removed outlier: 3.981A pdb=" N ASN C 117 " --> pdb=" O GLY C 113 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 171 removed outlier: 3.682A pdb=" N ILE C 171 " --> pdb=" O ASN C 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.543A pdb=" N SER C 211 " --> pdb=" O ASN C 207 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 265 removed outlier: 3.634A pdb=" N TYR C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU C 255 " --> pdb=" O TRP C 251 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C 262 " --> pdb=" O LYS C 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 60 Processing helix chain 'D' and resid 67 through 90 removed outlier: 3.855A pdb=" N ALA D 71 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE D 77 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE D 78 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D 84 " --> pdb=" O PHE D 80 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA D 85 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 110 Processing helix chain 'D' and resid 111 through 127 removed outlier: 3.982A pdb=" N ASN D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 171 removed outlier: 3.682A pdb=" N ILE D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 167 through 171' Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.543A pdb=" N SER D 211 " --> pdb=" O ASN D 207 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 265 removed outlier: 3.635A pdb=" N TYR D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU D 255 " --> pdb=" O TRP D 251 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP D 262 " --> pdb=" O LYS D 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 60 Processing helix chain 'E' and resid 67 through 90 removed outlier: 3.855A pdb=" N ALA E 71 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL E 73 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE E 77 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE E 78 " --> pdb=" O ARG E 74 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA E 85 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 110 Processing helix chain 'E' and resid 111 through 127 removed outlier: 3.981A pdb=" N ASN E 117 " --> pdb=" O GLY E 113 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU E 118 " --> pdb=" O SER E 114 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 171 removed outlier: 3.682A pdb=" N ILE E 171 " --> pdb=" O ASN E 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 167 through 171' Processing helix chain 'E' and resid 197 through 212 removed outlier: 3.543A pdb=" N SER E 211 " --> pdb=" O ASN E 207 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 265 removed outlier: 3.635A pdb=" N TYR E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU E 255 " --> pdb=" O TRP E 251 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP E 262 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 60 Processing helix chain 'F' and resid 67 through 90 removed outlier: 3.855A pdb=" N ALA F 71 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE F 77 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 78 " --> pdb=" O ARG F 74 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 84 " --> pdb=" O PHE F 80 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA F 85 " --> pdb=" O THR F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 110 Processing helix chain 'F' and resid 111 through 127 removed outlier: 3.982A pdb=" N ASN F 117 " --> pdb=" O GLY F 113 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU F 123 " --> pdb=" O ALA F 119 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL F 125 " --> pdb=" O GLY F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 171 removed outlier: 3.682A pdb=" N ILE F 171 " --> pdb=" O ASN F 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 167 through 171' Processing helix chain 'F' and resid 197 through 212 removed outlier: 3.542A pdb=" N SER F 211 " --> pdb=" O ASN F 207 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU F 212 " --> pdb=" O ILE F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 245 through 265 removed outlier: 3.635A pdb=" N TYR F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU F 255 " --> pdb=" O TRP F 251 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP F 262 " --> pdb=" O LYS F 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 60 Processing helix chain 'G' and resid 67 through 90 removed outlier: 3.855A pdb=" N ALA G 71 " --> pdb=" O ASP G 67 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL G 73 " --> pdb=" O LEU G 69 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE G 77 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE G 78 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA G 85 " --> pdb=" O THR G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 111 through 127 removed outlier: 3.981A pdb=" N ASN G 117 " --> pdb=" O GLY G 113 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU G 118 " --> pdb=" O SER G 114 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU G 123 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL G 125 " --> pdb=" O GLY G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 171 removed outlier: 3.682A pdb=" N ILE G 171 " --> pdb=" O ASN G 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 167 through 171' Processing helix chain 'G' and resid 197 through 212 removed outlier: 3.543A pdb=" N SER G 211 " --> pdb=" O ASN G 207 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU G 212 " --> pdb=" O ILE G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 265 removed outlier: 3.634A pdb=" N TYR G 250 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU G 255 " --> pdb=" O TRP G 251 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.817A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE A 162 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE G 162 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE F 162 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE E 162 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE D 162 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE C 162 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE B 162 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.349A pdb=" N VAL A 236 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU A 225 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ARG A 238 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL A 223 " --> pdb=" O ARG A 238 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N TRP A 240 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N MET A 221 " --> pdb=" O TRP A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 279 removed outlier: 8.605A pdb=" N MET B 273 " --> pdb=" O GLN A 272 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP A 274 " --> pdb=" O MET B 273 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL B 275 " --> pdb=" O ASP A 274 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASN A 276 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE B 277 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LYS A 278 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N ARG B 279 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N MET C 273 " --> pdb=" O GLN B 272 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP B 274 " --> pdb=" O MET C 273 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL C 275 " --> pdb=" O ASP B 274 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ASN B 276 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N PHE C 277 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS B 278 " --> pdb=" O PHE C 277 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ARG C 279 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N MET D 273 " --> pdb=" O GLN C 272 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP C 274 " --> pdb=" O MET D 273 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N VAL D 275 " --> pdb=" O ASP C 274 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASN C 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N PHE D 277 " --> pdb=" O ASN C 276 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS C 278 " --> pdb=" O PHE D 277 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N ARG D 279 " --> pdb=" O LYS C 278 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N MET E 273 " --> pdb=" O GLN D 272 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP D 274 " --> pdb=" O MET E 273 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL E 275 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN D 276 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N PHE E 277 " --> pdb=" O ASN D 276 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LYS D 278 " --> pdb=" O PHE E 277 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N ARG E 279 " --> pdb=" O LYS D 278 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N MET F 273 " --> pdb=" O GLN E 272 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASP E 274 " --> pdb=" O MET F 273 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL F 275 " --> pdb=" O ASP E 274 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ASN E 276 " --> pdb=" O VAL F 275 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N PHE F 277 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LYS E 278 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ARG F 279 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N MET G 273 " --> pdb=" O GLN F 272 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP F 274 " --> pdb=" O MET G 273 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL G 275 " --> pdb=" O ASP F 274 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN F 276 " --> pdb=" O VAL G 275 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N PHE G 277 " --> pdb=" O ASN F 276 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LYS F 278 " --> pdb=" O PHE G 277 " (cutoff:3.500A) removed outlier: 8.917A pdb=" N ARG G 279 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.350A pdb=" N VAL B 236 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU B 225 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ARG B 238 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL B 223 " --> pdb=" O ARG B 238 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N TRP B 240 " --> pdb=" O MET B 221 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N MET B 221 " --> pdb=" O TRP B 240 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.349A pdb=" N VAL C 236 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU C 225 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ARG C 238 " --> pdb=" O VAL C 223 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL C 223 " --> pdb=" O ARG C 238 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N TRP C 240 " --> pdb=" O MET C 221 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N MET C 221 " --> pdb=" O TRP C 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.350A pdb=" N VAL D 236 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU D 225 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ARG D 238 " --> pdb=" O VAL D 223 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL D 223 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N TRP D 240 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N MET D 221 " --> pdb=" O TRP D 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.349A pdb=" N VAL E 236 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU E 225 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ARG E 238 " --> pdb=" O VAL E 223 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL E 223 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N TRP E 240 " --> pdb=" O MET E 221 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N MET E 221 " --> pdb=" O TRP E 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.349A pdb=" N VAL F 236 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU F 225 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ARG F 238 " --> pdb=" O VAL F 223 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N VAL F 223 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N TRP F 240 " --> pdb=" O MET F 221 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N MET F 221 " --> pdb=" O TRP F 240 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.350A pdb=" N VAL G 236 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LEU G 225 " --> pdb=" O VAL G 236 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ARG G 238 " --> pdb=" O VAL G 223 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL G 223 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N TRP G 240 " --> pdb=" O MET G 221 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N MET G 221 " --> pdb=" O TRP G 240 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4712 1.34 - 1.47: 3218 1.47 - 1.60: 7407 1.60 - 1.73: 0 1.73 - 1.85: 112 Bond restraints: 15449 Sorted by residual: bond pdb=" O22 D21 E 304 " pdb=" P23 D21 E 304 " ideal model delta sigma weight residual 1.723 1.855 -0.132 2.00e-02 2.50e+03 4.33e+01 bond pdb=" O22 D21 B 304 " pdb=" P23 D21 B 304 " ideal model delta sigma weight residual 1.723 1.854 -0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" O22 D21 D 302 " pdb=" P23 D21 D 302 " ideal model delta sigma weight residual 1.723 1.854 -0.131 2.00e-02 2.50e+03 4.31e+01 bond pdb=" O22 D21 C 304 " pdb=" P23 D21 C 304 " ideal model delta sigma weight residual 1.723 1.854 -0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" O22 D21 E 305 " pdb=" P23 D21 E 305 " ideal model delta sigma weight residual 1.723 1.854 -0.131 2.00e-02 2.50e+03 4.29e+01 ... (remaining 15444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 19391 1.33 - 2.67: 826 2.67 - 4.00: 169 4.00 - 5.34: 122 5.34 - 6.67: 142 Bond angle restraints: 20650 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" C VAL C 125 " ideal model delta sigma weight residual 113.39 108.70 4.69 1.47e+00 4.63e-01 1.02e+01 angle pdb=" N VAL G 125 " pdb=" CA VAL G 125 " pdb=" C VAL G 125 " ideal model delta sigma weight residual 113.39 108.72 4.67 1.47e+00 4.63e-01 1.01e+01 angle pdb=" N VAL D 125 " pdb=" CA VAL D 125 " pdb=" C VAL D 125 " ideal model delta sigma weight residual 113.39 108.73 4.66 1.47e+00 4.63e-01 1.00e+01 angle pdb=" N VAL F 125 " pdb=" CA VAL F 125 " pdb=" C VAL F 125 " ideal model delta sigma weight residual 113.39 108.73 4.66 1.47e+00 4.63e-01 1.00e+01 angle pdb=" N VAL A 125 " pdb=" CA VAL A 125 " pdb=" C VAL A 125 " ideal model delta sigma weight residual 113.39 108.76 4.63 1.47e+00 4.63e-01 9.93e+00 ... (remaining 20645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.57: 9170 34.57 - 69.15: 588 69.15 - 103.72: 35 103.72 - 138.30: 14 138.30 - 172.87: 14 Dihedral angle restraints: 9821 sinusoidal: 4501 harmonic: 5320 Sorted by residual: dihedral pdb=" C21 D21 C 304 " pdb=" C20 D21 C 304 " pdb=" O30 D21 C 304 " pdb=" C31 D21 C 304 " ideal model delta sinusoidal sigma weight residual -84.16 88.71 -172.87 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 D21 E 304 " pdb=" C20 D21 E 304 " pdb=" O30 D21 E 304 " pdb=" C31 D21 E 304 " ideal model delta sinusoidal sigma weight residual -84.16 88.69 -172.85 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 D21 E 305 " pdb=" C20 D21 E 305 " pdb=" O30 D21 E 305 " pdb=" C31 D21 E 305 " ideal model delta sinusoidal sigma weight residual -84.16 88.68 -172.84 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 9818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1365 0.026 - 0.052: 530 0.052 - 0.078: 316 0.078 - 0.104: 113 0.104 - 0.130: 77 Chirality restraints: 2401 Sorted by residual: chirality pdb=" CA ILE E 165 " pdb=" N ILE E 165 " pdb=" C ILE E 165 " pdb=" CB ILE E 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE G 165 " pdb=" N ILE G 165 " pdb=" C ILE G 165 " pdb=" CB ILE G 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE E 175 " pdb=" N ILE E 175 " pdb=" C ILE E 175 " pdb=" CB ILE E 175 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 2398 not shown) Planarity restraints: 2527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 250 " -0.008 2.00e-02 2.50e+03 1.65e-02 2.71e+00 pdb=" C TYR A 250 " 0.028 2.00e-02 2.50e+03 pdb=" O TYR A 250 " -0.011 2.00e-02 2.50e+03 pdb=" N TRP A 251 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 250 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C TYR D 250 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR D 250 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP D 251 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 250 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C TYR C 250 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR C 250 " 0.011 2.00e-02 2.50e+03 pdb=" N TRP C 251 " 0.010 2.00e-02 2.50e+03 ... (remaining 2524 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 8981 3.05 - 3.51: 14547 3.51 - 3.97: 22947 3.97 - 4.44: 27996 4.44 - 4.90: 44845 Nonbonded interactions: 119316 Sorted by model distance: nonbonded pdb=" C14 D21 B 303 " pdb=" O18 D21 B 303 " model vdw 2.583 2.752 nonbonded pdb=" C14 D21 A 302 " pdb=" O18 D21 A 302 " model vdw 2.583 2.752 nonbonded pdb=" C14 D21 C 303 " pdb=" O18 D21 C 303 " model vdw 2.583 2.752 nonbonded pdb=" C14 D21 D 303 " pdb=" O18 D21 D 303 " model vdw 2.583 2.752 nonbonded pdb=" C14 D21 F 303 " pdb=" O18 D21 F 303 " model vdw 2.583 2.752 ... (remaining 119311 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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=0.45 max=1.00 mean=0.99 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.210 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: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.750 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.007 0.132 15449 Z= 0.370 Angle : 0.839 6.673 20650 Z= 0.369 Chirality : 0.042 0.130 2401 Planarity : 0.003 0.030 2527 Dihedral : 21.948 172.871 6391 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.14 % Allowed : 17.63 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 1841 helix: 0.16 (0.18), residues: 924 sheet: 1.42 (0.30), residues: 308 loop : -0.66 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 54 TYR 0.004 0.001 TYR E 135 PHE 0.010 0.001 PHE B 188 TRP 0.001 0.000 TRP E 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.37 (15449) covalent geometry : angle 0.83944 / 0.37 (20650) hydrogen bonds : bond 0.17556 / 11.55 ( 880) hydrogen bonds : angle 6.75755 / 4.89 ( 2598) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.548 Fit side-chains REVERT: A 56 MET cc_start: 0.4241 (ttp) cc_final: 0.3974 (ttp) REVERT: A 221 MET cc_start: 0.8875 (mtm) cc_final: 0.8482 (mtm) REVERT: A 279 ARG cc_start: 0.7677 (ttm170) cc_final: 0.7421 (ttm-80) REVERT: B 262 ASP cc_start: 0.7759 (m-30) cc_final: 0.7394 (m-30) REVERT: B 279 ARG cc_start: 0.7772 (ttm170) cc_final: 0.7477 (ttm-80) REVERT: C 279 ARG cc_start: 0.7680 (ttm170) cc_final: 0.7252 (ttt90) REVERT: D 128 ARG cc_start: 0.7725 (mtt-85) cc_final: 0.7120 (mtt-85) REVERT: D 151 PHE cc_start: 0.7718 (t80) cc_final: 0.6766 (m-80) REVERT: D 279 ARG cc_start: 0.7740 (ttm170) cc_final: 0.7527 (ttt-90) REVERT: E 128 ARG cc_start: 0.7772 (mtt-85) cc_final: 0.7160 (mtt-85) REVERT: E 151 PHE cc_start: 0.7838 (t80) cc_final: 0.6839 (m-80) REVERT: E 245 ASP cc_start: 0.8289 (m-30) cc_final: 0.8046 (m-30) REVERT: E 279 ARG cc_start: 0.7702 (ttm170) cc_final: 0.7337 (ttt-90) REVERT: F 279 ARG cc_start: 0.7671 (ttm170) cc_final: 0.7361 (ttm-80) REVERT: G 151 PHE cc_start: 0.7772 (t80) cc_final: 0.6893 (m-80) REVERT: G 245 ASP cc_start: 0.8422 (m-30) cc_final: 0.8114 (m-30) outliers start: 2 outliers final: 0 residues processed: 158 average time/residue: 0.5733 time to fit residues: 100.7082 Evaluate side-chains 137 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0020 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.190442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.129552 restraints weight = 16030.014| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.99 r_work: 0.3545 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15449 Z= 0.112 Angle : 0.444 4.677 20650 Z= 0.238 Chirality : 0.042 0.136 2401 Planarity : 0.003 0.029 2527 Dihedral : 20.839 178.312 3304 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.60 % Allowed : 16.81 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.20), residues: 1841 helix: 1.25 (0.18), residues: 931 sheet: 1.36 (0.29), residues: 308 loop : -0.63 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 128 TYR 0.006 0.001 TYR F 75 PHE 0.012 0.002 PHE A 188 TRP 0.004 0.001 TRP C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (15449) covalent geometry : angle 0.44380 / 0.24 (20650) hydrogen bonds : bond 0.04353 / 2.93 ( 880) hydrogen bonds : angle 3.89721 / 2.81 ( 2598) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.531 Fit side-chains REVERT: A 134 GLU cc_start: 0.8048 (tt0) cc_final: 0.7847 (tt0) REVERT: A 221 MET cc_start: 0.9047 (mtm) cc_final: 0.8689 (mtm) REVERT: A 262 ASP cc_start: 0.8382 (m-30) cc_final: 0.8035 (m-30) REVERT: A 279 ARG cc_start: 0.7679 (ttm170) cc_final: 0.7206 (ttm-80) REVERT: B 134 GLU cc_start: 0.8139 (tt0) cc_final: 0.7903 (tt0) REVERT: B 279 ARG cc_start: 0.7734 (ttm170) cc_final: 0.7239 (ttm-80) REVERT: C 134 GLU cc_start: 0.8094 (tt0) cc_final: 0.7855 (tt0) REVERT: C 262 ASP cc_start: 0.8335 (m-30) cc_final: 0.8130 (m-30) REVERT: C 279 ARG cc_start: 0.7688 (ttm170) cc_final: 0.7076 (ttt90) REVERT: D 128 ARG cc_start: 0.7391 (mtt-85) cc_final: 0.6699 (mtt-85) REVERT: D 134 GLU cc_start: 0.8021 (tt0) cc_final: 0.7735 (tt0) REVERT: D 151 PHE cc_start: 0.7605 (t80) cc_final: 0.6346 (m-80) REVERT: D 279 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7400 (ttt-90) REVERT: E 128 ARG cc_start: 0.7346 (mtt-85) cc_final: 0.6572 (mtt-85) REVERT: E 134 GLU cc_start: 0.8144 (tt0) cc_final: 0.7908 (tt0) REVERT: E 151 PHE cc_start: 0.7658 (t80) cc_final: 0.6359 (m-80) REVERT: E 279 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7177 (ttt-90) REVERT: F 197 ASP cc_start: 0.7801 (t0) cc_final: 0.7495 (t0) REVERT: F 279 ARG cc_start: 0.7592 (ttm170) cc_final: 0.7115 (ttm-80) REVERT: G 47 MET cc_start: 0.5528 (OUTLIER) cc_final: 0.5153 (mpt) REVERT: G 151 PHE cc_start: 0.7630 (t80) cc_final: 0.6453 (m-80) REVERT: G 171 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8605 (mm) REVERT: G 262 ASP cc_start: 0.8402 (m-30) cc_final: 0.8074 (m-30) outliers start: 38 outliers final: 14 residues processed: 188 average time/residue: 0.5424 time to fit residues: 113.1770 Evaluate side-chains 152 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 64 optimal weight: 3.9990 chunk 179 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 171 optimal weight: 0.0670 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.198592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.143717 restraints weight = 15788.991| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 1.71 r_work: 0.3728 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15449 Z= 0.143 Angle : 0.482 7.692 20650 Z= 0.255 Chirality : 0.043 0.145 2401 Planarity : 0.003 0.031 2527 Dihedral : 20.411 177.413 3304 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.42 % Allowed : 15.99 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 1841 helix: 1.56 (0.17), residues: 945 sheet: 1.11 (0.29), residues: 308 loop : -0.76 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 128 TYR 0.008 0.001 TYR G 135 PHE 0.014 0.002 PHE A 188 TRP 0.003 0.001 TRP B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (15449) covalent geometry : angle 0.48196 / 0.25 (20650) hydrogen bonds : bond 0.04539 / 3.05 ( 880) hydrogen bonds : angle 3.79479 / 2.75 ( 2598) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 157 time to evaluate : 0.379 Fit side-chains REVERT: A 134 GLU cc_start: 0.8076 (tt0) cc_final: 0.7874 (tt0) REVERT: A 262 ASP cc_start: 0.8273 (m-30) cc_final: 0.8033 (m-30) REVERT: A 279 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7426 (ttm-80) REVERT: B 189 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8423 (mt) REVERT: B 279 ARG cc_start: 0.7871 (ttm170) cc_final: 0.7320 (ttm-80) REVERT: C 262 ASP cc_start: 0.8186 (m-30) cc_final: 0.7956 (m-30) REVERT: C 279 ARG cc_start: 0.7760 (ttm170) cc_final: 0.7056 (mtp85) REVERT: D 128 ARG cc_start: 0.7565 (mtt-85) cc_final: 0.6878 (mtt-85) REVERT: D 134 GLU cc_start: 0.8068 (tt0) cc_final: 0.7850 (tt0) REVERT: D 151 PHE cc_start: 0.7691 (t80) cc_final: 0.6521 (m-80) REVERT: D 279 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7542 (ttm-80) REVERT: E 151 PHE cc_start: 0.7793 (t80) cc_final: 0.6584 (m-80) REVERT: E 279 ARG cc_start: 0.7916 (ttm170) cc_final: 0.7310 (mtp85) REVERT: F 159 ASP cc_start: 0.8004 (t0) cc_final: 0.7792 (t0) REVERT: F 197 ASP cc_start: 0.7862 (t0) cc_final: 0.7569 (t0) REVERT: F 219 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8320 (mtt180) REVERT: F 279 ARG cc_start: 0.7794 (ttm170) cc_final: 0.7304 (ttt-90) REVERT: G 47 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5375 (mpt) REVERT: G 151 PHE cc_start: 0.7717 (t80) cc_final: 0.6569 (m-80) REVERT: G 171 ILE cc_start: 0.8955 (OUTLIER) cc_final: 0.8749 (mm) REVERT: G 262 ASP cc_start: 0.8320 (m-30) cc_final: 0.8053 (m-30) outliers start: 50 outliers final: 24 residues processed: 191 average time/residue: 0.5260 time to fit residues: 111.4329 Evaluate side-chains 167 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 47 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 150 optimal weight: 0.0870 chunk 14 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 153 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.192733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.133150 restraints weight = 16125.610| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.90 r_work: 0.3535 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15449 Z= 0.119 Angle : 0.451 8.034 20650 Z= 0.241 Chirality : 0.042 0.143 2401 Planarity : 0.003 0.029 2527 Dihedral : 19.925 179.458 3304 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.08 % Allowed : 16.68 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.20), residues: 1841 helix: 1.90 (0.17), residues: 931 sheet: 1.08 (0.28), residues: 308 loop : -0.57 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 219 TYR 0.006 0.001 TYR C 135 PHE 0.012 0.001 PHE B 188 TRP 0.002 0.001 TRP G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15449) covalent geometry : angle 0.45150 / 0.24 (20650) hydrogen bonds : bond 0.04063 / 2.73 ( 880) hydrogen bonds : angle 3.61758 / 2.62 ( 2598) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 0.393 Fit side-chains REVERT: A 131 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7794 (ptp-170) REVERT: A 221 MET cc_start: 0.9069 (mtm) cc_final: 0.8789 (mtm) REVERT: A 262 ASP cc_start: 0.8360 (m-30) cc_final: 0.8108 (m-30) REVERT: A 279 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7207 (mtp85) REVERT: B 134 GLU cc_start: 0.8267 (tt0) cc_final: 0.8041 (tt0) REVERT: B 279 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7209 (ttm-80) REVERT: C 262 ASP cc_start: 0.8262 (m-30) cc_final: 0.8024 (m-30) REVERT: C 279 ARG cc_start: 0.7683 (ttm170) cc_final: 0.7041 (mtp85) REVERT: D 128 ARG cc_start: 0.7383 (mtt-85) cc_final: 0.6697 (mtt-85) REVERT: D 134 GLU cc_start: 0.8098 (tt0) cc_final: 0.7884 (tt0) REVERT: D 151 PHE cc_start: 0.7601 (t80) cc_final: 0.6393 (m-80) REVERT: D 262 ASP cc_start: 0.8210 (m-30) cc_final: 0.7896 (m-30) REVERT: D 279 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7370 (mtp85) REVERT: E 151 PHE cc_start: 0.7679 (t80) cc_final: 0.6433 (m-80) REVERT: E 279 ARG cc_start: 0.7766 (ttm170) cc_final: 0.7262 (mtp85) REVERT: F 159 ASP cc_start: 0.8003 (t0) cc_final: 0.7708 (t0) REVERT: F 219 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8172 (mtt180) REVERT: F 279 ARG cc_start: 0.7660 (ttm170) cc_final: 0.7204 (ttt-90) REVERT: G 47 MET cc_start: 0.5575 (OUTLIER) cc_final: 0.5269 (mpt) REVERT: G 131 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7704 (ptp-170) REVERT: G 151 PHE cc_start: 0.7683 (t80) cc_final: 0.6490 (m-80) REVERT: G 262 ASP cc_start: 0.8303 (m-30) cc_final: 0.7944 (m-30) outliers start: 45 outliers final: 24 residues processed: 172 average time/residue: 0.5320 time to fit residues: 101.2039 Evaluate side-chains 160 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 132 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 144 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.192719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.133268 restraints weight = 16052.996| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.87 r_work: 0.3535 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 15449 Z= 0.121 Angle : 0.453 7.324 20650 Z= 0.243 Chirality : 0.042 0.140 2401 Planarity : 0.003 0.028 2527 Dihedral : 19.424 179.143 3304 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.28 % Allowed : 17.09 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.20), residues: 1841 helix: 1.97 (0.17), residues: 931 sheet: 1.06 (0.28), residues: 308 loop : -0.57 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 219 TYR 0.006 0.001 TYR F 135 PHE 0.013 0.002 PHE B 188 TRP 0.002 0.001 TRP B 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (15449) covalent geometry : angle 0.45333 / 0.24 (20650) hydrogen bonds : bond 0.04048 / 2.72 ( 880) hydrogen bonds : angle 3.60789 / 2.61 ( 2598) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 0.461 Fit side-chains REVERT: A 131 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7805 (ptp-170) REVERT: A 221 MET cc_start: 0.9065 (mtm) cc_final: 0.8810 (mtm) REVERT: A 262 ASP cc_start: 0.8319 (m-30) cc_final: 0.7846 (m-30) REVERT: A 279 ARG cc_start: 0.7760 (ttm170) cc_final: 0.7217 (mtp85) REVERT: B 189 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8586 (mt) REVERT: B 262 ASP cc_start: 0.8312 (m-30) cc_final: 0.8055 (m-30) REVERT: B 279 ARG cc_start: 0.7718 (ttm170) cc_final: 0.7207 (ttm-80) REVERT: C 131 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7754 (ptp-170) REVERT: C 262 ASP cc_start: 0.8256 (m-30) cc_final: 0.8028 (m-30) REVERT: C 279 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7053 (mtp85) REVERT: D 128 ARG cc_start: 0.7338 (mtt-85) cc_final: 0.6668 (mtt-85) REVERT: D 151 PHE cc_start: 0.7606 (t80) cc_final: 0.6404 (m-80) REVERT: D 262 ASP cc_start: 0.8212 (m-30) cc_final: 0.7867 (m-30) REVERT: D 279 ARG cc_start: 0.7950 (ttm170) cc_final: 0.7398 (mtp85) REVERT: E 151 PHE cc_start: 0.7684 (t80) cc_final: 0.6439 (m-80) REVERT: E 262 ASP cc_start: 0.8417 (m-30) cc_final: 0.8096 (m-30) REVERT: E 279 ARG cc_start: 0.7786 (ttm170) cc_final: 0.7302 (mtp85) REVERT: F 131 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7831 (ptp-170) REVERT: F 159 ASP cc_start: 0.8031 (t0) cc_final: 0.7733 (t0) REVERT: F 219 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8201 (mtt180) REVERT: F 279 ARG cc_start: 0.7677 (ttm170) cc_final: 0.7116 (mtp85) REVERT: G 47 MET cc_start: 0.5585 (OUTLIER) cc_final: 0.5259 (mpt) REVERT: G 131 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7726 (ptp-170) REVERT: G 151 PHE cc_start: 0.7690 (t80) cc_final: 0.6489 (m-80) REVERT: G 171 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8603 (mm) REVERT: G 262 ASP cc_start: 0.8284 (m-30) cc_final: 0.7992 (m-30) outliers start: 48 outliers final: 28 residues processed: 171 average time/residue: 0.5502 time to fit residues: 103.7117 Evaluate side-chains 171 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 135 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 152 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.192055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.132440 restraints weight = 16016.370| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.89 r_work: 0.3523 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 15449 Z= 0.131 Angle : 0.469 6.965 20650 Z= 0.251 Chirality : 0.043 0.141 2401 Planarity : 0.003 0.029 2527 Dihedral : 19.089 176.453 3304 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.28 % Allowed : 17.43 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 1841 helix: 1.89 (0.17), residues: 945 sheet: 1.26 (0.30), residues: 273 loop : -0.74 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 128 TYR 0.008 0.001 TYR C 135 PHE 0.013 0.002 PHE B 188 TRP 0.002 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (15449) covalent geometry : angle 0.46928 / 0.25 (20650) hydrogen bonds : bond 0.04166 / 2.80 ( 880) hydrogen bonds : angle 3.63190 / 2.63 ( 2598) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 140 time to evaluate : 0.536 Fit side-chains REVERT: A 131 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7865 (ptp-170) REVERT: A 262 ASP cc_start: 0.8334 (m-30) cc_final: 0.7847 (m-30) REVERT: A 279 ARG cc_start: 0.7760 (ttm170) cc_final: 0.7220 (mtp85) REVERT: B 262 ASP cc_start: 0.8322 (m-30) cc_final: 0.8072 (m-30) REVERT: B 279 ARG cc_start: 0.7689 (ttm170) cc_final: 0.7215 (ttm-80) REVERT: C 131 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7829 (ptp-170) REVERT: C 262 ASP cc_start: 0.8238 (m-30) cc_final: 0.7998 (m-30) REVERT: C 279 ARG cc_start: 0.7681 (ttm170) cc_final: 0.7065 (mtp85) REVERT: D 128 ARG cc_start: 0.7350 (mtt-85) cc_final: 0.6682 (mtt-85) REVERT: D 151 PHE cc_start: 0.7607 (t80) cc_final: 0.6437 (m-80) REVERT: D 245 ASP cc_start: 0.8952 (m-30) cc_final: 0.8453 (m-30) REVERT: D 262 ASP cc_start: 0.8201 (m-30) cc_final: 0.7823 (m-30) REVERT: D 279 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7407 (mtp85) REVERT: E 47 MET cc_start: 0.5995 (mmt) cc_final: 0.5793 (mmt) REVERT: E 151 PHE cc_start: 0.7694 (t80) cc_final: 0.6488 (m-80) REVERT: E 279 ARG cc_start: 0.7767 (ttm170) cc_final: 0.7300 (mtp85) REVERT: F 131 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7868 (ptp-170) REVERT: F 219 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8188 (mtt180) REVERT: F 279 ARG cc_start: 0.7665 (ttm170) cc_final: 0.7123 (mtp85) REVERT: G 47 MET cc_start: 0.5591 (OUTLIER) cc_final: 0.5299 (mpt) REVERT: G 151 PHE cc_start: 0.7700 (t80) cc_final: 0.6506 (m-80) REVERT: G 171 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8621 (mm) REVERT: G 262 ASP cc_start: 0.8302 (m-30) cc_final: 0.7897 (m-30) outliers start: 48 outliers final: 29 residues processed: 173 average time/residue: 0.5636 time to fit residues: 107.7890 Evaluate side-chains 167 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 274 ASP Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 239 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 164 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 171 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.190861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.131483 restraints weight = 15594.103| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.85 r_work: 0.3524 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3394 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3394 r_free = 0.3394 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3394 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15449 Z= 0.144 Angle : 0.486 6.653 20650 Z= 0.261 Chirality : 0.043 0.142 2401 Planarity : 0.003 0.029 2527 Dihedral : 18.992 172.581 3304 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.28 % Allowed : 17.70 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.19), residues: 1841 helix: 1.88 (0.17), residues: 945 sheet: 1.23 (0.30), residues: 273 loop : -0.74 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 128 TYR 0.008 0.001 TYR C 135 PHE 0.014 0.002 PHE B 188 TRP 0.002 0.001 TRP C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (15449) covalent geometry : angle 0.48572 / 0.26 (20650) hydrogen bonds : bond 0.04307 / 2.90 ( 880) hydrogen bonds : angle 3.66570 / 2.66 ( 2598) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.520 Fit side-chains REVERT: A 131 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7901 (ptp-170) REVERT: A 279 ARG cc_start: 0.7743 (ttm170) cc_final: 0.7283 (ttm-80) REVERT: B 189 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8591 (mt) REVERT: B 279 ARG cc_start: 0.7664 (ttm170) cc_final: 0.7208 (ttm-80) REVERT: C 131 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7777 (ptp-170) REVERT: C 262 ASP cc_start: 0.8253 (m-30) cc_final: 0.8040 (m-30) REVERT: C 279 ARG cc_start: 0.7716 (ttm170) cc_final: 0.7118 (mtp85) REVERT: D 131 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7890 (ptp-170) REVERT: D 151 PHE cc_start: 0.7650 (t80) cc_final: 0.6458 (m-80) REVERT: D 262 ASP cc_start: 0.8213 (m-30) cc_final: 0.7846 (m-30) REVERT: D 279 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7380 (ttm-80) REVERT: E 47 MET cc_start: 0.6031 (mmt) cc_final: 0.5821 (mmt) REVERT: E 131 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7864 (ptp-170) REVERT: E 151 PHE cc_start: 0.7718 (t80) cc_final: 0.6526 (m-80) REVERT: E 279 ARG cc_start: 0.7750 (ttm170) cc_final: 0.7295 (mtp85) REVERT: F 131 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7812 (ptp-170) REVERT: F 197 ASP cc_start: 0.7806 (t0) cc_final: 0.7440 (t0) REVERT: F 219 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8181 (mtt180) REVERT: F 279 ARG cc_start: 0.7663 (ttm170) cc_final: 0.7136 (mtp85) REVERT: G 47 MET cc_start: 0.5543 (OUTLIER) cc_final: 0.5205 (mpt) REVERT: G 151 PHE cc_start: 0.7720 (t80) cc_final: 0.6567 (m-80) REVERT: G 171 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8625 (mm) REVERT: G 262 ASP cc_start: 0.8259 (m-30) cc_final: 0.7858 (m-30) outliers start: 48 outliers final: 34 residues processed: 178 average time/residue: 0.5255 time to fit residues: 103.2806 Evaluate side-chains 182 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 139 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 171 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain E residue 171 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 171 ILE Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 274 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 100 optimal weight: 0.9990 chunk 169 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 82 optimal weight: 0.0980 chunk 148 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.193410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134277 restraints weight = 15759.546| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.86 r_work: 0.3563 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3430 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3430 r_free = 0.3430 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3430 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15449 Z= 0.101 Angle : 0.448 6.466 20650 Z= 0.242 Chirality : 0.042 0.138 2401 Planarity : 0.003 0.029 2527 Dihedral : 18.597 169.737 3304 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.32 % Allowed : 18.93 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.20), residues: 1841 helix: 2.06 (0.17), residues: 945 sheet: 1.38 (0.30), residues: 273 loop : -0.67 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 128 TYR 0.005 0.001 TYR B 135 PHE 0.010 0.001 PHE B 188 TRP 0.002 0.001 TRP F 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (15449) covalent geometry : angle 0.44843 / 0.24 (20650) hydrogen bonds : bond 0.03676 / 2.48 ( 880) hydrogen bonds : angle 3.50068 / 2.53 ( 2598) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.353 Fit side-chains REVERT: A 131 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7872 (ptp-170) REVERT: A 262 ASP cc_start: 0.8318 (m-30) cc_final: 0.7975 (m-30) REVERT: A 279 ARG cc_start: 0.7757 (ttm170) cc_final: 0.7217 (mtp85) REVERT: B 118 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7836 (pt) REVERT: B 189 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8580 (mt) REVERT: B 262 ASP cc_start: 0.8253 (m-30) cc_final: 0.8018 (m-30) REVERT: B 279 ARG cc_start: 0.7686 (ttm170) cc_final: 0.7151 (mtp85) REVERT: C 131 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7752 (ptp-170) REVERT: C 262 ASP cc_start: 0.8258 (m-30) cc_final: 0.8008 (m-30) REVERT: C 279 ARG cc_start: 0.7701 (ttm170) cc_final: 0.7059 (mtp85) REVERT: D 131 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7893 (ptp-170) REVERT: D 151 PHE cc_start: 0.7634 (t80) cc_final: 0.6457 (m-80) REVERT: D 245 ASP cc_start: 0.8902 (m-30) cc_final: 0.8424 (m-30) REVERT: D 262 ASP cc_start: 0.8205 (m-30) cc_final: 0.7776 (m-30) REVERT: D 279 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7413 (mtp85) REVERT: E 47 MET cc_start: 0.6002 (mmt) cc_final: 0.5751 (mmt) REVERT: E 151 PHE cc_start: 0.7641 (t80) cc_final: 0.6454 (m-80) REVERT: E 279 ARG cc_start: 0.7774 (ttm170) cc_final: 0.7296 (mtp85) REVERT: F 131 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7791 (ptp-170) REVERT: F 219 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8187 (mtt180) REVERT: F 279 ARG cc_start: 0.7727 (ttm170) cc_final: 0.7187 (mtp85) REVERT: G 47 MET cc_start: 0.5574 (OUTLIER) cc_final: 0.5272 (mpt) REVERT: G 151 PHE cc_start: 0.7706 (t80) cc_final: 0.6518 (m-80) REVERT: G 262 ASP cc_start: 0.8295 (m-30) cc_final: 0.7876 (m-30) outliers start: 34 outliers final: 21 residues processed: 172 average time/residue: 0.5478 time to fit residues: 103.7070 Evaluate side-chains 162 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 274 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 138 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 177 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.192289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.133135 restraints weight = 15665.037| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.86 r_work: 0.3545 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3412 r_free = 0.3412 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 15449 Z= 0.120 Angle : 0.471 7.287 20650 Z= 0.254 Chirality : 0.043 0.139 2401 Planarity : 0.003 0.028 2527 Dihedral : 18.334 166.478 3304 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.32 % Allowed : 19.34 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 1841 helix: 1.95 (0.17), residues: 945 sheet: 1.30 (0.30), residues: 273 loop : -0.66 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 128 TYR 0.007 0.001 TYR D 135 PHE 0.013 0.001 PHE B 188 TRP 0.002 0.001 TRP F 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (15449) covalent geometry : angle 0.47139 / 0.25 (20650) hydrogen bonds : bond 0.03941 / 2.65 ( 880) hydrogen bonds : angle 3.55651 / 2.58 ( 2598) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.476 Fit side-chains REVERT: A 131 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7909 (ptp-170) REVERT: A 262 ASP cc_start: 0.8341 (m-30) cc_final: 0.7957 (m-30) REVERT: A 279 ARG cc_start: 0.7750 (ttm170) cc_final: 0.7190 (mtp85) REVERT: B 118 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7810 (pt) REVERT: B 189 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8583 (mt) REVERT: B 262 ASP cc_start: 0.8318 (m-30) cc_final: 0.8021 (m-30) REVERT: B 279 ARG cc_start: 0.7673 (ttm170) cc_final: 0.7134 (mtp85) REVERT: C 131 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7738 (ptp-170) REVERT: C 279 ARG cc_start: 0.7685 (ttm170) cc_final: 0.7047 (mtp85) REVERT: D 131 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7888 (ptp-170) REVERT: D 151 PHE cc_start: 0.7651 (t80) cc_final: 0.6481 (m-80) REVERT: D 181 GLU cc_start: 0.7648 (tp30) cc_final: 0.6013 (pm20) REVERT: D 262 ASP cc_start: 0.8207 (m-30) cc_final: 0.7801 (m-30) REVERT: D 279 ARG cc_start: 0.7950 (ttm170) cc_final: 0.7414 (mtp85) REVERT: E 47 MET cc_start: 0.6095 (mmt) cc_final: 0.5843 (mmt) REVERT: E 151 PHE cc_start: 0.7640 (t80) cc_final: 0.6464 (m-80) REVERT: E 279 ARG cc_start: 0.7765 (ttm170) cc_final: 0.7308 (mtp85) REVERT: F 131 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7808 (ptp-170) REVERT: F 219 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8182 (mtt180) REVERT: F 279 ARG cc_start: 0.7722 (ttm170) cc_final: 0.7261 (mtp85) REVERT: G 47 MET cc_start: 0.5518 (OUTLIER) cc_final: 0.5220 (mpt) REVERT: G 151 PHE cc_start: 0.7687 (t80) cc_final: 0.6515 (m-80) REVERT: G 262 ASP cc_start: 0.8322 (m-30) cc_final: 0.7898 (m-30) outliers start: 34 outliers final: 23 residues processed: 164 average time/residue: 0.5739 time to fit residues: 103.5332 Evaluate side-chains 171 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 274 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 147 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 171 optimal weight: 0.0570 chunk 42 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 170 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 133 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.193632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134736 restraints weight = 15668.055| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.86 r_work: 0.3562 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15449 Z= 0.106 Angle : 0.457 7.017 20650 Z= 0.248 Chirality : 0.043 0.137 2401 Planarity : 0.003 0.029 2527 Dihedral : 17.966 162.760 3304 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.32 % Allowed : 19.96 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1841 helix: 2.02 (0.17), residues: 945 sheet: 1.34 (0.30), residues: 273 loop : -0.64 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 128 TYR 0.006 0.001 TYR E 135 PHE 0.012 0.001 PHE G 277 TRP 0.002 0.001 TRP G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (15449) covalent geometry : angle 0.45716 / 0.25 (20650) hydrogen bonds : bond 0.03665 / 2.47 ( 880) hydrogen bonds : angle 3.48064 / 2.53 ( 2598) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3682 Ramachandran restraints generated. 1841 Oldfield, 0 Emsley, 1841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.517 Fit side-chains REVERT: A 131 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7906 (ptp-170) REVERT: A 187 GLU cc_start: 0.8490 (tt0) cc_final: 0.8191 (tt0) REVERT: A 262 ASP cc_start: 0.8320 (m-30) cc_final: 0.7936 (m-30) REVERT: A 279 ARG cc_start: 0.7748 (ttm170) cc_final: 0.7244 (mtp85) REVERT: B 118 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7809 (pt) REVERT: B 189 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8559 (mt) REVERT: B 262 ASP cc_start: 0.8266 (m-30) cc_final: 0.7993 (m-30) REVERT: B 279 ARG cc_start: 0.7695 (ttm170) cc_final: 0.7147 (mtp85) REVERT: C 131 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7719 (ptp-170) REVERT: C 245 ASP cc_start: 0.8927 (m-30) cc_final: 0.8511 (m-30) REVERT: C 262 ASP cc_start: 0.8341 (m-30) cc_final: 0.8095 (m-30) REVERT: C 279 ARG cc_start: 0.7700 (ttm170) cc_final: 0.7067 (mtp85) REVERT: D 131 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7907 (ptp-170) REVERT: D 151 PHE cc_start: 0.7601 (t80) cc_final: 0.6427 (m-80) REVERT: D 262 ASP cc_start: 0.8209 (m-30) cc_final: 0.7746 (m-30) REVERT: D 279 ARG cc_start: 0.7874 (ttm170) cc_final: 0.7314 (mtp85) REVERT: E 151 PHE cc_start: 0.7651 (t80) cc_final: 0.6440 (m-80) REVERT: E 279 ARG cc_start: 0.7803 (ttm170) cc_final: 0.7330 (mtp85) REVERT: F 131 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7787 (ptp-170) REVERT: F 187 GLU cc_start: 0.8434 (tt0) cc_final: 0.8205 (tt0) REVERT: F 219 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8118 (mtt180) REVERT: F 279 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7304 (mtp85) REVERT: G 47 MET cc_start: 0.5476 (OUTLIER) cc_final: 0.5170 (mpt) REVERT: G 151 PHE cc_start: 0.7698 (t80) cc_final: 0.6522 (m-80) REVERT: G 262 ASP cc_start: 0.8313 (m-30) cc_final: 0.7924 (m-30) outliers start: 34 outliers final: 20 residues processed: 171 average time/residue: 0.6076 time to fit residues: 114.5773 Evaluate side-chains 169 residues out of total 1505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 47 MET Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 131 ARG Chi-restraints excluded: chain F residue 219 ARG Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 131 ARG Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 274 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 64 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 157 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 180 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.192308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.133403 restraints weight = 15630.590| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.84 r_work: 0.3549 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15449 Z= 0.123 Angle : 0.475 6.835 20650 Z= 0.257 Chirality : 0.043 0.139 2401 Planarity : 0.003 0.030 2527 Dihedral : 17.884 161.055 3304 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.12 % Allowed : 20.10 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.19), residues: 1841 helix: 1.94 (0.17), residues: 945 sheet: 1.30 (0.30), residues: 273 loop : -0.64 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 128 TYR 0.007 0.001 TYR D 135 PHE 0.013 0.001 PHE G 277 TRP 0.002 0.001 TRP G 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15449) covalent geometry : angle 0.47533 / 0.26 (20650) hydrogen bonds : bond 0.03917 / 2.64 ( 880) hydrogen bonds : angle 3.54593 / 2.58 ( 2598) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5147.42 seconds wall clock time: 88 minutes 15.43 seconds (5295.43 seconds total)