Starting phenix.real_space_refine on Mon Aug 25 06:18:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekw_28214/08_2025/8ekw_28214.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekw_28214/08_2025/8ekw_28214.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ekw_28214/08_2025/8ekw_28214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekw_28214/08_2025/8ekw_28214.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ekw_28214/08_2025/8ekw_28214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekw_28214/08_2025/8ekw_28214.map" } resolution = 2.83 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= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14082 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 9120 2.51 5 N 2380 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14552 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "B" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "C" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "E" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "F" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "G" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "I" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1415 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Time building chain proxies: 2.81, per 1000 atoms: 0.19 Number of scatterers: 14552 At special positions: 0 Unit cell: (143.64, 140.4, 61.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 3022 8.00 N 2380 7.00 C 9120 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: 0.83 Conformation dependent library (CDL) restraints added in 463.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 5 sheets defined 34.7% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 104 through 107 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 134 through 140 removed outlier: 3.759A pdb=" N PHE A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 163 through 167 Processing helix chain 'A' and resid 182 through 188 Processing helix chain 'A' and resid 224 through 241 Processing helix chain 'B' and resid 104 through 107 Processing helix chain 'B' and resid 125 through 134 Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 163 through 167 Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'B' and resid 224 through 241 Processing helix chain 'C' and resid 104 through 107 Processing helix chain 'C' and resid 125 through 134 Processing helix chain 'C' and resid 134 through 140 removed outlier: 3.752A pdb=" N PHE C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 162 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 224 through 241 Processing helix chain 'D' and resid 104 through 107 Processing helix chain 'D' and resid 125 through 134 Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 152 through 162 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 182 through 188 Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'E' and resid 104 through 107 Processing helix chain 'E' and resid 125 through 134 Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 152 through 161 Processing helix chain 'E' and resid 163 through 167 Processing helix chain 'E' and resid 182 through 188 Processing helix chain 'E' and resid 224 through 241 Processing helix chain 'F' and resid 104 through 107 Processing helix chain 'F' and resid 125 through 134 Processing helix chain 'F' and resid 134 through 140 removed outlier: 3.645A pdb=" N PHE F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 162 Processing helix chain 'F' and resid 163 through 167 Processing helix chain 'F' and resid 182 through 188 Processing helix chain 'F' and resid 224 through 241 Processing helix chain 'G' and resid 104 through 107 Processing helix chain 'G' and resid 125 through 134 Processing helix chain 'G' and resid 134 through 140 removed outlier: 3.708A pdb=" N PHE G 138 " --> pdb=" O ARG G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 162 Processing helix chain 'G' and resid 163 through 167 Processing helix chain 'G' and resid 182 through 188 Processing helix chain 'G' and resid 224 through 241 Processing helix chain 'H' and resid 104 through 107 Processing helix chain 'H' and resid 125 through 134 Processing helix chain 'H' and resid 134 through 140 removed outlier: 3.737A pdb=" N PHE H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 162 Processing helix chain 'H' and resid 163 through 167 Processing helix chain 'H' and resid 182 through 188 Processing helix chain 'H' and resid 224 through 241 Processing helix chain 'I' and resid 104 through 107 Processing helix chain 'I' and resid 125 through 134 Processing helix chain 'I' and resid 134 through 140 removed outlier: 3.570A pdb=" N PHE I 138 " --> pdb=" O ARG I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 162 Processing helix chain 'I' and resid 182 through 188 Processing helix chain 'I' and resid 224 through 241 Processing helix chain 'J' and resid 104 through 107 Processing helix chain 'J' and resid 125 through 134 Processing helix chain 'J' and resid 135 through 140 Processing helix chain 'J' and resid 152 through 161 Processing helix chain 'J' and resid 163 through 167 Processing helix chain 'J' and resid 182 through 188 Processing helix chain 'J' and resid 224 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 102 removed outlier: 4.702A pdb=" N THR A 91 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N LEU A 177 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA A 147 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR A 110 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL A 146 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL A 112 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N CYS A 148 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE A 114 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY A 201 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG A 200 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU A 216 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU A 202 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE A 214 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 204 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C 204 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE C 214 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C 202 " --> pdb=" O ILE C 214 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU C 216 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ARG C 200 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY C 201 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR C 110 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL C 146 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C 112 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N CYS C 148 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE C 114 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N LEU C 177 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA C 147 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR C 91 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 102 removed outlier: 4.750A pdb=" N THR B 91 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LEU B 177 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA B 147 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR B 110 " --> pdb=" O GLU B 144 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL B 146 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL B 112 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N CYS B 148 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE B 114 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY B 201 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 200 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN B 213 " --> pdb=" O ILE B 204 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE D 204 " --> pdb=" O ARG D 212 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE D 214 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU D 202 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU D 216 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ARG D 200 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR D 110 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL D 146 " --> pdb=" O TYR D 110 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL D 112 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS D 148 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N PHE D 114 " --> pdb=" O CYS D 148 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LEU D 177 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA D 147 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR D 91 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 97 through 102 removed outlier: 4.849A pdb=" N THR E 91 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N LEU E 177 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA E 147 " --> pdb=" O LEU E 177 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TYR E 110 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N VAL E 146 " --> pdb=" O TYR E 110 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL E 112 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS E 148 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE E 114 " --> pdb=" O CYS E 148 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY E 201 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG E 200 " --> pdb=" O ASN E 217 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN E 213 " --> pdb=" O ILE E 204 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE J 204 " --> pdb=" O ARG J 212 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ILE J 214 " --> pdb=" O LEU J 202 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU J 202 " --> pdb=" O ILE J 214 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU J 216 " --> pdb=" O ARG J 200 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ARG J 200 " --> pdb=" O LEU J 216 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N TYR J 110 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL J 146 " --> pdb=" O TYR J 110 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL J 112 " --> pdb=" O VAL J 146 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N CYS J 148 " --> pdb=" O VAL J 112 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N PHE J 114 " --> pdb=" O CYS J 148 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N LEU J 177 " --> pdb=" O VAL J 145 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA J 147 " --> pdb=" O LEU J 177 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N THR J 91 " --> pdb=" O SER J 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 97 through 102 removed outlier: 4.782A pdb=" N THR F 91 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N LEU F 177 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA F 147 " --> pdb=" O LEU F 177 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TYR F 110 " --> pdb=" O GLU F 144 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL F 146 " --> pdb=" O TYR F 110 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL F 112 " --> pdb=" O VAL F 146 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N CYS F 148 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE F 114 " --> pdb=" O CYS F 148 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY F 201 " --> pdb=" O PHE F 115 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG F 200 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU F 216 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU F 202 " --> pdb=" O ILE F 214 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE F 214 " --> pdb=" O LEU F 202 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE F 204 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN G 213 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG G 200 " --> pdb=" O ASN G 217 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY G 201 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TYR G 110 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL G 146 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL G 112 " --> pdb=" O VAL G 146 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N CYS G 148 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N PHE G 114 " --> pdb=" O CYS G 148 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N LEU G 177 " --> pdb=" O VAL G 145 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA G 147 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR G 91 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 97 through 102 removed outlier: 4.832A pdb=" N THR H 91 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU H 177 " --> pdb=" O VAL H 145 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA H 147 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N TYR H 110 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL H 146 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL H 112 " --> pdb=" O VAL H 146 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N CYS H 148 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N PHE H 114 " --> pdb=" O CYS H 148 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY H 201 " --> pdb=" O PHE H 115 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG H 200 " --> pdb=" O ASN H 217 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN H 213 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN I 213 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG I 200 " --> pdb=" O ASN I 217 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY I 201 " --> pdb=" O PHE I 115 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR I 110 " --> pdb=" O GLU I 144 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL I 146 " --> pdb=" O TYR I 110 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL I 112 " --> pdb=" O VAL I 146 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N CYS I 148 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE I 114 " --> pdb=" O CYS I 148 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N LEU I 177 " --> pdb=" O VAL I 145 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA I 147 " --> pdb=" O LEU I 177 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N THR I 91 " --> pdb=" O SER I 178 " (cutoff:3.500A) 535 hydrogen bonds defined for protein. 1461 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: 1.85 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2352 1.31 - 1.43: 3974 1.43 - 1.56: 8143 1.56 - 1.68: 1 1.68 - 1.81: 30 Bond restraints: 14500 Sorted by residual: bond pdb=" CA PRO C 220 " pdb=" C PRO C 220 " ideal model delta sigma weight residual 1.516 1.431 0.085 1.42e-02 4.96e+03 3.57e+01 bond pdb=" CA ASP C 218 " pdb=" C ASP C 218 " ideal model delta sigma weight residual 1.528 1.450 0.078 1.33e-02 5.65e+03 3.40e+01 bond pdb=" CA PRO D 220 " pdb=" C PRO D 220 " ideal model delta sigma weight residual 1.516 1.429 0.087 1.61e-02 3.86e+03 2.93e+01 bond pdb=" CA SER E 178 " pdb=" CB SER E 178 " ideal model delta sigma weight residual 1.531 1.453 0.077 1.52e-02 4.33e+03 2.60e+01 bond pdb=" CA ASP D 218 " pdb=" C ASP D 218 " ideal model delta sigma weight residual 1.528 1.460 0.068 1.37e-02 5.33e+03 2.44e+01 ... (remaining 14495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 19564 3.26 - 6.52: 94 6.52 - 9.77: 11 9.77 - 13.03: 0 13.03 - 16.29: 1 Bond angle restraints: 19670 Sorted by residual: angle pdb=" N ASP D 218 " pdb=" CA ASP D 218 " pdb=" C ASP D 218 " ideal model delta sigma weight residual 110.53 100.81 9.72 1.29e+00 6.01e-01 5.68e+01 angle pdb=" N LEU D 219 " pdb=" CA LEU D 219 " pdb=" C LEU D 219 " ideal model delta sigma weight residual 113.16 122.09 -8.93 1.42e+00 4.96e-01 3.95e+01 angle pdb=" C PRO D 220 " pdb=" CA PRO D 220 " pdb=" CB PRO D 220 " ideal model delta sigma weight residual 112.21 103.94 8.27 1.56e+00 4.11e-01 2.81e+01 angle pdb=" N VAL C 221 " pdb=" CA VAL C 221 " pdb=" C VAL C 221 " ideal model delta sigma weight residual 109.21 116.15 -6.94 1.36e+00 5.41e-01 2.60e+01 angle pdb=" N LEU C 219 " pdb=" CA LEU C 219 " pdb=" C LEU C 219 " ideal model delta sigma weight residual 113.16 120.38 -7.22 1.42e+00 4.96e-01 2.58e+01 ... (remaining 19665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.45: 7694 17.45 - 34.91: 697 34.91 - 52.36: 121 52.36 - 69.82: 13 69.82 - 87.27: 15 Dihedral angle restraints: 8540 sinusoidal: 3460 harmonic: 5080 Sorted by residual: dihedral pdb=" C VAL C 221 " pdb=" N VAL C 221 " pdb=" CA VAL C 221 " pdb=" CB VAL C 221 " ideal model delta harmonic sigma weight residual -122.00 -134.72 12.72 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" N ARG A 223 " pdb=" C ARG A 223 " pdb=" CA ARG A 223 " pdb=" CB ARG A 223 " ideal model delta harmonic sigma weight residual 122.80 133.58 -10.78 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" N LEU D 219 " pdb=" C LEU D 219 " pdb=" CA LEU D 219 " pdb=" CB LEU D 219 " ideal model delta harmonic sigma weight residual 122.80 133.43 -10.63 0 2.50e+00 1.60e-01 1.81e+01 ... (remaining 8537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 2135 0.123 - 0.245: 50 0.245 - 0.368: 1 0.368 - 0.490: 0 0.490 - 0.613: 4 Chirality restraints: 2190 Sorted by residual: chirality pdb=" CA LEU C 219 " pdb=" N LEU C 219 " pdb=" C LEU C 219 " pdb=" CB LEU C 219 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.39e+00 chirality pdb=" CA LEU D 219 " pdb=" N LEU D 219 " pdb=" C LEU D 219 " pdb=" CB LEU D 219 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" CA VAL C 221 " pdb=" N VAL C 221 " pdb=" C VAL C 221 " pdb=" CB VAL C 221 " both_signs ideal model delta sigma weight residual False 2.44 1.91 0.53 2.00e-01 2.50e+01 7.15e+00 ... (remaining 2187 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 218 " -0.016 2.00e-02 2.50e+03 3.09e-02 9.57e+00 pdb=" C ASP C 218 " 0.053 2.00e-02 2.50e+03 pdb=" O ASP C 218 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU C 219 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR G 162 " 0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO G 163 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO G 163 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 163 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 218 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.06e+00 pdb=" C ASP D 218 " 0.043 2.00e-02 2.50e+03 pdb=" O ASP D 218 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU D 219 " -0.014 2.00e-02 2.50e+03 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1838 2.75 - 3.28: 13540 3.28 - 3.82: 24618 3.82 - 4.36: 32206 4.36 - 4.90: 53262 Nonbonded interactions: 125464 Sorted by model distance: nonbonded pdb=" OD2 ASP F 179 " pdb=" OG SER F 185 " model vdw 2.207 3.040 nonbonded pdb=" OD2 ASP C 179 " pdb=" OG SER C 185 " model vdw 2.216 3.040 nonbonded pdb=" NZ LYS B 80 " pdb=" O HOH B 301 " model vdw 2.228 3.120 nonbonded pdb=" NZ LYS H 80 " pdb=" O HOH H 301 " model vdw 2.244 3.120 nonbonded pdb=" NE ARG H 200 " pdb=" O LEU H 219 " model vdw 2.244 3.120 ... (remaining 125459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.870 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:8.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 14500 Z= 0.316 Angle : 0.659 16.290 19670 Z= 0.360 Chirality : 0.054 0.613 2190 Planarity : 0.006 0.082 2520 Dihedral : 13.689 87.275 5280 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.26 % Allowed : 0.32 % Favored : 99.42 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.20), residues: 1740 helix: 0.54 (0.23), residues: 550 sheet: -0.26 (0.22), residues: 450 loop : 0.17 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 223 TYR 0.009 0.002 TYR B 110 PHE 0.019 0.002 PHE D 115 TRP 0.011 0.002 TRP E 88 HIS 0.003 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00574 (14500) covalent geometry : angle 0.65949 (19670) hydrogen bonds : bond 0.16682 ( 535) hydrogen bonds : angle 4.93010 ( 1461) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 311 time to evaluate : 0.458 Fit side-chains REVERT: A 140 SER cc_start: 0.8106 (p) cc_final: 0.7824 (p) REVERT: B 142 ASN cc_start: 0.8187 (t0) cc_final: 0.7845 (t0) REVERT: B 151 ASP cc_start: 0.8923 (m-30) cc_final: 0.8694 (m-30) REVERT: B 206 ASP cc_start: 0.8353 (p0) cc_final: 0.8130 (p0) REVERT: C 78 LYS cc_start: 0.8226 (mttp) cc_final: 0.8026 (mtmt) REVERT: C 140 SER cc_start: 0.8190 (p) cc_final: 0.7902 (p) REVERT: C 206 ASP cc_start: 0.8278 (p0) cc_final: 0.8035 (p0) REVERT: D 218 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: E 151 ASP cc_start: 0.8958 (m-30) cc_final: 0.8729 (m-30) REVERT: E 179 ASP cc_start: 0.8690 (t0) cc_final: 0.8405 (t0) REVERT: E 206 ASP cc_start: 0.8244 (p0) cc_final: 0.7922 (p0) REVERT: F 78 LYS cc_start: 0.8451 (mttp) cc_final: 0.8132 (mtpt) REVERT: F 99 LYS cc_start: 0.8423 (mmmm) cc_final: 0.8200 (mmtp) REVERT: F 142 ASN cc_start: 0.8381 (t0) cc_final: 0.7902 (t0) REVERT: G 142 ASN cc_start: 0.8338 (t0) cc_final: 0.7767 (t0) REVERT: H 142 ASN cc_start: 0.8202 (t0) cc_final: 0.7596 (t0) REVERT: H 179 ASP cc_start: 0.8727 (t0) cc_final: 0.8426 (t0) REVERT: I 78 LYS cc_start: 0.8398 (mttp) cc_final: 0.8190 (mtpt) outliers start: 4 outliers final: 1 residues processed: 312 average time/residue: 0.7727 time to fit residues: 256.0882 Evaluate side-chains 223 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain J residue 95 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0970 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 149 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS B 142 ASN B 166 GLN D 217 ASN I 217 ASN J 217 ASN J 233 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.137240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.107559 restraints weight = 16211.574| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 1.87 r_work: 0.3013 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14500 Z= 0.101 Angle : 0.491 4.681 19670 Z= 0.262 Chirality : 0.043 0.146 2190 Planarity : 0.005 0.060 2520 Dihedral : 4.278 57.927 1924 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.23 % Allowed : 10.06 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.21), residues: 1740 helix: 1.23 (0.23), residues: 540 sheet: 0.09 (0.21), residues: 480 loop : 0.38 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 107 TYR 0.019 0.002 TYR D 237 PHE 0.015 0.001 PHE J 114 TRP 0.008 0.001 TRP B 88 HIS 0.001 0.000 HIS D 197 Details of bonding type rmsd covalent geometry : bond 0.00221 (14500) covalent geometry : angle 0.49141 (19670) hydrogen bonds : bond 0.03417 ( 535) hydrogen bonds : angle 3.95594 ( 1461) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 SER cc_start: 0.8329 (p) cc_final: 0.8026 (p) REVERT: A 142 ASN cc_start: 0.8392 (t0) cc_final: 0.7761 (t0) REVERT: B 97 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7651 (mt-10) REVERT: B 142 ASN cc_start: 0.8154 (t0) cc_final: 0.7815 (t0) REVERT: B 166 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: B 193 GLU cc_start: 0.8315 (mp0) cc_final: 0.7928 (mp0) REVERT: C 78 LYS cc_start: 0.8558 (mttp) cc_final: 0.8272 (mtmt) REVERT: C 140 SER cc_start: 0.8359 (p) cc_final: 0.8050 (p) REVERT: C 142 ASN cc_start: 0.8394 (t0) cc_final: 0.7684 (t0) REVERT: D 137 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7819 (mt-10) REVERT: D 218 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: E 97 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7693 (mt-10) REVERT: E 163 PRO cc_start: 0.8147 (Cg_exo) cc_final: 0.7935 (Cg_endo) REVERT: E 193 GLU cc_start: 0.8352 (mp0) cc_final: 0.7939 (mp0) REVERT: F 78 LYS cc_start: 0.8527 (mttp) cc_final: 0.8265 (mtpt) REVERT: F 142 ASN cc_start: 0.8343 (t0) cc_final: 0.7721 (t0) REVERT: G 142 ASN cc_start: 0.8245 (t0) cc_final: 0.7649 (t0) REVERT: G 173 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.6969 (mtm110) REVERT: H 142 ASN cc_start: 0.8293 (t0) cc_final: 0.7724 (t0) REVERT: H 173 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7019 (mtm110) REVERT: I 78 LYS cc_start: 0.8652 (mttp) cc_final: 0.8360 (mtpt) REVERT: I 166 GLN cc_start: 0.8483 (mt0) cc_final: 0.7886 (mp10) outliers start: 19 outliers final: 3 residues processed: 252 average time/residue: 0.8462 time to fit residues: 225.9342 Evaluate side-chains 226 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 217 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain J residue 95 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN F 233 GLN G 213 GLN I 217 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.134505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.104545 restraints weight = 16284.737| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.85 r_work: 0.3007 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14500 Z= 0.119 Angle : 0.495 4.743 19670 Z= 0.262 Chirality : 0.044 0.158 2190 Planarity : 0.004 0.056 2520 Dihedral : 4.192 53.282 1924 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.29 % Allowed : 12.77 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.21), residues: 1740 helix: 1.40 (0.22), residues: 540 sheet: 0.48 (0.21), residues: 460 loop : 0.16 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 107 TYR 0.020 0.002 TYR C 237 PHE 0.016 0.001 PHE G 114 TRP 0.006 0.001 TRP B 88 HIS 0.002 0.001 HIS F 156 Details of bonding type rmsd covalent geometry : bond 0.00283 (14500) covalent geometry : angle 0.49520 (19670) hydrogen bonds : bond 0.03442 ( 535) hydrogen bonds : angle 3.82648 ( 1461) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7344 (mtpp) REVERT: A 140 SER cc_start: 0.8346 (p) cc_final: 0.8028 (p) REVERT: A 142 ASN cc_start: 0.8381 (t0) cc_final: 0.7286 (t0) REVERT: A 213 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.8566 (tt0) REVERT: B 97 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7674 (mt-10) REVERT: B 142 ASN cc_start: 0.8088 (t0) cc_final: 0.7778 (t0) REVERT: B 193 GLU cc_start: 0.8442 (mp0) cc_final: 0.8008 (mp0) REVERT: C 78 LYS cc_start: 0.8588 (mttp) cc_final: 0.8332 (mtmt) REVERT: C 140 SER cc_start: 0.8409 (p) cc_final: 0.8119 (p) REVERT: C 142 ASN cc_start: 0.8389 (t0) cc_final: 0.7658 (t0) REVERT: D 166 GLN cc_start: 0.8204 (mt0) cc_final: 0.7738 (mp10) REVERT: D 218 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8305 (m-30) REVERT: E 78 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8379 (mtpt) REVERT: E 97 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: E 193 GLU cc_start: 0.8439 (mp0) cc_final: 0.8012 (mp0) REVERT: F 78 LYS cc_start: 0.8542 (mttp) cc_final: 0.8297 (mtpt) REVERT: F 142 ASN cc_start: 0.8298 (t0) cc_final: 0.7651 (t0) REVERT: F 166 GLN cc_start: 0.8418 (mt0) cc_final: 0.7848 (mp10) REVERT: F 200 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8732 (mtt-85) REVERT: G 142 ASN cc_start: 0.8210 (t0) cc_final: 0.7585 (t0) REVERT: G 173 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7032 (mtm110) REVERT: H 142 ASN cc_start: 0.8212 (t0) cc_final: 0.7608 (t0) REVERT: H 173 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7018 (mtm110) REVERT: I 78 LYS cc_start: 0.8610 (mttp) cc_final: 0.8301 (mtpt) REVERT: I 164 ARG cc_start: 0.7601 (ttm170) cc_final: 0.7332 (ttm170) REVERT: I 166 GLN cc_start: 0.8452 (mt0) cc_final: 0.7841 (mp10) REVERT: J 166 GLN cc_start: 0.8258 (mt0) cc_final: 0.7591 (mp10) outliers start: 20 outliers final: 4 residues processed: 229 average time/residue: 0.8332 time to fit residues: 201.9377 Evaluate side-chains 227 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 215 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 200 ARG Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 207 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 106 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN G 213 GLN H 213 GLN J 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.099202 restraints weight = 16272.372| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.86 r_work: 0.2899 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14500 Z= 0.239 Angle : 0.618 5.506 19670 Z= 0.326 Chirality : 0.049 0.192 2190 Planarity : 0.005 0.055 2520 Dihedral : 4.743 52.297 1924 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.13 % Allowed : 14.26 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.20), residues: 1740 helix: 1.12 (0.22), residues: 540 sheet: 0.32 (0.21), residues: 460 loop : 0.08 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 200 TYR 0.020 0.003 TYR B 237 PHE 0.022 0.002 PHE G 114 TRP 0.006 0.002 TRP C 88 HIS 0.005 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00609 (14500) covalent geometry : angle 0.61783 (19670) hydrogen bonds : bond 0.04529 ( 535) hydrogen bonds : angle 3.97900 ( 1461) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 0.325 Fit side-chains REVERT: A 140 SER cc_start: 0.8624 (p) cc_final: 0.8360 (p) REVERT: A 213 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: B 97 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: B 99 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8256 (mmtm) REVERT: B 142 ASN cc_start: 0.8232 (t0) cc_final: 0.7698 (t0) REVERT: C 78 LYS cc_start: 0.8644 (mttp) cc_final: 0.8342 (mtmt) REVERT: C 140 SER cc_start: 0.8598 (p) cc_final: 0.8328 (p) REVERT: C 213 GLN cc_start: 0.9393 (OUTLIER) cc_final: 0.8455 (tt0) REVERT: D 193 GLU cc_start: 0.8467 (mp0) cc_final: 0.8244 (mp0) REVERT: D 218 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: E 97 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: F 78 LYS cc_start: 0.8764 (mttp) cc_final: 0.8467 (mtpt) REVERT: F 142 ASN cc_start: 0.8358 (t0) cc_final: 0.7745 (t0) REVERT: F 166 GLN cc_start: 0.8404 (mt0) cc_final: 0.7830 (mp10) REVERT: F 200 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8825 (mtp85) REVERT: G 173 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7168 (mtm110) REVERT: H 173 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7124 (mtm110) REVERT: I 78 LYS cc_start: 0.8784 (mttp) cc_final: 0.8496 (mtpt) REVERT: I 166 GLN cc_start: 0.8515 (mt0) cc_final: 0.7812 (mp10) REVERT: I 193 GLU cc_start: 0.8486 (mp0) cc_final: 0.7887 (mp0) REVERT: J 78 LYS cc_start: 0.9008 (mtpm) cc_final: 0.8664 (mtpt) REVERT: J 166 GLN cc_start: 0.8250 (mt0) cc_final: 0.7512 (mp10) REVERT: J 193 GLU cc_start: 0.8489 (mp0) cc_final: 0.8280 (mp0) outliers start: 33 outliers final: 12 residues processed: 237 average time/residue: 0.8373 time to fit residues: 209.4057 Evaluate side-chains 239 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 218 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 200 ARG Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain J residue 207 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN G 72 HIS G 213 GLN H 213 GLN J 213 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.098894 restraints weight = 16286.676| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.88 r_work: 0.2887 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14500 Z= 0.181 Angle : 0.553 5.474 19670 Z= 0.293 Chirality : 0.046 0.177 2190 Planarity : 0.005 0.054 2520 Dihedral : 4.534 48.059 1924 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.81 % Allowed : 15.55 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.20), residues: 1740 helix: 1.19 (0.22), residues: 540 sheet: 0.32 (0.21), residues: 460 loop : 0.05 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 200 TYR 0.019 0.002 TYR C 237 PHE 0.020 0.002 PHE G 114 TRP 0.006 0.002 TRP B 88 HIS 0.003 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00455 (14500) covalent geometry : angle 0.55314 (19670) hydrogen bonds : bond 0.03978 ( 535) hydrogen bonds : angle 3.87614 ( 1461) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 140 SER cc_start: 0.8617 (p) cc_final: 0.8345 (p) REVERT: A 213 GLN cc_start: 0.9317 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: B 97 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7824 (mt-10) REVERT: B 99 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8283 (mmtm) REVERT: B 142 ASN cc_start: 0.8190 (t0) cc_final: 0.7639 (t0) REVERT: C 78 LYS cc_start: 0.8637 (mttp) cc_final: 0.8324 (mtmt) REVERT: C 95 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7989 (t0) REVERT: C 99 LYS cc_start: 0.8434 (mttm) cc_final: 0.8166 (mttp) REVERT: C 109 LYS cc_start: 0.8645 (mtmm) cc_final: 0.7913 (mttm) REVERT: C 140 SER cc_start: 0.8506 (p) cc_final: 0.8231 (p) REVERT: C 213 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: D 166 GLN cc_start: 0.8240 (mt0) cc_final: 0.7750 (mp10) REVERT: D 193 GLU cc_start: 0.8467 (mp0) cc_final: 0.8238 (mp0) REVERT: E 97 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: F 78 LYS cc_start: 0.8627 (mttp) cc_final: 0.8372 (mtpt) REVERT: F 142 ASN cc_start: 0.8405 (t0) cc_final: 0.7739 (t0) REVERT: F 193 GLU cc_start: 0.8397 (mp0) cc_final: 0.7795 (mp0) REVERT: F 200 ARG cc_start: 0.9112 (mtp85) cc_final: 0.8860 (mtp85) REVERT: G 173 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7133 (mtm110) REVERT: H 173 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7161 (mtm110) REVERT: I 78 LYS cc_start: 0.8717 (mttp) cc_final: 0.8438 (mtpt) REVERT: I 95 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7992 (t0) REVERT: I 166 GLN cc_start: 0.8509 (mt0) cc_final: 0.7808 (mp10) REVERT: J 78 LYS cc_start: 0.9033 (mtpm) cc_final: 0.8697 (mtmt) REVERT: J 166 GLN cc_start: 0.8281 (mt0) cc_final: 0.7553 (mp10) outliers start: 28 outliers final: 10 residues processed: 229 average time/residue: 0.8651 time to fit residues: 209.4964 Evaluate side-chains 229 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain C residue 213 GLN Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 95 ASP Chi-restraints excluded: chain J residue 207 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 29 optimal weight: 0.3980 chunk 49 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN H 213 GLN I 217 ASN J 213 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.103361 restraints weight = 16043.411| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.87 r_work: 0.2925 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14500 Z= 0.097 Angle : 0.468 6.059 19670 Z= 0.249 Chirality : 0.043 0.148 2190 Planarity : 0.004 0.053 2520 Dihedral : 3.996 44.456 1922 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.68 % Allowed : 16.26 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.20), residues: 1740 helix: 1.49 (0.22), residues: 540 sheet: 0.49 (0.21), residues: 460 loop : 0.08 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 107 TYR 0.019 0.001 TYR A 237 PHE 0.013 0.001 PHE G 114 TRP 0.004 0.001 TRP E 88 HIS 0.002 0.000 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00220 (14500) covalent geometry : angle 0.46818 (19670) hydrogen bonds : bond 0.03056 ( 535) hydrogen bonds : angle 3.73930 ( 1461) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.524 Fit side-chains REVERT: A 99 LYS cc_start: 0.8485 (mttm) cc_final: 0.8235 (mttp) REVERT: A 109 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.7345 (mtpp) REVERT: A 140 SER cc_start: 0.8447 (p) cc_final: 0.8169 (p) REVERT: A 142 ASN cc_start: 0.8281 (t0) cc_final: 0.8047 (t0) REVERT: A 213 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8461 (tt0) REVERT: B 97 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7719 (mt-10) REVERT: B 99 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8238 (mmtm) REVERT: B 142 ASN cc_start: 0.8081 (t0) cc_final: 0.7688 (t0) REVERT: C 78 LYS cc_start: 0.8606 (mttp) cc_final: 0.8288 (mtmt) REVERT: C 99 LYS cc_start: 0.8464 (mttm) cc_final: 0.8172 (mttp) REVERT: C 109 LYS cc_start: 0.8539 (mtmm) cc_final: 0.7765 (mttm) REVERT: C 140 SER cc_start: 0.8445 (p) cc_final: 0.8158 (p) REVERT: C 142 ASN cc_start: 0.8303 (t0) cc_final: 0.7594 (t0) REVERT: C 200 ARG cc_start: 0.9021 (mtp85) cc_final: 0.8807 (mtt-85) REVERT: D 166 GLN cc_start: 0.8182 (mt0) cc_final: 0.7613 (mp10) REVERT: D 193 GLU cc_start: 0.8486 (mp0) cc_final: 0.8283 (mp0) REVERT: E 97 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: F 78 LYS cc_start: 0.8610 (mttp) cc_final: 0.8351 (mtpt) REVERT: F 142 ASN cc_start: 0.8206 (t0) cc_final: 0.7513 (t0) REVERT: F 166 GLN cc_start: 0.8373 (mt0) cc_final: 0.7805 (mp10) REVERT: F 193 GLU cc_start: 0.8366 (mp0) cc_final: 0.7767 (mp0) REVERT: F 200 ARG cc_start: 0.9047 (mtp85) cc_final: 0.8792 (mtt-85) REVERT: G 173 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7067 (mtm110) REVERT: I 78 LYS cc_start: 0.8644 (mttp) cc_final: 0.8351 (mtpt) REVERT: I 95 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7970 (t0) REVERT: J 78 LYS cc_start: 0.9011 (mtpm) cc_final: 0.8739 (mtmt) REVERT: J 218 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8341 (m-30) outliers start: 26 outliers final: 4 residues processed: 232 average time/residue: 0.8297 time to fit residues: 203.4384 Evaluate side-chains 212 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain J residue 218 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 166 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN G 213 GLN H 213 GLN J 166 GLN J 213 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.129366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099025 restraints weight = 16355.302| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.87 r_work: 0.2927 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14500 Z= 0.127 Angle : 0.502 5.964 19670 Z= 0.266 Chirality : 0.044 0.157 2190 Planarity : 0.004 0.052 2520 Dihedral : 3.924 15.684 1920 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.74 % Allowed : 16.65 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.20), residues: 1740 helix: 1.52 (0.22), residues: 540 sheet: 0.47 (0.22), residues: 460 loop : 0.08 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 200 TYR 0.019 0.002 TYR C 237 PHE 0.016 0.001 PHE D 114 TRP 0.004 0.001 TRP C 88 HIS 0.002 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00309 (14500) covalent geometry : angle 0.50238 (19670) hydrogen bonds : bond 0.03380 ( 535) hydrogen bonds : angle 3.72708 ( 1461) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.428 Fit side-chains REVERT: A 99 LYS cc_start: 0.8500 (mttm) cc_final: 0.8258 (mttp) REVERT: A 109 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.7278 (mtpp) REVERT: A 140 SER cc_start: 0.8472 (p) cc_final: 0.8188 (p) REVERT: A 142 ASN cc_start: 0.8330 (t0) cc_final: 0.7329 (t0) REVERT: A 194 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: A 213 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.8578 (tt0) REVERT: B 97 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: B 99 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8226 (mmtm) REVERT: B 142 ASN cc_start: 0.8100 (t0) cc_final: 0.7708 (t0) REVERT: C 78 LYS cc_start: 0.8577 (mttp) cc_final: 0.8277 (mtmt) REVERT: C 99 LYS cc_start: 0.8458 (mttm) cc_final: 0.8167 (mttp) REVERT: C 140 SER cc_start: 0.8486 (p) cc_final: 0.8198 (p) REVERT: C 142 ASN cc_start: 0.8325 (t0) cc_final: 0.7498 (t0) REVERT: D 166 GLN cc_start: 0.8210 (mt0) cc_final: 0.7643 (mp10) REVERT: D 193 GLU cc_start: 0.8489 (mp0) cc_final: 0.8271 (mp0) REVERT: E 97 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: F 78 LYS cc_start: 0.8653 (mttp) cc_final: 0.8363 (mtpt) REVERT: F 142 ASN cc_start: 0.8235 (t0) cc_final: 0.7507 (t0) REVERT: F 166 GLN cc_start: 0.8391 (mt0) cc_final: 0.7835 (mp10) REVERT: F 193 GLU cc_start: 0.8373 (mp0) cc_final: 0.7745 (mp0) REVERT: F 200 ARG cc_start: 0.9042 (mtp85) cc_final: 0.8774 (mtt-85) REVERT: F 218 ASP cc_start: 0.8392 (m-30) cc_final: 0.8155 (m-30) REVERT: G 164 ARG cc_start: 0.7472 (ttm170) cc_final: 0.7242 (ttm170) REVERT: G 173 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7133 (mtm110) REVERT: H 173 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7132 (mtm110) REVERT: I 78 LYS cc_start: 0.8657 (mttp) cc_final: 0.8369 (mtpt) REVERT: I 95 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8018 (t0) REVERT: I 166 GLN cc_start: 0.8507 (mt0) cc_final: 0.7893 (mp10) REVERT: I 218 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8362 (m-30) REVERT: J 78 LYS cc_start: 0.9020 (mtpm) cc_final: 0.8746 (mtmt) REVERT: J 166 GLN cc_start: 0.8178 (mt0) cc_final: 0.7683 (mp10) REVERT: J 218 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8435 (m-30) outliers start: 27 outliers final: 9 residues processed: 219 average time/residue: 0.8864 time to fit residues: 204.5355 Evaluate side-chains 216 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain I residue 218 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 218 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 110 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN G 213 GLN H 213 GLN J 213 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.129278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.098896 restraints weight = 16268.857| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.87 r_work: 0.2925 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14500 Z= 0.132 Angle : 0.507 6.431 19670 Z= 0.268 Chirality : 0.044 0.154 2190 Planarity : 0.005 0.056 2520 Dihedral : 3.928 16.077 1920 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.87 % Allowed : 16.58 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.20), residues: 1740 helix: 1.53 (0.22), residues: 540 sheet: 0.47 (0.22), residues: 460 loop : 0.09 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 200 TYR 0.019 0.002 TYR A 237 PHE 0.016 0.001 PHE D 114 TRP 0.004 0.001 TRP C 88 HIS 0.003 0.001 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00323 (14500) covalent geometry : angle 0.50710 (19670) hydrogen bonds : bond 0.03395 ( 535) hydrogen bonds : angle 3.72967 ( 1461) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.343 Fit side-chains REVERT: A 78 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8563 (mtmt) REVERT: A 109 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.7232 (mtpp) REVERT: A 140 SER cc_start: 0.8580 (p) cc_final: 0.8293 (p) REVERT: A 142 ASN cc_start: 0.8282 (t0) cc_final: 0.7208 (t0) REVERT: A 194 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7841 (m-30) REVERT: A 213 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: B 97 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7706 (mt-10) REVERT: B 99 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8200 (mmtm) REVERT: B 142 ASN cc_start: 0.8092 (t0) cc_final: 0.7696 (t0) REVERT: C 78 LYS cc_start: 0.8554 (mttp) cc_final: 0.8262 (mtmt) REVERT: C 99 LYS cc_start: 0.8456 (mttm) cc_final: 0.8176 (mttp) REVERT: C 140 SER cc_start: 0.8473 (p) cc_final: 0.8181 (p) REVERT: C 142 ASN cc_start: 0.8310 (t0) cc_final: 0.7510 (t0) REVERT: D 139 ARG cc_start: 0.8069 (ptp-170) cc_final: 0.7837 (ptp-170) REVERT: D 166 GLN cc_start: 0.8199 (mt0) cc_final: 0.7692 (mp10) REVERT: D 193 GLU cc_start: 0.8474 (mp0) cc_final: 0.8248 (mp0) REVERT: E 97 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7724 (mt-10) REVERT: F 78 LYS cc_start: 0.8595 (mttp) cc_final: 0.8309 (mtpt) REVERT: F 95 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7984 (t0) REVERT: F 142 ASN cc_start: 0.8212 (t0) cc_final: 0.7485 (t0) REVERT: F 166 GLN cc_start: 0.8395 (mt0) cc_final: 0.7814 (mp10) REVERT: F 193 GLU cc_start: 0.8355 (mp0) cc_final: 0.7758 (mp0) REVERT: F 218 ASP cc_start: 0.8406 (m-30) cc_final: 0.8147 (m-30) REVERT: G 164 ARG cc_start: 0.7441 (ttm170) cc_final: 0.7232 (ttm170) REVERT: G 173 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7113 (mtm110) REVERT: H 173 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7125 (mtm110) REVERT: I 78 LYS cc_start: 0.8634 (mttp) cc_final: 0.8330 (mtpt) REVERT: I 95 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8007 (t0) REVERT: I 166 GLN cc_start: 0.8454 (mt0) cc_final: 0.7830 (mp10) REVERT: J 78 LYS cc_start: 0.9005 (mtpm) cc_final: 0.8724 (mtmt) REVERT: J 166 GLN cc_start: 0.8198 (mt0) cc_final: 0.7564 (mp10) REVERT: J 218 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8304 (m-30) outliers start: 29 outliers final: 12 residues processed: 219 average time/residue: 0.9151 time to fit residues: 211.2768 Evaluate side-chains 217 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain J residue 207 ASP Chi-restraints excluded: chain J residue 218 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 128 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 154 optimal weight: 0.0010 chunk 71 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN H 213 GLN J 213 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.132391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102059 restraints weight = 16138.693| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.89 r_work: 0.2926 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14500 Z= 0.108 Angle : 0.482 6.897 19670 Z= 0.255 Chirality : 0.043 0.143 2190 Planarity : 0.004 0.053 2520 Dihedral : 3.794 17.041 1920 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.68 % Allowed : 17.16 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.20), residues: 1740 helix: 1.61 (0.22), residues: 540 sheet: 0.55 (0.22), residues: 460 loop : 0.11 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 200 TYR 0.018 0.001 TYR C 237 PHE 0.014 0.001 PHE D 114 TRP 0.004 0.001 TRP I 88 HIS 0.002 0.000 HIS F 197 Details of bonding type rmsd covalent geometry : bond 0.00254 (14500) covalent geometry : angle 0.48154 (19670) hydrogen bonds : bond 0.03108 ( 535) hydrogen bonds : angle 3.67371 ( 1461) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.465 Fit side-chains REVERT: A 78 LYS cc_start: 0.9025 (mtpp) cc_final: 0.8559 (mtmt) REVERT: A 99 LYS cc_start: 0.8483 (mttm) cc_final: 0.8249 (mttp) REVERT: A 109 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.7213 (mtpp) REVERT: A 140 SER cc_start: 0.8459 (p) cc_final: 0.8171 (p) REVERT: A 142 ASN cc_start: 0.8282 (t0) cc_final: 0.7262 (t0) REVERT: A 213 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: B 97 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: B 99 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8267 (mttp) REVERT: B 142 ASN cc_start: 0.8045 (t0) cc_final: 0.7699 (t0) REVERT: C 78 LYS cc_start: 0.8544 (mttp) cc_final: 0.8193 (mtmt) REVERT: C 99 LYS cc_start: 0.8421 (mttm) cc_final: 0.8142 (mttp) REVERT: C 140 SER cc_start: 0.8436 (p) cc_final: 0.8129 (p) REVERT: C 142 ASN cc_start: 0.8329 (t0) cc_final: 0.7590 (t0) REVERT: D 193 GLU cc_start: 0.8504 (mp0) cc_final: 0.8286 (mp0) REVERT: E 97 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: F 78 LYS cc_start: 0.8617 (mttp) cc_final: 0.8350 (mtpt) REVERT: F 119 ASP cc_start: 0.9177 (m-30) cc_final: 0.8912 (m-30) REVERT: F 142 ASN cc_start: 0.8195 (t0) cc_final: 0.7508 (t0) REVERT: F 166 GLN cc_start: 0.8327 (mt0) cc_final: 0.7741 (mp10) REVERT: F 193 GLU cc_start: 0.8381 (mp0) cc_final: 0.7800 (mp0) REVERT: F 218 ASP cc_start: 0.8289 (m-30) cc_final: 0.8037 (m-30) REVERT: G 173 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7074 (mtm110) REVERT: H 173 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7124 (mtm110) REVERT: I 78 LYS cc_start: 0.8604 (mttp) cc_final: 0.8320 (mtpt) REVERT: I 95 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8069 (t0) REVERT: I 166 GLN cc_start: 0.8501 (mt0) cc_final: 0.7769 (mp10) REVERT: J 78 LYS cc_start: 0.9035 (mtpm) cc_final: 0.8742 (mtmt) REVERT: J 166 GLN cc_start: 0.8203 (mt0) cc_final: 0.7641 (mp10) REVERT: J 218 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8255 (m-30) outliers start: 26 outliers final: 11 residues processed: 215 average time/residue: 0.8543 time to fit residues: 194.2026 Evaluate side-chains 220 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain J residue 218 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 148 optimal weight: 0.3980 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.0050 chunk 116 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 3 optimal weight: 0.0670 overall best weight: 0.6734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 166 GLN D 213 GLN H 213 GLN I 72 HIS I 217 ASN J 213 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.130975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.100679 restraints weight = 16267.933| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.87 r_work: 0.2939 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14500 Z= 0.105 Angle : 0.480 7.059 19670 Z= 0.254 Chirality : 0.043 0.143 2190 Planarity : 0.005 0.085 2520 Dihedral : 3.771 18.095 1920 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.55 % Allowed : 17.42 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.20), residues: 1740 helix: 1.68 (0.22), residues: 540 sheet: 0.57 (0.22), residues: 460 loop : 0.15 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG J 200 TYR 0.018 0.001 TYR J 237 PHE 0.013 0.001 PHE D 114 TRP 0.004 0.001 TRP C 88 HIS 0.002 0.000 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00246 (14500) covalent geometry : angle 0.48014 (19670) hydrogen bonds : bond 0.03056 ( 535) hydrogen bonds : angle 3.65299 ( 1461) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.464 Fit side-chains REVERT: A 99 LYS cc_start: 0.8472 (mttm) cc_final: 0.8246 (mttp) REVERT: A 109 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7226 (mtpp) REVERT: A 140 SER cc_start: 0.8474 (p) cc_final: 0.8182 (p) REVERT: A 142 ASN cc_start: 0.8285 (t0) cc_final: 0.7285 (t0) REVERT: A 213 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: B 97 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7669 (mt-10) REVERT: B 99 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8273 (mttp) REVERT: B 100 GLU cc_start: 0.8168 (tp30) cc_final: 0.7632 (tp30) REVERT: B 142 ASN cc_start: 0.8024 (t0) cc_final: 0.7719 (t0) REVERT: C 78 LYS cc_start: 0.8576 (mttp) cc_final: 0.8309 (mtmt) REVERT: C 99 LYS cc_start: 0.8416 (mttm) cc_final: 0.8149 (mttp) REVERT: C 140 SER cc_start: 0.8415 (p) cc_final: 0.8113 (p) REVERT: C 142 ASN cc_start: 0.8323 (t0) cc_final: 0.7617 (t0) REVERT: D 166 GLN cc_start: 0.8208 (mt0) cc_final: 0.7773 (mp10) REVERT: D 193 GLU cc_start: 0.8504 (mp0) cc_final: 0.8299 (mp0) REVERT: E 97 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7697 (mt-10) REVERT: F 78 LYS cc_start: 0.8625 (mttp) cc_final: 0.8369 (mtpt) REVERT: F 119 ASP cc_start: 0.9165 (m-30) cc_final: 0.8896 (m-30) REVERT: F 142 ASN cc_start: 0.8200 (t0) cc_final: 0.7493 (t0) REVERT: F 166 GLN cc_start: 0.8303 (mt0) cc_final: 0.7704 (mp10) REVERT: F 193 GLU cc_start: 0.8405 (mp0) cc_final: 0.7831 (mp0) REVERT: F 218 ASP cc_start: 0.8283 (m-30) cc_final: 0.8039 (m-30) REVERT: G 142 ASN cc_start: 0.8188 (t0) cc_final: 0.7585 (t0) REVERT: G 173 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7072 (mtm110) REVERT: H 173 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7125 (mtm110) REVERT: I 78 LYS cc_start: 0.8610 (mttp) cc_final: 0.8383 (mtpt) REVERT: I 95 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8049 (t0) REVERT: I 166 GLN cc_start: 0.8460 (mt0) cc_final: 0.7726 (mp10) REVERT: J 78 LYS cc_start: 0.9031 (mtpm) cc_final: 0.8721 (mtmt) REVERT: J 166 GLN cc_start: 0.8243 (mt0) cc_final: 0.7684 (mp10) REVERT: J 218 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8133 (m-30) outliers start: 24 outliers final: 12 residues processed: 215 average time/residue: 0.8829 time to fit residues: 200.5443 Evaluate side-chains 218 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 207 ASP Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 207 ASP Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 229 LEU Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain J residue 207 ASP Chi-restraints excluded: chain J residue 218 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 53 optimal weight: 0.0270 chunk 120 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 37 optimal weight: 0.0470 chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 0.0020 chunk 134 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 103 optimal weight: 0.0980 overall best weight: 0.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 GLN D 217 ASN G 142 ASN H 213 GLN I 217 ASN J 213 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.138228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.108828 restraints weight = 15876.086| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.82 r_work: 0.3019 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14500 Z= 0.079 Angle : 0.439 6.954 19670 Z= 0.231 Chirality : 0.041 0.138 2190 Planarity : 0.004 0.052 2520 Dihedral : 3.396 15.083 1920 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.16 % Allowed : 17.87 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.21), residues: 1740 helix: 1.81 (0.22), residues: 550 sheet: 0.51 (0.23), residues: 460 loop : 0.44 (0.25), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 200 TYR 0.018 0.001 TYR C 237 PHE 0.010 0.001 PHE G 114 TRP 0.005 0.001 TRP E 88 HIS 0.001 0.000 HIS E 197 Details of bonding type rmsd covalent geometry : bond 0.00166 (14500) covalent geometry : angle 0.43875 (19670) hydrogen bonds : bond 0.02388 ( 535) hydrogen bonds : angle 3.58293 ( 1461) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4929.61 seconds wall clock time: 84 minutes 26.08 seconds (5066.08 seconds total)