Starting phenix.real_space_refine on Thu Sep 18 10:21:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kto_62304/09_2025/9kto_62304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kto_62304/09_2025/9kto_62304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kto_62304/09_2025/9kto_62304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kto_62304/09_2025/9kto_62304.map" model { file = "/net/cci-nas-00/data/ceres_data/9kto_62304/09_2025/9kto_62304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kto_62304/09_2025/9kto_62304.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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 7 5.49 5 S 49 5.16 5 C 10038 2.51 5 N 2709 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15974 Number of models: 1 Model: "" Number of chains: 12 Chain: "G" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2259 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "A" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2259 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "B" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2259 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "C" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2259 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "D" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2259 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2259 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "F" Number of atoms: 2259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2259 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 1 Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'P1O': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 45 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P1O': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 4.04, per 1000 atoms: 0.25 Number of scatterers: 15974 At special positions: 0 Unit cell: (112.24, 110.4, 96.6, 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 49 16.00 P 7 15.00 O 3171 8.00 N 2709 7.00 C 10038 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: 1.26 Conformation dependent library (CDL) restraints added in 664.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3668 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 34 sheets defined 6.1% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'G' and resid 1 through 6 Processing helix chain 'G' and resid 205 through 209 Processing helix chain 'G' and resid 217 through 222 removed outlier: 4.258A pdb=" N SER G 221 " --> pdb=" O SER G 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 217 through 222 removed outlier: 4.279A pdb=" N SER A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 6 Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'B' and resid 217 through 222 removed outlier: 4.280A pdb=" N SER B 221 " --> pdb=" O SER B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 217 through 222 removed outlier: 4.270A pdb=" N SER C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 6 Processing helix chain 'D' and resid 205 through 209 Processing helix chain 'D' and resid 217 through 222 removed outlier: 4.299A pdb=" N SER D 221 " --> pdb=" O SER D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 6 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 217 through 222 removed outlier: 4.307A pdb=" N SER E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 6 Processing helix chain 'F' and resid 205 through 209 Processing helix chain 'F' and resid 217 through 222 removed outlier: 4.247A pdb=" N SER F 221 " --> pdb=" O SER F 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'G' and resid 26 through 29 Processing sheet with id=AA3, first strand: chain 'G' and resid 75 through 76 removed outlier: 6.372A pdb=" N ASP G 246 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU G 88 " --> pdb=" O ASP G 246 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE G 248 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL G 86 " --> pdb=" O ILE G 248 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLU G 250 " --> pdb=" O PHE G 84 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE G 84 " --> pdb=" O GLU G 250 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL G 252 " --> pdb=" O SER G 82 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N SER G 82 " --> pdb=" O PHE G 171 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL G 165 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY G 166 " --> pdb=" O GLU G 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 75 through 76 removed outlier: 7.204A pdb=" N ASP G 255 " --> pdb=" O ASP G 272 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASP G 272 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N GLN G 257 " --> pdb=" O THR G 270 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR G 270 " --> pdb=" O GLN G 257 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N HIS G 259 " --> pdb=" O THR G 268 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N THR G 268 " --> pdb=" O HIS G 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 111 through 120 removed outlier: 3.517A pdb=" N GLY E 143 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 174 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA8, first strand: chain 'A' and resid 26 through 29 Processing sheet with id=AA9, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.373A pdb=" N ASP A 246 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A 88 " --> pdb=" O ASP A 246 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE A 248 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL A 86 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU A 250 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A 84 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 252 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N SER A 82 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A 165 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY A 166 " --> pdb=" O GLU A 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.174A pdb=" N ASP A 255 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ASP A 272 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN A 257 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N THR A 270 " --> pdb=" O GLN A 257 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N HIS A 259 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N THR A 268 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AB3, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AB4, first strand: chain 'B' and resid 26 through 29 Processing sheet with id=AB5, first strand: chain 'B' and resid 153 through 158 removed outlier: 4.421A pdb=" N GLY B 166 " --> pdb=" O GLU B 158 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 165 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N SER B 82 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL B 252 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 84 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU B 250 " --> pdb=" O PHE B 84 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL B 86 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 248 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU B 88 " --> pdb=" O ASP B 246 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 246 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ASP B 255 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ASP B 272 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLN B 257 " --> pdb=" O THR B 270 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR B 270 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N HIS B 259 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N THR B 268 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AB7, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AB8, first strand: chain 'C' and resid 26 through 29 Processing sheet with id=AB9, first strand: chain 'C' and resid 153 through 158 removed outlier: 4.430A pdb=" N GLY C 166 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 165 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N SER C 82 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL C 252 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE C 84 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU C 250 " --> pdb=" O PHE C 84 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 86 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 248 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU C 88 " --> pdb=" O ASP C 246 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP C 246 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ASP C 255 " --> pdb=" O ASP C 272 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N ASP C 272 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N GLN C 257 " --> pdb=" O THR C 270 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR C 270 " --> pdb=" O GLN C 257 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N HIS C 259 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N THR C 268 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AC2, first strand: chain 'D' and resid 21 through 22 Processing sheet with id=AC3, first strand: chain 'D' and resid 26 through 29 Processing sheet with id=AC4, first strand: chain 'D' and resid 75 through 76 removed outlier: 6.423A pdb=" N ASP D 246 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N LEU D 88 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE D 248 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL D 86 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU D 250 " --> pdb=" O PHE D 84 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE D 84 " --> pdb=" O GLU D 250 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL D 252 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N SER D 82 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 165 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY D 166 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 75 through 76 removed outlier: 7.214A pdb=" N ASP D 255 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ASP D 272 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N GLN D 257 " --> pdb=" O THR D 270 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N THR D 270 " --> pdb=" O GLN D 257 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS D 259 " --> pdb=" O THR D 268 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N THR D 268 " --> pdb=" O HIS D 259 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 174 through 175 Processing sheet with id=AC7, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AC8, first strand: chain 'E' and resid 26 through 29 Processing sheet with id=AC9, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.348A pdb=" N ASP E 246 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU E 88 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE E 248 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL E 86 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU E 250 " --> pdb=" O PHE E 84 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE E 84 " --> pdb=" O GLU E 250 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL E 252 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N SER E 82 " --> pdb=" O PHE E 171 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 165 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY E 166 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 75 through 76 removed outlier: 7.205A pdb=" N ASP E 255 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP E 272 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N GLN E 257 " --> pdb=" O THR E 270 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR E 270 " --> pdb=" O GLN E 257 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N HIS E 259 " --> pdb=" O THR E 268 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR E 268 " --> pdb=" O HIS E 259 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 174 through 175 Processing sheet with id=AD3, first strand: chain 'F' and resid 21 through 22 Processing sheet with id=AD4, first strand: chain 'F' and resid 26 through 29 Processing sheet with id=AD5, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.347A pdb=" N ASP F 246 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LEU F 88 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE F 248 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL F 86 " --> pdb=" O ILE F 248 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU F 250 " --> pdb=" O PHE F 84 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N PHE F 84 " --> pdb=" O GLU F 250 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL F 252 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N SER F 82 " --> pdb=" O PHE F 171 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL F 165 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLY F 166 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 75 through 76 removed outlier: 7.199A pdb=" N ASP F 255 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ASP F 272 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N GLN F 257 " --> pdb=" O THR F 270 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR F 270 " --> pdb=" O GLN F 257 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N HIS F 259 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N THR F 268 " --> pdb=" O HIS F 259 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 174 through 175 561 hydrogen bonds defined for protein. 1431 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: 2.67 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2732 1.32 - 1.44: 4507 1.44 - 1.56: 8973 1.56 - 1.68: 14 1.68 - 1.80: 98 Bond restraints: 16324 Sorted by residual: bond pdb=" C1 P1O G 301 " pdb=" O3 P1O G 301 " ideal model delta sigma weight residual 1.407 1.452 -0.045 2.00e-02 2.50e+03 5.12e+00 bond pdb=" C1 P1O C 301 " pdb=" O3 P1O C 301 " ideal model delta sigma weight residual 1.407 1.452 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" C1 P1O F 301 " pdb=" O3 P1O F 301 " ideal model delta sigma weight residual 1.407 1.452 -0.045 2.00e-02 2.50e+03 5.01e+00 bond pdb=" C1 P1O E 301 " pdb=" O3 P1O E 301 " ideal model delta sigma weight residual 1.407 1.452 -0.045 2.00e-02 2.50e+03 5.00e+00 bond pdb=" C1 P1O G 303 " pdb=" O3 P1O G 303 " ideal model delta sigma weight residual 1.407 1.452 -0.045 2.00e-02 2.50e+03 4.99e+00 ... (remaining 16319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 21737 2.25 - 4.51: 319 4.51 - 6.76: 22 6.76 - 9.02: 7 9.02 - 11.27: 7 Bond angle restraints: 22092 Sorted by residual: angle pdb=" O3 P1O G 303 " pdb=" P1 P1O G 303 " pdb=" O4 P1O G 303 " ideal model delta sigma weight residual 93.71 104.98 -11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" O3 P1O G 301 " pdb=" P1 P1O G 301 " pdb=" O4 P1O G 301 " ideal model delta sigma weight residual 93.71 104.61 -10.90 3.00e+00 1.11e-01 1.32e+01 angle pdb=" O3 P1O C 301 " pdb=" P1 P1O C 301 " pdb=" O4 P1O C 301 " ideal model delta sigma weight residual 93.71 104.41 -10.70 3.00e+00 1.11e-01 1.27e+01 angle pdb=" CA TRP C 179 " pdb=" CB TRP C 179 " pdb=" CG TRP C 179 " ideal model delta sigma weight residual 113.60 120.14 -6.54 1.90e+00 2.77e-01 1.19e+01 angle pdb=" O3 P1O G 302 " pdb=" P1 P1O G 302 " pdb=" O4 P1O G 302 " ideal model delta sigma weight residual 93.71 104.00 -10.29 3.00e+00 1.11e-01 1.18e+01 ... (remaining 22087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 8797 16.91 - 33.83: 672 33.83 - 50.74: 188 50.74 - 67.65: 67 67.65 - 84.57: 20 Dihedral angle restraints: 9744 sinusoidal: 4032 harmonic: 5712 Sorted by residual: dihedral pdb=" CA GLY A 180 " pdb=" C GLY A 180 " pdb=" N PRO A 181 " pdb=" CA PRO A 181 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA GLY B 180 " pdb=" C GLY B 180 " pdb=" N PRO B 181 " pdb=" CA PRO B 181 " ideal model delta harmonic sigma weight residual 180.00 163.95 16.05 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA PRO D 226 " pdb=" C PRO D 226 " pdb=" N ASP D 227 " pdb=" CA ASP D 227 " ideal model delta harmonic sigma weight residual 180.00 164.24 15.76 0 5.00e+00 4.00e-02 9.94e+00 ... (remaining 9741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1229 0.030 - 0.059: 684 0.059 - 0.088: 236 0.088 - 0.118: 163 0.118 - 0.147: 26 Chirality restraints: 2338 Sorted by residual: chirality pdb=" CA ILE C 61 " pdb=" N ILE C 61 " pdb=" C ILE C 61 " pdb=" CB ILE C 61 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE F 61 " pdb=" N ILE F 61 " pdb=" C ILE F 61 " pdb=" CB ILE F 61 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA ILE E 61 " pdb=" N ILE E 61 " pdb=" C ILE E 61 " pdb=" CB ILE E 61 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 2335 not shown) Planarity restraints: 2828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 38 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C VAL F 38 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL F 38 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE F 39 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 38 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.54e+00 pdb=" C VAL B 38 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL B 38 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE B 39 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 180 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO F 181 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO F 181 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 181 " -0.022 5.00e-02 4.00e+02 ... (remaining 2825 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1080 2.73 - 3.27: 15001 3.27 - 3.81: 24555 3.81 - 4.36: 30960 4.36 - 4.90: 57716 Nonbonded interactions: 129312 Sorted by model distance: nonbonded pdb=" OG SER E 218 " pdb=" OD1 ASN F 105 " model vdw 2.183 3.040 nonbonded pdb=" OG SER D 218 " pdb=" OD1 ASN E 105 " model vdw 2.196 3.040 nonbonded pdb=" OG SER C 218 " pdb=" OD1 ASN D 105 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP F 29 " pdb=" ND2 ASN F 32 " model vdw 2.205 3.120 nonbonded pdb=" OG SER B 218 " pdb=" OD1 ASN C 105 " model vdw 2.211 3.040 ... (remaining 129307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 1 through 293) selection = (chain 'D' and resid 1 through 293) selection = (chain 'E' and resid 1 through 293) selection = (chain 'F' and resid 1 through 293) selection = (chain 'G' and resid 1 through 293) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 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: 0.140 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 15.770 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5689 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 0.045 16324 Z= 0.297 Angle : 0.711 11.275 22092 Z= 0.365 Chirality : 0.046 0.147 2338 Planarity : 0.004 0.039 2828 Dihedral : 14.519 84.565 6076 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 6.23 % Allowed : 9.43 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.19), residues: 1932 helix: -3.17 (0.40), residues: 42 sheet: -0.88 (0.17), residues: 938 loop : -1.16 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 184 TYR 0.018 0.002 TYR B 65 PHE 0.013 0.002 PHE B 196 TRP 0.020 0.002 TRP F 179 HIS 0.004 0.001 HIS F 144 Details of bonding type rmsd covalent geometry : bond 0.00700 (16324) covalent geometry : angle 0.71123 (22092) hydrogen bonds : bond 0.28349 ( 551) hydrogen bonds : angle 10.64738 ( 1431) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 532 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 5 ILE cc_start: 0.2677 (OUTLIER) cc_final: 0.2376 (pt) REVERT: G 51 LYS cc_start: 0.7034 (mttm) cc_final: 0.6571 (mtmt) REVERT: G 64 GLN cc_start: 0.6651 (mm-40) cc_final: 0.6088 (mp10) REVERT: G 89 GLN cc_start: 0.6934 (mt0) cc_final: 0.6625 (mt0) REVERT: G 100 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7146 (m-30) REVERT: G 142 ILE cc_start: 0.6530 (mt) cc_final: 0.6247 (mp) REVERT: G 164 LYS cc_start: 0.5985 (tttm) cc_final: 0.5711 (ttpt) REVERT: G 174 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6467 (tmm) REVERT: G 200 ARG cc_start: 0.5411 (mtt180) cc_final: 0.5119 (mtt180) REVERT: G 205 LYS cc_start: 0.5604 (ttmt) cc_final: 0.4635 (mtmm) REVERT: G 215 LYS cc_start: 0.5654 (mmtt) cc_final: 0.5218 (mmmm) REVERT: G 242 GLN cc_start: 0.6764 (tt0) cc_final: 0.6525 (tt0) REVERT: G 244 ASN cc_start: 0.7058 (OUTLIER) cc_final: 0.6675 (p0) REVERT: G 288 LYS cc_start: 0.6407 (mmtp) cc_final: 0.5697 (mppt) REVERT: A 5 ILE cc_start: 0.2754 (OUTLIER) cc_final: 0.2267 (pt) REVERT: A 21 LYS cc_start: 0.6977 (mttm) cc_final: 0.6485 (mtpt) REVERT: A 51 LYS cc_start: 0.7052 (mttm) cc_final: 0.6630 (mtmt) REVERT: A 64 GLN cc_start: 0.6794 (mm-40) cc_final: 0.6314 (mp10) REVERT: A 89 GLN cc_start: 0.6937 (mt0) cc_final: 0.6534 (mt0) REVERT: A 100 ASP cc_start: 0.7712 (OUTLIER) cc_final: 0.7507 (t0) REVERT: A 111 GLU cc_start: 0.6402 (mt-10) cc_final: 0.6132 (mt-10) REVERT: A 142 ILE cc_start: 0.6612 (mt) cc_final: 0.6344 (pt) REVERT: A 150 GLN cc_start: 0.7582 (mt0) cc_final: 0.7352 (mt0) REVERT: A 164 LYS cc_start: 0.5891 (tttm) cc_final: 0.5653 (ttpp) REVERT: A 174 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6687 (ppp) REVERT: A 185 ASP cc_start: 0.5265 (m-30) cc_final: 0.4989 (t0) REVERT: A 198 LYS cc_start: 0.5566 (tttp) cc_final: 0.5297 (tmmm) REVERT: A 205 LYS cc_start: 0.5639 (ttmt) cc_final: 0.4295 (mtmm) REVERT: A 242 GLN cc_start: 0.6687 (tt0) cc_final: 0.6399 (tt0) REVERT: A 244 ASN cc_start: 0.6900 (OUTLIER) cc_final: 0.6563 (p0) REVERT: A 281 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.7018 (ttm-80) REVERT: A 288 LYS cc_start: 0.6167 (mmtp) cc_final: 0.5481 (mppt) REVERT: A 291 MET cc_start: 0.7588 (ptt) cc_final: 0.7246 (ptt) REVERT: B 5 ILE cc_start: 0.2982 (OUTLIER) cc_final: 0.2621 (pt) REVERT: B 21 LYS cc_start: 0.6799 (mttm) cc_final: 0.6182 (mtmt) REVERT: B 51 LYS cc_start: 0.6898 (mttm) cc_final: 0.6335 (mttt) REVERT: B 64 GLN cc_start: 0.6863 (mm-40) cc_final: 0.6309 (mm110) REVERT: B 99 SER cc_start: 0.6694 (t) cc_final: 0.6077 (m) REVERT: B 113 MET cc_start: 0.7138 (ttt) cc_final: 0.6434 (tmt) REVERT: B 142 ILE cc_start: 0.6570 (mt) cc_final: 0.6320 (pt) REVERT: B 150 GLN cc_start: 0.7642 (mt0) cc_final: 0.7413 (mt0) REVERT: B 164 LYS cc_start: 0.5953 (tttm) cc_final: 0.5740 (ttpp) REVERT: B 174 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.6789 (ppp) REVERT: B 200 ARG cc_start: 0.5286 (mtt180) cc_final: 0.4820 (mtt180) REVERT: B 205 LYS cc_start: 0.5316 (ttmt) cc_final: 0.4250 (mtmm) REVERT: B 242 GLN cc_start: 0.6658 (tt0) cc_final: 0.6304 (tt0) REVERT: B 244 ASN cc_start: 0.6916 (OUTLIER) cc_final: 0.6536 (p0) REVERT: B 288 LYS cc_start: 0.6269 (mmtp) cc_final: 0.5746 (mtmt) REVERT: C 5 ILE cc_start: 0.2895 (OUTLIER) cc_final: 0.2550 (pt) REVERT: C 21 LYS cc_start: 0.7088 (mttm) cc_final: 0.6726 (mttt) REVERT: C 51 LYS cc_start: 0.6984 (mttm) cc_final: 0.6437 (mtmm) REVERT: C 64 GLN cc_start: 0.6799 (mm-40) cc_final: 0.6034 (mp10) REVERT: C 100 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7025 (m-30) REVERT: C 150 GLN cc_start: 0.7613 (mt0) cc_final: 0.7407 (mt0) REVERT: C 200 ARG cc_start: 0.5369 (mtt180) cc_final: 0.4965 (mtt180) REVERT: C 205 LYS cc_start: 0.5650 (ttmt) cc_final: 0.4838 (mtmm) REVERT: C 215 LYS cc_start: 0.5467 (mmtt) cc_final: 0.5093 (mmmm) REVERT: C 231 VAL cc_start: 0.6854 (OUTLIER) cc_final: 0.6652 (m) REVERT: C 244 ASN cc_start: 0.7063 (OUTLIER) cc_final: 0.6707 (p0) REVERT: C 246 ASP cc_start: 0.6023 (OUTLIER) cc_final: 0.5473 (m-30) REVERT: C 271 LYS cc_start: 0.6414 (mtmm) cc_final: 0.6115 (mttt) REVERT: C 288 LYS cc_start: 0.6322 (mmtp) cc_final: 0.5516 (mppt) REVERT: D 5 ILE cc_start: 0.2902 (OUTLIER) cc_final: 0.2595 (pt) REVERT: D 21 LYS cc_start: 0.7011 (mttm) cc_final: 0.6619 (mttt) REVERT: D 51 LYS cc_start: 0.7013 (mttm) cc_final: 0.6520 (mtmt) REVERT: D 64 GLN cc_start: 0.6770 (mm-40) cc_final: 0.6297 (mp10) REVERT: D 100 ASP cc_start: 0.7694 (OUTLIER) cc_final: 0.7178 (m-30) REVERT: D 113 MET cc_start: 0.7165 (ttt) cc_final: 0.6570 (tmm) REVERT: D 142 ILE cc_start: 0.6504 (mt) cc_final: 0.6221 (mp) REVERT: D 150 GLN cc_start: 0.7681 (mt0) cc_final: 0.7106 (mt0) REVERT: D 162 ASP cc_start: 0.7017 (t0) cc_final: 0.5834 (p0) REVERT: D 200 ARG cc_start: 0.5527 (mtt180) cc_final: 0.5147 (mtt180) REVERT: D 205 LYS cc_start: 0.5717 (ttmt) cc_final: 0.4529 (mtmm) REVERT: D 215 LYS cc_start: 0.5525 (mmtt) cc_final: 0.5194 (mmmm) REVERT: D 244 ASN cc_start: 0.7070 (OUTLIER) cc_final: 0.6689 (p0) REVERT: D 288 LYS cc_start: 0.6344 (mmtp) cc_final: 0.5656 (mppt) REVERT: E 5 ILE cc_start: 0.2885 (OUTLIER) cc_final: 0.2505 (pt) REVERT: E 21 LYS cc_start: 0.7132 (mttm) cc_final: 0.6272 (mtmt) REVERT: E 51 LYS cc_start: 0.7009 (mttm) cc_final: 0.6637 (mtmt) REVERT: E 100 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7171 (m-30) REVERT: E 113 MET cc_start: 0.6999 (ttt) cc_final: 0.6387 (tmt) REVERT: E 142 ILE cc_start: 0.6558 (mt) cc_final: 0.6313 (pt) REVERT: E 150 GLN cc_start: 0.7610 (mt0) cc_final: 0.7326 (mt0) REVERT: E 162 ASP cc_start: 0.7077 (t0) cc_final: 0.6030 (p0) REVERT: E 164 LYS cc_start: 0.5988 (tttm) cc_final: 0.5757 (ttpt) REVERT: E 174 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6399 (tmm) REVERT: E 183 ASP cc_start: 0.7078 (p0) cc_final: 0.6853 (p0) REVERT: E 200 ARG cc_start: 0.5393 (mtt180) cc_final: 0.4995 (mtt180) REVERT: E 205 LYS cc_start: 0.5542 (ttmt) cc_final: 0.4612 (mtmm) REVERT: E 231 VAL cc_start: 0.6693 (OUTLIER) cc_final: 0.6318 (p) REVERT: E 242 GLN cc_start: 0.6771 (tt0) cc_final: 0.6568 (tt0) REVERT: E 244 ASN cc_start: 0.7010 (OUTLIER) cc_final: 0.6678 (p0) REVERT: E 281 ARG cc_start: 0.7204 (ttm-80) cc_final: 0.6966 (ttm-80) REVERT: E 288 LYS cc_start: 0.6422 (mmtp) cc_final: 0.5582 (mppt) REVERT: E 291 MET cc_start: 0.7631 (ptt) cc_final: 0.7326 (ptt) REVERT: F 5 ILE cc_start: 0.3080 (OUTLIER) cc_final: 0.2811 (pt) REVERT: F 21 LYS cc_start: 0.6994 (mttm) cc_final: 0.6793 (mttp) REVERT: F 51 LYS cc_start: 0.7015 (mttm) cc_final: 0.6541 (mtmt) REVERT: F 64 GLN cc_start: 0.6761 (mm-40) cc_final: 0.6115 (mp10) REVERT: F 113 MET cc_start: 0.7127 (ttt) cc_final: 0.6516 (tmm) REVERT: F 142 ILE cc_start: 0.6578 (mt) cc_final: 0.6348 (pt) REVERT: F 150 GLN cc_start: 0.7705 (mt0) cc_final: 0.7404 (mt0) REVERT: F 162 ASP cc_start: 0.7005 (t0) cc_final: 0.6216 (t70) REVERT: F 185 ASP cc_start: 0.5222 (m-30) cc_final: 0.4955 (t0) REVERT: F 200 ARG cc_start: 0.5708 (mtt180) cc_final: 0.4679 (mtt180) REVERT: F 205 LYS cc_start: 0.5741 (ttmt) cc_final: 0.4888 (mtmm) REVERT: F 212 ASP cc_start: 0.5773 (t70) cc_final: 0.5472 (t0) REVERT: F 215 LYS cc_start: 0.5633 (mmtt) cc_final: 0.5143 (mmmm) REVERT: F 231 VAL cc_start: 0.6899 (OUTLIER) cc_final: 0.6472 (p) REVERT: F 237 LYS cc_start: 0.6737 (mtmm) cc_final: 0.6441 (mtmt) REVERT: F 244 ASN cc_start: 0.7214 (OUTLIER) cc_final: 0.6907 (p0) REVERT: F 288 LYS cc_start: 0.6114 (mmtp) cc_final: 0.5433 (mppt) outliers start: 109 outliers final: 11 residues processed: 617 average time/residue: 0.6332 time to fit residues: 428.8689 Evaluate side-chains 358 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 320 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 179 TRP Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 174 MET Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 244 ASN Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 179 TRP Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 244 ASN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 244 ASN Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 179 TRP Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 244 ASN Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 244 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 17 ASN G 269 ASN A 17 ASN A 269 ASN B 17 ASN C 17 ASN C 269 ASN D 17 ASN D 144 HIS D 194 GLN D 269 ASN E 17 ASN E 269 ASN F 17 ASN F 269 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.186531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.170028 restraints weight = 17469.944| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.46 r_work: 0.3907 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16324 Z= 0.160 Angle : 0.659 10.179 22092 Z= 0.345 Chirality : 0.047 0.141 2338 Planarity : 0.005 0.058 2828 Dihedral : 9.777 63.140 2313 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 6.51 % Allowed : 21.09 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.19), residues: 1932 helix: -4.18 (0.26), residues: 42 sheet: -0.45 (0.16), residues: 1057 loop : -0.90 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 281 TYR 0.015 0.002 TYR E 118 PHE 0.013 0.002 PHE F 84 TRP 0.016 0.002 TRP G 179 HIS 0.005 0.002 HIS A 144 Details of bonding type rmsd covalent geometry : bond 0.00364 (16324) covalent geometry : angle 0.65892 (22092) hydrogen bonds : bond 0.04304 ( 551) hydrogen bonds : angle 6.60864 ( 1431) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 337 time to evaluate : 0.621 Fit side-chains REVERT: G 64 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7300 (mp10) REVERT: G 98 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7342 (mt) REVERT: G 100 ASP cc_start: 0.8041 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: G 111 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6554 (mt-10) REVERT: G 183 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7157 (p0) REVERT: G 200 ARG cc_start: 0.6607 (mtt180) cc_final: 0.5884 (mtt180) REVERT: G 242 GLN cc_start: 0.7582 (tt0) cc_final: 0.7370 (tt0) REVERT: G 288 LYS cc_start: 0.7841 (mmtp) cc_final: 0.7545 (mppt) REVERT: A 64 GLN cc_start: 0.7702 (mm-40) cc_final: 0.7363 (mt0) REVERT: A 100 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: A 200 ARG cc_start: 0.6414 (mtt180) cc_final: 0.5754 (mtt180) REVERT: A 235 ASP cc_start: 0.6950 (t0) cc_final: 0.6655 (t70) REVERT: A 288 LYS cc_start: 0.7839 (mmtp) cc_final: 0.7504 (mppt) REVERT: B 64 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7433 (mt0) REVERT: B 100 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: B 200 ARG cc_start: 0.6512 (mtt180) cc_final: 0.5816 (mtt180) REVERT: B 208 ASP cc_start: 0.7382 (p0) cc_final: 0.7068 (p0) REVERT: B 242 GLN cc_start: 0.7557 (tt0) cc_final: 0.7316 (tt0) REVERT: B 288 LYS cc_start: 0.7868 (mmtp) cc_final: 0.7642 (mtmt) REVERT: C 14 ILE cc_start: 0.4975 (OUTLIER) cc_final: 0.4641 (pt) REVERT: C 64 GLN cc_start: 0.7672 (mm-40) cc_final: 0.7333 (mp10) REVERT: C 100 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7533 (m-30) REVERT: C 200 ARG cc_start: 0.6506 (mtt180) cc_final: 0.5807 (mtt180) REVERT: C 215 LYS cc_start: 0.7214 (mmtt) cc_final: 0.6828 (mmmm) REVERT: C 251 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.6836 (ptp90) REVERT: D 87 GLN cc_start: 0.7600 (mt0) cc_final: 0.7351 (mt0) REVERT: D 100 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: D 200 ARG cc_start: 0.6382 (mtt180) cc_final: 0.5791 (mtt180) REVERT: D 280 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6800 (mm-30) REVERT: D 288 LYS cc_start: 0.7757 (mmtp) cc_final: 0.7438 (mppt) REVERT: E 100 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7418 (m-30) REVERT: E 162 ASP cc_start: 0.7325 (t0) cc_final: 0.7092 (t70) REVERT: E 200 ARG cc_start: 0.6497 (mtt180) cc_final: 0.5790 (mtt180) REVERT: E 242 GLN cc_start: 0.7570 (tt0) cc_final: 0.7333 (tt0) REVERT: E 271 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7346 (mttt) REVERT: F 5 ILE cc_start: 0.4398 (OUTLIER) cc_final: 0.4117 (pt) REVERT: F 64 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7372 (mt0) REVERT: F 100 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: F 215 LYS cc_start: 0.7068 (mmtt) cc_final: 0.6807 (mttt) REVERT: F 218 SER cc_start: 0.7560 (m) cc_final: 0.7241 (p) REVERT: F 266 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7113 (ttmm) outliers start: 114 outliers final: 25 residues processed: 420 average time/residue: 0.7506 time to fit residues: 342.9460 Evaluate side-chains 293 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 254 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 253 ARG Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 251 ARG Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 250 GLU Chi-restraints excluded: chain E residue 253 ARG Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 244 ASN Chi-restraints excluded: chain F residue 266 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 23 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 187 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 HIS G 150 GLN G 178 ASN A 35 HIS A 48 HIS B 35 HIS C 35 HIS C 269 ASN D 35 HIS F 35 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.182613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165107 restraints weight = 17733.160| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.52 r_work: 0.3852 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16324 Z= 0.176 Angle : 0.634 9.600 22092 Z= 0.330 Chirality : 0.046 0.216 2338 Planarity : 0.004 0.042 2828 Dihedral : 8.465 59.916 2256 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 7.77 % Allowed : 24.29 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.18), residues: 1932 helix: -4.48 (0.17), residues: 42 sheet: -0.18 (0.15), residues: 1071 loop : -1.30 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 66 TYR 0.014 0.002 TYR C 65 PHE 0.012 0.002 PHE F 84 TRP 0.012 0.002 TRP D 260 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00417 (16324) covalent geometry : angle 0.63396 (22092) hydrogen bonds : bond 0.04015 ( 551) hydrogen bonds : angle 6.24688 ( 1431) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 322 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: G 5 ILE cc_start: 0.4473 (OUTLIER) cc_final: 0.4100 (pt) REVERT: G 64 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7387 (mt0) REVERT: G 100 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7712 (m-30) REVERT: G 183 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7314 (p0) REVERT: G 198 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.7079 (tmmt) REVERT: G 208 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6809 (p0) REVERT: G 215 LYS cc_start: 0.7511 (mmtt) cc_final: 0.7280 (mtpt) REVERT: G 242 GLN cc_start: 0.7614 (tt0) cc_final: 0.7343 (tt0) REVERT: G 287 GLU cc_start: 0.7373 (tt0) cc_final: 0.7131 (tp30) REVERT: G 288 LYS cc_start: 0.8054 (mmtp) cc_final: 0.7713 (mppt) REVERT: A 5 ILE cc_start: 0.4416 (OUTLIER) cc_final: 0.4028 (pt) REVERT: A 64 GLN cc_start: 0.7731 (mm-40) cc_final: 0.7359 (mt0) REVERT: A 88 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 136 ILE cc_start: 0.1440 (OUTLIER) cc_final: 0.1156 (mp) REVERT: A 183 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7404 (p0) REVERT: A 199 THR cc_start: 0.7494 (m) cc_final: 0.7282 (t) REVERT: A 215 LYS cc_start: 0.7427 (mmtt) cc_final: 0.7203 (mtpt) REVERT: A 288 LYS cc_start: 0.8065 (mmtp) cc_final: 0.7750 (mppt) REVERT: B 5 ILE cc_start: 0.4553 (OUTLIER) cc_final: 0.3775 (pt) REVERT: B 64 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7523 (mt0) REVERT: B 75 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7517 (tttt) REVERT: B 100 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: B 183 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7463 (p0) REVERT: B 215 LYS cc_start: 0.7352 (mmtt) cc_final: 0.7129 (mtpt) REVERT: B 242 GLN cc_start: 0.7509 (tt0) cc_final: 0.7209 (tt0) REVERT: B 287 GLU cc_start: 0.7272 (tt0) cc_final: 0.6678 (tp30) REVERT: B 288 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7644 (mtmt) REVERT: C 5 ILE cc_start: 0.4495 (OUTLIER) cc_final: 0.4057 (pt) REVERT: C 64 GLN cc_start: 0.7762 (mm-40) cc_final: 0.7422 (mt0) REVERT: C 100 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: C 113 MET cc_start: 0.8245 (ttp) cc_final: 0.7972 (tmm) REVERT: C 179 TRP cc_start: 0.6781 (OUTLIER) cc_final: 0.6374 (t60) REVERT: C 198 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7254 (tmmt) REVERT: C 199 THR cc_start: 0.7529 (m) cc_final: 0.7309 (t) REVERT: C 208 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6957 (p0) REVERT: C 287 GLU cc_start: 0.7361 (tt0) cc_final: 0.7007 (tp30) REVERT: C 288 LYS cc_start: 0.8088 (mmtp) cc_final: 0.7815 (mtmt) REVERT: D 5 ILE cc_start: 0.4956 (OUTLIER) cc_final: 0.4450 (mt) REVERT: D 89 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: D 179 TRP cc_start: 0.6428 (OUTLIER) cc_final: 0.6009 (t60) REVERT: D 288 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7714 (mppt) REVERT: E 5 ILE cc_start: 0.4178 (OUTLIER) cc_final: 0.3741 (pt) REVERT: E 75 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7440 (mttt) REVERT: E 100 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: E 208 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6806 (p0) REVERT: E 234 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7566 (ttm) REVERT: E 242 GLN cc_start: 0.7685 (tt0) cc_final: 0.7448 (tt0) REVERT: E 246 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7539 (t0) REVERT: F 30 LYS cc_start: 0.6553 (OUTLIER) cc_final: 0.6159 (mttp) REVERT: F 66 ARG cc_start: 0.7252 (ptm-80) cc_final: 0.7016 (ptm-80) REVERT: F 100 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: F 154 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7786 (mtpt) REVERT: F 179 TRP cc_start: 0.6233 (OUTLIER) cc_final: 0.5607 (t60) REVERT: F 198 LYS cc_start: 0.7401 (OUTLIER) cc_final: 0.7118 (tmmt) REVERT: F 208 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.7052 (p0) REVERT: F 291 MET cc_start: 0.8511 (ptt) cc_final: 0.8154 (ptt) outliers start: 136 outliers final: 32 residues processed: 422 average time/residue: 0.6988 time to fit residues: 321.8106 Evaluate side-chains 325 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 260 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 198 LYS Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 253 ARG Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 114 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 253 ARG Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 179 TRP Chi-restraints excluded: chain C residue 198 LYS Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 139 ASN Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 244 ASN Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 179 TRP Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 253 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 88 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 149 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN D 242 GLN E 35 HIS ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.178045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.162161 restraints weight = 17832.889| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.36 r_work: 0.3828 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.6108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16324 Z= 0.149 Angle : 0.596 10.214 22092 Z= 0.312 Chirality : 0.045 0.186 2338 Planarity : 0.004 0.034 2828 Dihedral : 7.907 59.329 2248 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 9.03 % Allowed : 25.26 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.18), residues: 1932 helix: -4.55 (0.15), residues: 42 sheet: -0.01 (0.15), residues: 1071 loop : -1.42 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 200 TYR 0.014 0.001 TYR C 65 PHE 0.011 0.001 PHE D 42 TRP 0.011 0.002 TRP D 167 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00351 (16324) covalent geometry : angle 0.59594 (22092) hydrogen bonds : bond 0.03557 ( 551) hydrogen bonds : angle 6.04899 ( 1431) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 283 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 5 ILE cc_start: 0.4603 (OUTLIER) cc_final: 0.4264 (pt) REVERT: G 100 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: G 179 TRP cc_start: 0.6476 (OUTLIER) cc_final: 0.5683 (t60) REVERT: G 183 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7267 (p0) REVERT: G 208 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6785 (p0) REVERT: G 215 LYS cc_start: 0.7440 (mmtt) cc_final: 0.7194 (mttt) REVERT: G 237 LYS cc_start: 0.8301 (mttp) cc_final: 0.7504 (pmtt) REVERT: G 242 GLN cc_start: 0.7501 (tt0) cc_final: 0.7239 (tt0) REVERT: G 288 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7718 (mppt) REVERT: A 64 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7448 (mt0) REVERT: A 136 ILE cc_start: 0.1618 (OUTLIER) cc_final: 0.1407 (mp) REVERT: A 179 TRP cc_start: 0.6539 (OUTLIER) cc_final: 0.5782 (t60) REVERT: A 208 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6946 (p0) REVERT: B 5 ILE cc_start: 0.4675 (OUTLIER) cc_final: 0.4121 (mt) REVERT: B 64 GLN cc_start: 0.7741 (mm-40) cc_final: 0.7451 (mt0) REVERT: B 75 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7493 (tttt) REVERT: B 100 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7573 (m-30) REVERT: B 113 MET cc_start: 0.7877 (tmm) cc_final: 0.7674 (tmm) REVERT: B 179 TRP cc_start: 0.6551 (OUTLIER) cc_final: 0.5481 (t60) REVERT: B 208 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6888 (p0) REVERT: B 212 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6700 (t0) REVERT: B 234 MET cc_start: 0.8222 (ttm) cc_final: 0.7386 (ttm) REVERT: B 242 GLN cc_start: 0.7489 (tt0) cc_final: 0.7215 (tt0) REVERT: B 281 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7525 (ttt-90) REVERT: C 5 ILE cc_start: 0.4570 (OUTLIER) cc_final: 0.4193 (pt) REVERT: C 113 MET cc_start: 0.8331 (ttp) cc_final: 0.8050 (tmm) REVERT: C 136 ILE cc_start: 0.2070 (OUTLIER) cc_final: 0.1853 (mp) REVERT: C 179 TRP cc_start: 0.6574 (OUTLIER) cc_final: 0.5211 (t60) REVERT: C 183 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.7328 (p0) REVERT: C 200 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6579 (mpt180) REVERT: C 208 ASP cc_start: 0.7230 (OUTLIER) cc_final: 0.6871 (p0) REVERT: D 5 ILE cc_start: 0.4939 (OUTLIER) cc_final: 0.4514 (mt) REVERT: D 89 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: D 100 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: D 179 TRP cc_start: 0.6407 (OUTLIER) cc_final: 0.5005 (t60) REVERT: D 183 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7280 (p0) REVERT: D 205 LYS cc_start: 0.7324 (mtmm) cc_final: 0.6772 (mtmm) REVERT: D 208 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7119 (p0) REVERT: D 288 LYS cc_start: 0.7857 (mmtp) cc_final: 0.7653 (mppt) REVERT: E 5 ILE cc_start: 0.4214 (OUTLIER) cc_final: 0.3851 (pt) REVERT: E 75 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7373 (mttt) REVERT: E 100 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: E 108 ASP cc_start: 0.7273 (p0) cc_final: 0.7041 (p0) REVERT: E 179 TRP cc_start: 0.6257 (OUTLIER) cc_final: 0.5445 (t60) REVERT: E 183 ASP cc_start: 0.7483 (OUTLIER) cc_final: 0.7210 (p0) REVERT: E 208 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6806 (p0) REVERT: E 215 LYS cc_start: 0.7419 (mmtt) cc_final: 0.7210 (mtpt) REVERT: E 234 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7438 (ttm) REVERT: E 242 GLN cc_start: 0.7595 (tt0) cc_final: 0.7318 (tt0) REVERT: E 246 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7341 (t0) REVERT: F 100 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7513 (m-30) REVERT: F 121 ASN cc_start: 0.7455 (p0) cc_final: 0.7242 (p0) REVERT: F 154 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7645 (mtpt) REVERT: F 179 TRP cc_start: 0.6326 (OUTLIER) cc_final: 0.6017 (t60) REVERT: F 198 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7191 (tmmt) REVERT: F 205 LYS cc_start: 0.7263 (mtmm) cc_final: 0.6711 (mtmm) REVERT: F 208 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.6914 (p0) REVERT: F 215 LYS cc_start: 0.7485 (mmtt) cc_final: 0.7192 (mttt) REVERT: F 234 MET cc_start: 0.8275 (ttm) cc_final: 0.7406 (ttm) REVERT: F 253 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7876 (mtp-110) outliers start: 158 outliers final: 48 residues processed: 410 average time/residue: 0.7191 time to fit residues: 321.7030 Evaluate side-chains 349 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 260 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 179 TRP Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 241 GLN Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 179 TRP Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 179 TRP Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 179 TRP Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 253 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 126 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 114 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 GLN A 242 GLN D 242 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.179702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.162460 restraints weight = 17716.499| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.49 r_work: 0.3829 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3691 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.6536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16324 Z= 0.206 Angle : 0.650 9.953 22092 Z= 0.342 Chirality : 0.047 0.200 2338 Planarity : 0.004 0.041 2828 Dihedral : 8.245 59.452 2246 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 8.91 % Allowed : 25.14 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.18), residues: 1932 helix: -4.69 (0.12), residues: 42 sheet: -0.09 (0.15), residues: 1071 loop : -1.52 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 281 TYR 0.017 0.002 TYR E 65 PHE 0.013 0.002 PHE D 42 TRP 0.016 0.002 TRP G 260 HIS 0.003 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00491 (16324) covalent geometry : angle 0.64969 (22092) hydrogen bonds : bond 0.03766 ( 551) hydrogen bonds : angle 6.13142 ( 1431) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 255 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 5 ILE cc_start: 0.4997 (OUTLIER) cc_final: 0.4377 (pt) REVERT: G 100 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: G 179 TRP cc_start: 0.6635 (OUTLIER) cc_final: 0.5788 (t60) REVERT: G 183 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7392 (p0) REVERT: G 208 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6609 (p0) REVERT: G 215 LYS cc_start: 0.7674 (mmtt) cc_final: 0.7318 (mttt) REVERT: G 242 GLN cc_start: 0.7467 (tt0) cc_final: 0.7239 (tt0) REVERT: G 288 LYS cc_start: 0.8075 (mmtp) cc_final: 0.7642 (mtmt) REVERT: A 179 TRP cc_start: 0.6511 (OUTLIER) cc_final: 0.6222 (t60) REVERT: A 208 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6792 (p0) REVERT: A 287 GLU cc_start: 0.7427 (tp30) cc_final: 0.7079 (tp30) REVERT: B 5 ILE cc_start: 0.4654 (OUTLIER) cc_final: 0.4140 (mt) REVERT: B 64 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7537 (mt0) REVERT: B 75 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7523 (tttt) REVERT: B 179 TRP cc_start: 0.6540 (OUTLIER) cc_final: 0.5519 (t60) REVERT: B 183 ASP cc_start: 0.7769 (OUTLIER) cc_final: 0.7447 (p0) REVERT: B 208 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.7007 (p0) REVERT: B 234 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7419 (ttm) REVERT: B 242 GLN cc_start: 0.7501 (tt0) cc_final: 0.7183 (tt0) REVERT: B 281 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7593 (ttt-90) REVERT: C 113 MET cc_start: 0.8385 (ttp) cc_final: 0.8142 (tmm) REVERT: C 136 ILE cc_start: 0.2083 (OUTLIER) cc_final: 0.1863 (mp) REVERT: C 179 TRP cc_start: 0.6702 (OUTLIER) cc_final: 0.5406 (t60) REVERT: C 200 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6591 (mpt180) REVERT: C 288 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7434 (mppt) REVERT: D 89 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7795 (mt0) REVERT: D 178 ASN cc_start: 0.7467 (p0) cc_final: 0.7202 (p0) REVERT: D 183 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7432 (p0) REVERT: D 205 LYS cc_start: 0.7341 (mtmm) cc_final: 0.6916 (mtmm) REVERT: D 208 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7180 (p0) REVERT: E 75 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7430 (tttt) REVERT: E 100 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7460 (m-30) REVERT: E 108 ASP cc_start: 0.7413 (p0) cc_final: 0.7168 (p0) REVERT: E 179 TRP cc_start: 0.6374 (OUTLIER) cc_final: 0.5173 (t60) REVERT: E 183 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7487 (p0) REVERT: E 200 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6459 (mpt180) REVERT: E 208 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6929 (m-30) REVERT: E 215 LYS cc_start: 0.7590 (mmtt) cc_final: 0.7352 (mtpt) REVERT: E 234 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7480 (ttm) REVERT: E 242 GLN cc_start: 0.7471 (tt0) cc_final: 0.7188 (tt0) REVERT: E 246 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7560 (t0) REVERT: F 100 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: F 154 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7903 (mtpt) REVERT: F 179 TRP cc_start: 0.6608 (OUTLIER) cc_final: 0.6327 (t60) REVERT: F 198 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7191 (ttmt) REVERT: F 205 LYS cc_start: 0.7279 (mtmm) cc_final: 0.6681 (mtmm) REVERT: F 208 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6882 (p0) REVERT: F 215 LYS cc_start: 0.7473 (mmtt) cc_final: 0.7175 (mtpt) REVERT: F 234 MET cc_start: 0.8371 (ttm) cc_final: 0.7553 (ttm) REVERT: F 253 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7769 (mtp-110) outliers start: 156 outliers final: 69 residues processed: 373 average time/residue: 0.6657 time to fit residues: 270.5528 Evaluate side-chains 349 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 246 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 118 TYR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 179 TRP Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 241 GLN Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 179 TRP Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 82 SER Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 179 TRP Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 179 TRP Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 118 TYR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 154 LYS Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 179 TRP Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 253 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 46 optimal weight: 0.4980 chunk 127 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 147 optimal weight: 20.0000 chunk 76 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.0010 chunk 66 optimal weight: 1.9990 chunk 141 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 GLN A 242 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.182813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.165465 restraints weight = 17638.265| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.52 r_work: 0.3862 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16324 Z= 0.112 Angle : 0.550 9.358 22092 Z= 0.290 Chirality : 0.045 0.151 2338 Planarity : 0.004 0.073 2828 Dihedral : 7.772 59.733 2246 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 7.89 % Allowed : 25.71 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.18), residues: 1932 helix: -4.65 (0.11), residues: 42 sheet: 0.04 (0.16), residues: 1071 loop : -1.41 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 66 TYR 0.012 0.001 TYR D 65 PHE 0.010 0.001 PHE D 42 TRP 0.015 0.001 TRP F 167 HIS 0.002 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00253 (16324) covalent geometry : angle 0.55040 (22092) hydrogen bonds : bond 0.03137 ( 551) hydrogen bonds : angle 5.84781 ( 1431) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 263 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 5 ILE cc_start: 0.4725 (OUTLIER) cc_final: 0.4125 (pt) REVERT: G 75 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7438 (mttp) REVERT: G 100 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7595 (m-30) REVERT: G 179 TRP cc_start: 0.6514 (OUTLIER) cc_final: 0.5748 (t60) REVERT: G 183 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7393 (p0) REVERT: G 208 ASP cc_start: 0.6984 (OUTLIER) cc_final: 0.6607 (p0) REVERT: G 215 LYS cc_start: 0.7569 (mmtt) cc_final: 0.7251 (mttt) REVERT: G 242 GLN cc_start: 0.7468 (tt0) cc_final: 0.7245 (tt0) REVERT: G 288 LYS cc_start: 0.7898 (mmtp) cc_final: 0.7685 (mtmt) REVERT: A 100 ASP cc_start: 0.7946 (m-30) cc_final: 0.7730 (m-30) REVERT: A 205 LYS cc_start: 0.7301 (mtmm) cc_final: 0.6689 (mtmm) REVERT: A 208 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6798 (p0) REVERT: A 212 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6650 (t0) REVERT: A 287 GLU cc_start: 0.7314 (tp30) cc_final: 0.6884 (tp30) REVERT: B 5 ILE cc_start: 0.4647 (OUTLIER) cc_final: 0.4161 (mp) REVERT: B 64 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7474 (mt0) REVERT: B 75 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7531 (tttt) REVERT: B 113 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7881 (tmm) REVERT: B 179 TRP cc_start: 0.6310 (OUTLIER) cc_final: 0.5353 (t60) REVERT: B 183 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7390 (p0) REVERT: B 208 ASP cc_start: 0.7284 (OUTLIER) cc_final: 0.6982 (p0) REVERT: B 212 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6853 (t0) REVERT: B 234 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7348 (ttm) REVERT: B 242 GLN cc_start: 0.7499 (tt0) cc_final: 0.7167 (tt0) REVERT: B 251 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8163 (ptp90) REVERT: C 113 MET cc_start: 0.8354 (ttp) cc_final: 0.8093 (tmm) REVERT: C 179 TRP cc_start: 0.6530 (OUTLIER) cc_final: 0.5318 (t60) REVERT: C 200 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6726 (mpt180) REVERT: C 205 LYS cc_start: 0.7238 (mtmm) cc_final: 0.6784 (mtmm) REVERT: C 208 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6924 (p0) REVERT: C 288 LYS cc_start: 0.7983 (mtmt) cc_final: 0.7377 (mppt) REVERT: D 179 TRP cc_start: 0.6340 (OUTLIER) cc_final: 0.5964 (t60) REVERT: D 183 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7398 (p0) REVERT: D 205 LYS cc_start: 0.7272 (mtmm) cc_final: 0.6814 (mtmm) REVERT: D 208 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7183 (p0) REVERT: E 100 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: E 208 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6851 (p0) REVERT: E 242 GLN cc_start: 0.7468 (tt0) cc_final: 0.7199 (tt0) REVERT: E 246 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7486 (t0) REVERT: F 100 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: F 179 TRP cc_start: 0.6321 (OUTLIER) cc_final: 0.6054 (t60) REVERT: F 198 LYS cc_start: 0.7398 (OUTLIER) cc_final: 0.7104 (tmmt) REVERT: F 200 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.7049 (mpt180) REVERT: F 205 LYS cc_start: 0.7214 (mtmm) cc_final: 0.6699 (mtmm) REVERT: F 208 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6874 (p0) REVERT: F 215 LYS cc_start: 0.7473 (mmtt) cc_final: 0.7147 (mtpt) REVERT: F 234 MET cc_start: 0.8346 (ttm) cc_final: 0.7508 (ttm) outliers start: 138 outliers final: 56 residues processed: 369 average time/residue: 0.6372 time to fit residues: 256.5479 Evaluate side-chains 332 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 245 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 TYR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 179 TRP Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 241 GLN Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 179 TRP Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 208 ASP Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 118 TYR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 179 TRP Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 200 ARG Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 218 SER Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 246 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 187 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 35 optimal weight: 0.0020 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 164 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 GLN G 201 ASN A 242 GLN D 242 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.178418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.161092 restraints weight = 17793.320| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 1.51 r_work: 0.3817 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.6887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16324 Z= 0.244 Angle : 0.688 11.070 22092 Z= 0.362 Chirality : 0.049 0.230 2338 Planarity : 0.004 0.070 2828 Dihedral : 8.505 60.814 2246 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 8.57 % Allowed : 24.63 % Favored : 66.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.18), residues: 1932 helix: -4.77 (0.10), residues: 42 sheet: -0.09 (0.15), residues: 1057 loop : -1.69 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 281 TYR 0.020 0.002 TYR D 65 PHE 0.014 0.002 PHE D 42 TRP 0.015 0.002 TRP A 260 HIS 0.003 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00588 (16324) covalent geometry : angle 0.68780 (22092) hydrogen bonds : bond 0.03871 ( 551) hydrogen bonds : angle 6.19788 ( 1431) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 253 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 5 ILE cc_start: 0.4612 (OUTLIER) cc_final: 0.3968 (pt) REVERT: G 75 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7434 (mttp) REVERT: G 179 TRP cc_start: 0.6472 (OUTLIER) cc_final: 0.5402 (t60) REVERT: G 183 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7462 (p0) REVERT: G 208 ASP cc_start: 0.6911 (OUTLIER) cc_final: 0.6569 (p0) REVERT: G 215 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7314 (mttt) REVERT: G 242 GLN cc_start: 0.7494 (tt0) cc_final: 0.7269 (tt0) REVERT: G 288 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7718 (mtmt) REVERT: A 88 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 205 LYS cc_start: 0.7378 (mtmm) cc_final: 0.6894 (mtmm) REVERT: A 208 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6790 (p0) REVERT: B 5 ILE cc_start: 0.4658 (OUTLIER) cc_final: 0.4106 (mp) REVERT: B 64 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7368 (mm110) REVERT: B 75 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7541 (tttt) REVERT: B 179 TRP cc_start: 0.6642 (OUTLIER) cc_final: 0.6315 (t60) REVERT: B 208 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.7000 (p0) REVERT: B 212 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.6921 (t70) REVERT: B 234 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7477 (ttm) REVERT: B 242 GLN cc_start: 0.7511 (tt0) cc_final: 0.7160 (tt0) REVERT: B 281 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7655 (ttt-90) REVERT: C 179 TRP cc_start: 0.6655 (OUTLIER) cc_final: 0.5372 (t60) REVERT: C 205 LYS cc_start: 0.7288 (mtmm) cc_final: 0.6778 (mtmm) REVERT: C 208 ASP cc_start: 0.6989 (OUTLIER) cc_final: 0.6614 (p0) REVERT: C 214 ASN cc_start: 0.7200 (p0) cc_final: 0.6974 (m-40) REVERT: D 89 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7827 (mt0) REVERT: D 152 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.6950 (m-30) REVERT: D 179 TRP cc_start: 0.6502 (OUTLIER) cc_final: 0.6227 (t60) REVERT: D 183 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7463 (p0) REVERT: D 205 LYS cc_start: 0.7298 (mtmm) cc_final: 0.6841 (mtmm) REVERT: D 208 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.7065 (p0) REVERT: E 5 ILE cc_start: 0.4525 (OUTLIER) cc_final: 0.3923 (mp) REVERT: E 75 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7412 (mttt) REVERT: E 100 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7591 (m-30) REVERT: E 179 TRP cc_start: 0.6448 (OUTLIER) cc_final: 0.5263 (t60) REVERT: E 200 ARG cc_start: 0.7538 (mpt180) cc_final: 0.6645 (mpt180) REVERT: E 242 GLN cc_start: 0.7494 (tt0) cc_final: 0.7213 (tt0) REVERT: E 246 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7525 (m-30) REVERT: F 100 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7614 (m-30) REVERT: F 179 TRP cc_start: 0.6856 (OUTLIER) cc_final: 0.6504 (t60) REVERT: F 198 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7181 (ttmt) REVERT: F 205 LYS cc_start: 0.7343 (mtmm) cc_final: 0.6767 (mtmm) REVERT: F 208 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6856 (p0) REVERT: F 215 LYS cc_start: 0.7421 (mmtt) cc_final: 0.7144 (mtpt) REVERT: F 234 MET cc_start: 0.8451 (ttm) cc_final: 0.7699 (ttm) REVERT: F 253 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7526 (mtp-110) outliers start: 150 outliers final: 71 residues processed: 373 average time/residue: 0.6259 time to fit residues: 255.4440 Evaluate side-chains 333 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 231 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 TYR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 179 TRP Chi-restraints excluded: chain G residue 183 ASP Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 241 GLN Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 118 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 179 TRP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 234 MET Chi-restraints excluded: chain B residue 241 GLN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 281 ARG Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 179 TRP Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 99 SER Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 82 SER Chi-restraints excluded: chain E residue 90 LEU Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 109 THR Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 179 TRP Chi-restraints excluded: chain E residue 241 GLN Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain F residue 99 SER Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 179 TRP Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 241 GLN Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 253 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 92 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 chunk 24 optimal weight: 0.0770 chunk 53 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 0.0970 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 201 ASN G 259 HIS A 242 GLN A 259 HIS E 241 GLN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.183826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.166622 restraints weight = 17752.654| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.53 r_work: 0.3880 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.6964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16324 Z= 0.097 Angle : 0.532 10.487 22092 Z= 0.282 Chirality : 0.044 0.179 2338 Planarity : 0.004 0.055 2828 Dihedral : 7.562 58.906 2244 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.89 % Allowed : 28.17 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.18), residues: 1932 helix: -4.68 (0.11), residues: 42 sheet: 0.05 (0.16), residues: 1064 loop : -1.35 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 66 TYR 0.010 0.001 TYR D 65 PHE 0.007 0.001 PHE C 42 TRP 0.013 0.001 TRP F 167 HIS 0.003 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00212 (16324) covalent geometry : angle 0.53230 (22092) hydrogen bonds : bond 0.02897 ( 551) hydrogen bonds : angle 5.66173 ( 1431) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 252 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: G 5 ILE cc_start: 0.4595 (OUTLIER) cc_final: 0.3940 (pt) REVERT: G 179 TRP cc_start: 0.6320 (OUTLIER) cc_final: 0.5652 (t60) REVERT: G 208 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6639 (p0) REVERT: G 215 LYS cc_start: 0.7534 (mmtt) cc_final: 0.7239 (mttt) REVERT: G 242 GLN cc_start: 0.7418 (tt0) cc_final: 0.7154 (tt0) REVERT: A 5 ILE cc_start: 0.4740 (OUTLIER) cc_final: 0.4448 (mt) REVERT: A 100 ASP cc_start: 0.7950 (m-30) cc_final: 0.7687 (m-30) REVERT: A 205 LYS cc_start: 0.7262 (mtmm) cc_final: 0.6759 (mtmm) REVERT: A 208 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6830 (p0) REVERT: B 5 ILE cc_start: 0.4817 (OUTLIER) cc_final: 0.4276 (mp) REVERT: B 64 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7263 (mm110) REVERT: B 113 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7806 (tmm) REVERT: B 200 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7332 (mpt180) REVERT: B 208 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.7017 (p0) REVERT: B 212 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6872 (t0) REVERT: B 234 MET cc_start: 0.8133 (ttm) cc_final: 0.7253 (ttm) REVERT: B 242 GLN cc_start: 0.7488 (tt0) cc_final: 0.7162 (tt0) REVERT: C 179 TRP cc_start: 0.6345 (OUTLIER) cc_final: 0.5103 (t60) REVERT: C 183 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7451 (p0) REVERT: C 200 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.6792 (mpt180) REVERT: C 205 LYS cc_start: 0.7341 (mtmm) cc_final: 0.6890 (mtmm) REVERT: C 208 ASP cc_start: 0.7202 (OUTLIER) cc_final: 0.6873 (p0) REVERT: D 5 ILE cc_start: 0.4663 (OUTLIER) cc_final: 0.4175 (mp) REVERT: D 93 ASN cc_start: 0.5849 (p0) cc_final: 0.5602 (p0) REVERT: D 113 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7872 (tmm) REVERT: D 179 TRP cc_start: 0.6166 (OUTLIER) cc_final: 0.5858 (t60) REVERT: D 184 ARG cc_start: 0.8147 (mtp180) cc_final: 0.7903 (mtp85) REVERT: D 205 LYS cc_start: 0.7203 (mtmm) cc_final: 0.6810 (mtmm) REVERT: D 208 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7174 (p0) REVERT: E 5 ILE cc_start: 0.4513 (OUTLIER) cc_final: 0.3955 (mp) REVERT: E 75 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7322 (tttt) REVERT: E 95 VAL cc_start: 0.8111 (m) cc_final: 0.7878 (p) REVERT: E 100 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: E 149 VAL cc_start: 0.8432 (t) cc_final: 0.8223 (p) REVERT: E 242 GLN cc_start: 0.7483 (tt0) cc_final: 0.7182 (tt0) REVERT: E 281 ARG cc_start: 0.8054 (ttm-80) cc_final: 0.7805 (ttt90) REVERT: F 30 LYS cc_start: 0.6605 (OUTLIER) cc_final: 0.6192 (mttm) REVERT: F 66 ARG cc_start: 0.7313 (ptm-80) cc_final: 0.7057 (ptm-80) REVERT: F 179 TRP cc_start: 0.6277 (OUTLIER) cc_final: 0.6018 (t60) REVERT: F 198 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7170 (tmmt) REVERT: F 205 LYS cc_start: 0.7210 (mtmm) cc_final: 0.6667 (mtmm) REVERT: F 208 ASP cc_start: 0.7330 (OUTLIER) cc_final: 0.6897 (p0) REVERT: F 212 ASP cc_start: 0.7127 (t70) cc_final: 0.6824 (t0) REVERT: F 215 LYS cc_start: 0.7421 (mmtt) cc_final: 0.7127 (mtpt) outliers start: 103 outliers final: 43 residues processed: 334 average time/residue: 0.6121 time to fit residues: 223.3398 Evaluate side-chains 309 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 241 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 TYR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 179 TRP Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 244 ASN Chi-restraints excluded: chain G residue 246 ASP Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 200 ARG Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 118 TYR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 179 TRP Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 118 TYR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 179 TRP Chi-restraints excluded: chain F residue 198 LYS Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 246 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 149 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 144 HIS G 201 ASN A 242 GLN C 17 ASN D 87 GLN D 242 GLN E 64 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.183466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.165952 restraints weight = 17640.718| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 1.54 r_work: 0.3868 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16324 Z= 0.109 Angle : 0.563 10.752 22092 Z= 0.301 Chirality : 0.045 0.205 2338 Planarity : 0.004 0.055 2828 Dihedral : 7.448 59.710 2244 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 5.37 % Allowed : 28.97 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.18), residues: 1932 helix: -4.61 (0.11), residues: 42 sheet: 0.12 (0.15), residues: 1071 loop : -1.40 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 66 TYR 0.012 0.001 TYR G 65 PHE 0.009 0.001 PHE D 42 TRP 0.017 0.001 TRP A 179 HIS 0.003 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00241 (16324) covalent geometry : angle 0.56344 (22092) hydrogen bonds : bond 0.02847 ( 551) hydrogen bonds : angle 5.50636 ( 1431) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 238 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 5 ILE cc_start: 0.4568 (OUTLIER) cc_final: 0.3974 (mp) REVERT: G 121 ASN cc_start: 0.6162 (t0) cc_final: 0.5897 (t0) REVERT: G 179 TRP cc_start: 0.6168 (OUTLIER) cc_final: 0.5470 (t60) REVERT: G 208 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6644 (p0) REVERT: G 215 LYS cc_start: 0.7526 (mmtt) cc_final: 0.7240 (mttt) REVERT: G 242 GLN cc_start: 0.7439 (tt0) cc_final: 0.7121 (tt0) REVERT: A 5 ILE cc_start: 0.4617 (OUTLIER) cc_final: 0.4076 (mt) REVERT: A 100 ASP cc_start: 0.7773 (m-30) cc_final: 0.7533 (m-30) REVERT: A 184 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7944 (mtp85) REVERT: A 205 LYS cc_start: 0.7221 (mtmm) cc_final: 0.6748 (mtmm) REVERT: A 208 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6777 (p0) REVERT: B 5 ILE cc_start: 0.4518 (OUTLIER) cc_final: 0.4035 (mp) REVERT: B 34 MET cc_start: 0.7329 (mtt) cc_final: 0.6805 (mtm) REVERT: B 64 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7242 (mm-40) REVERT: B 75 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7575 (tttt) REVERT: B 95 VAL cc_start: 0.7891 (m) cc_final: 0.7459 (t) REVERT: B 113 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7836 (tmm) REVERT: B 183 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7409 (p0) REVERT: B 208 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6977 (p0) REVERT: B 212 ASP cc_start: 0.7222 (OUTLIER) cc_final: 0.6875 (t0) REVERT: B 242 GLN cc_start: 0.7463 (tt0) cc_final: 0.7154 (tt0) REVERT: C 179 TRP cc_start: 0.6347 (OUTLIER) cc_final: 0.5149 (t60) REVERT: C 205 LYS cc_start: 0.7265 (mtmm) cc_final: 0.6798 (mtmm) REVERT: C 208 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6920 (p0) REVERT: C 234 MET cc_start: 0.8087 (ttm) cc_final: 0.7557 (ttm) REVERT: D 5 ILE cc_start: 0.4645 (OUTLIER) cc_final: 0.4147 (mp) REVERT: D 179 TRP cc_start: 0.6078 (OUTLIER) cc_final: 0.5850 (t60) REVERT: D 183 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7380 (p0) REVERT: D 184 ARG cc_start: 0.8170 (mtp180) cc_final: 0.7887 (mtp85) REVERT: D 200 ARG cc_start: 0.7217 (mpt-90) cc_final: 0.6764 (mpt-90) REVERT: D 205 LYS cc_start: 0.7220 (mtmm) cc_final: 0.6825 (mtmm) REVERT: D 208 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7183 (p0) REVERT: E 5 ILE cc_start: 0.4371 (OUTLIER) cc_final: 0.3798 (mp) REVERT: E 75 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7343 (mttt) REVERT: E 95 VAL cc_start: 0.8127 (m) cc_final: 0.7902 (p) REVERT: E 242 GLN cc_start: 0.7562 (tt0) cc_final: 0.7232 (tt0) REVERT: E 281 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7752 (ttt90) REVERT: F 30 LYS cc_start: 0.6577 (OUTLIER) cc_final: 0.6186 (mttm) REVERT: F 100 ASP cc_start: 0.7920 (m-30) cc_final: 0.7680 (m-30) REVERT: F 179 TRP cc_start: 0.6210 (OUTLIER) cc_final: 0.5935 (t60) REVERT: F 200 ARG cc_start: 0.7458 (mpt180) cc_final: 0.6993 (mpt180) REVERT: F 205 LYS cc_start: 0.7207 (mtmm) cc_final: 0.6645 (mtmm) REVERT: F 208 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6890 (p0) REVERT: F 212 ASP cc_start: 0.7099 (t70) cc_final: 0.6822 (t0) REVERT: F 215 LYS cc_start: 0.7466 (mmtt) cc_final: 0.7175 (mtpt) REVERT: F 234 MET cc_start: 0.8314 (ttm) cc_final: 0.7548 (ttm) outliers start: 94 outliers final: 43 residues processed: 316 average time/residue: 0.7445 time to fit residues: 255.3545 Evaluate side-chains 296 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 231 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 TYR Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 179 TRP Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 118 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 179 TRP Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 118 TYR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 179 TRP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 222 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 128 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 GLN G 201 ASN A 242 GLN D 242 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.180226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.162647 restraints weight = 17727.242| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 1.53 r_work: 0.3836 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16324 Z= 0.187 Angle : 0.647 10.955 22092 Z= 0.341 Chirality : 0.047 0.210 2338 Planarity : 0.004 0.054 2828 Dihedral : 7.726 59.137 2240 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.26 % Allowed : 29.14 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.18), residues: 1932 helix: -4.70 (0.11), residues: 42 sheet: -0.00 (0.15), residues: 1071 loop : -1.53 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 281 TYR 0.017 0.002 TYR G 65 PHE 0.011 0.002 PHE D 42 TRP 0.025 0.002 TRP A 179 HIS 0.003 0.001 HIS G 35 Details of bonding type rmsd covalent geometry : bond 0.00444 (16324) covalent geometry : angle 0.64730 (22092) hydrogen bonds : bond 0.03326 ( 551) hydrogen bonds : angle 5.76488 ( 1431) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 241 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: G 5 ILE cc_start: 0.4546 (OUTLIER) cc_final: 0.3983 (mp) REVERT: G 75 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7385 (mttp) REVERT: G 121 ASN cc_start: 0.6198 (t0) cc_final: 0.5927 (t0) REVERT: G 179 TRP cc_start: 0.6436 (OUTLIER) cc_final: 0.5592 (t60) REVERT: G 208 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6670 (p0) REVERT: G 215 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7247 (mttt) REVERT: G 242 GLN cc_start: 0.7419 (tt0) cc_final: 0.7174 (tt0) REVERT: A 5 ILE cc_start: 0.4666 (OUTLIER) cc_final: 0.4186 (mt) REVERT: A 100 ASP cc_start: 0.7797 (m-30) cc_final: 0.7570 (m-30) REVERT: A 184 ARG cc_start: 0.8203 (mtp180) cc_final: 0.7926 (mtp85) REVERT: A 205 LYS cc_start: 0.7297 (mtmm) cc_final: 0.6770 (mtmm) REVERT: A 208 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6789 (p0) REVERT: B 5 ILE cc_start: 0.4594 (OUTLIER) cc_final: 0.4097 (mp) REVERT: B 34 MET cc_start: 0.7259 (mtt) cc_final: 0.6740 (mtm) REVERT: B 64 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7294 (mm110) REVERT: B 75 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7569 (tttt) REVERT: B 95 VAL cc_start: 0.7965 (m) cc_final: 0.7528 (t) REVERT: B 113 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7886 (tmm) REVERT: B 208 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7099 (p0) REVERT: B 212 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6917 (t70) REVERT: B 242 GLN cc_start: 0.7503 (tt0) cc_final: 0.7174 (tt0) REVERT: C 179 TRP cc_start: 0.6456 (OUTLIER) cc_final: 0.4911 (t60) REVERT: C 205 LYS cc_start: 0.7383 (mtmm) cc_final: 0.7034 (mtmm) REVERT: C 208 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6802 (p0) REVERT: C 221 SER cc_start: 0.7507 (OUTLIER) cc_final: 0.7189 (t) REVERT: D 152 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7056 (m-30) REVERT: D 179 TRP cc_start: 0.6314 (OUTLIER) cc_final: 0.5932 (t60) REVERT: D 183 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7427 (p0) REVERT: D 200 ARG cc_start: 0.7272 (mpt-90) cc_final: 0.6831 (mpt-90) REVERT: D 205 LYS cc_start: 0.7324 (mtmm) cc_final: 0.6905 (mtmm) REVERT: D 208 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.7179 (p0) REVERT: D 250 GLU cc_start: 0.7841 (tt0) cc_final: 0.7633 (tt0) REVERT: E 5 ILE cc_start: 0.4347 (OUTLIER) cc_final: 0.3739 (mp) REVERT: E 75 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7351 (mttt) REVERT: E 95 VAL cc_start: 0.8127 (m) cc_final: 0.7876 (p) REVERT: E 242 GLN cc_start: 0.7585 (tt0) cc_final: 0.7290 (tt0) REVERT: F 5 ILE cc_start: 0.4943 (OUTLIER) cc_final: 0.4506 (mp) REVERT: F 179 TRP cc_start: 0.6382 (OUTLIER) cc_final: 0.6108 (t60) REVERT: F 205 LYS cc_start: 0.7276 (mtmm) cc_final: 0.6677 (mtmm) REVERT: F 208 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6818 (p0) REVERT: F 215 LYS cc_start: 0.7441 (mmtt) cc_final: 0.7127 (mtpt) REVERT: F 234 MET cc_start: 0.8374 (ttm) cc_final: 0.7650 (ttm) outliers start: 92 outliers final: 48 residues processed: 315 average time/residue: 0.6907 time to fit residues: 236.6390 Evaluate side-chains 305 residues out of total 1750 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 234 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 30 LYS Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 118 TYR Chi-restraints excluded: chain G residue 157 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 179 TRP Chi-restraints excluded: chain G residue 200 ARG Chi-restraints excluded: chain G residue 208 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 118 TYR Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 222 SER Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain B residue 5 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 113 MET Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain B residue 212 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 179 TRP Chi-restraints excluded: chain C residue 208 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 222 SER Chi-restraints excluded: chain C residue 241 GLN Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 152 ASP Chi-restraints excluded: chain D residue 179 TRP Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 208 ASP Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain E residue 118 TYR Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain F residue 5 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 118 TYR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 179 TRP Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 222 SER Chi-restraints excluded: chain F residue 241 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 188 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 201 ASN A 242 GLN D 242 GLN E 194 GLN ** E 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.180864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.163413 restraints weight = 17646.323| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.51 r_work: 0.3840 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16324 Z= 0.159 Angle : 0.620 11.045 22092 Z= 0.327 Chirality : 0.047 0.209 2338 Planarity : 0.004 0.055 2828 Dihedral : 7.707 59.033 2240 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 5.03 % Allowed : 29.31 % Favored : 65.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.18), residues: 1932 helix: -4.68 (0.11), residues: 42 sheet: -0.03 (0.15), residues: 1071 loop : -1.58 (0.19), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 66 TYR 0.016 0.001 TYR G 65 PHE 0.010 0.002 PHE D 42 TRP 0.020 0.002 TRP A 179 HIS 0.003 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00374 (16324) covalent geometry : angle 0.62025 (22092) hydrogen bonds : bond 0.03175 ( 551) hydrogen bonds : angle 5.74618 ( 1431) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6333.45 seconds wall clock time: 108 minutes 36.15 seconds (6516.15 seconds total)