Starting phenix.real_space_refine on Sat May 24 19:40:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekw_28214/05_2025/8ekw_28214.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekw_28214/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ekw_28214/05_2025/8ekw_28214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekw_28214/05_2025/8ekw_28214.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekw_28214/05_2025/8ekw_28214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekw_28214/05_2025/8ekw_28214.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.074 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 7.82, per 1000 atoms: 0.54 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: 3.26 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.57 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: 3.90 Time building geometry restraints manager: 3.72 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: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.170 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 30.520 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.370 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (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 TRP 0.011 0.002 TRP E 88 HIS 0.003 0.001 HIS F 197 PHE 0.019 0.002 PHE D 115 TYR 0.009 0.002 TYR B 110 ARG 0.012 0.001 ARG J 223 Details of bonding type rmsd hydrogen bonds : bond 0.16682 ( 535) hydrogen bonds : angle 4.93010 ( 1461) covalent geometry : bond 0.00574 (14500) covalent geometry : angle 0.65949 (19670) *********************** 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 : 1.710 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: 0.7844 (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: 0.7901 (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: 0.8404 (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: 1.7752 time to fit residues: 591.4204 Evaluate side-chains 224 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 143 optimal weight: 3.9990 chunk 128 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 142 ASN ** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 HIS B 166 GLN D 213 GLN D 217 ASN G 213 GLN J 213 GLN J 217 ASN J 233 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.128171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.098325 restraints weight = 16462.556| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.87 r_work: 0.2946 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14500 Z= 0.191 Angle : 0.587 5.527 19670 Z= 0.312 Chirality : 0.047 0.176 2190 Planarity : 0.005 0.057 2520 Dihedral : 4.644 55.812 1924 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.06 % Allowed : 10.00 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1740 helix: 1.01 (0.22), residues: 540 sheet: 0.33 (0.21), residues: 460 loop : 0.15 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 88 HIS 0.004 0.001 HIS F 197 PHE 0.021 0.002 PHE H 114 TYR 0.019 0.002 TYR B 237 ARG 0.005 0.001 ARG H 107 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 535) hydrogen bonds : angle 4.03696 ( 1461) covalent geometry : bond 0.00470 (14500) covalent geometry : angle 0.58732 (19670) *********************** 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 270 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 SER cc_start: 0.8518 (p) cc_final: 0.8253 (p) REVERT: B 97 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7779 (mt-10) REVERT: B 142 ASN cc_start: 0.8323 (t0) cc_final: 0.7823 (t0) REVERT: B 218 ASP cc_start: 0.8932 (t0) cc_final: 0.8728 (m-30) REVERT: C 78 LYS cc_start: 0.8561 (mttp) cc_final: 0.8286 (mtmt) REVERT: C 95 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.8002 (t0) REVERT: C 140 SER cc_start: 0.8512 (p) cc_final: 0.8247 (p) REVERT: D 164 ARG cc_start: 0.7434 (ttm170) cc_final: 0.7085 (ttm170) REVERT: D 166 GLN cc_start: 0.8329 (mt0) cc_final: 0.7753 (mp10) REVERT: D 218 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: E 97 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: E 218 ASP cc_start: 0.8917 (t0) cc_final: 0.8698 (m-30) REVERT: F 78 LYS cc_start: 0.8634 (mttp) cc_final: 0.8427 (mtpt) REVERT: F 142 ASN cc_start: 0.8452 (t0) cc_final: 0.7745 (t0) REVERT: G 142 ASN cc_start: 0.8365 (t0) cc_final: 0.7612 (t0) REVERT: G 173 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7085 (mtm110) REVERT: H 142 ASN cc_start: 0.8365 (t0) cc_final: 0.7609 (t0) REVERT: H 173 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7100 (mtm110) REVERT: H 218 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8466 (m-30) REVERT: I 78 LYS cc_start: 0.8783 (mttp) cc_final: 0.8505 (mtpt) REVERT: I 164 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7292 (ttm170) REVERT: I 166 GLN cc_start: 0.8565 (mt0) cc_final: 0.7934 (mp10) outliers start: 32 outliers final: 8 residues processed: 252 average time/residue: 1.9016 time to fit residues: 509.9470 Evaluate side-chains 234 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 219 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 95 ASP Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain D residue 95 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 G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain H residue 218 ASP Chi-restraints excluded: chain H residue 229 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 124 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 217 ASN B 166 GLN C 213 GLN D 213 GLN G 213 GLN I 217 ASN J 213 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.128996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.098742 restraints weight = 16377.172| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.86 r_work: 0.2955 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14500 Z= 0.130 Angle : 0.501 4.797 19670 Z= 0.267 Chirality : 0.044 0.166 2190 Planarity : 0.005 0.055 2520 Dihedral : 4.322 52.205 1924 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.06 % Allowed : 13.10 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.20), residues: 1740 helix: 1.25 (0.22), residues: 540 sheet: 0.40 (0.21), residues: 460 loop : 0.09 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 88 HIS 0.002 0.001 HIS I 197 PHE 0.016 0.001 PHE B 114 TYR 0.019 0.002 TYR J 237 ARG 0.004 0.000 ARG I 200 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 535) hydrogen bonds : angle 3.83070 ( 1461) covalent geometry : bond 0.00315 (14500) covalent geometry : angle 0.50090 (19670) *********************** 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 247 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 1.612 Fit side-chains revert: symmetry clash REVERT: A 140 SER cc_start: 0.8356 (p) cc_final: 0.8043 (p) REVERT: A 166 GLN cc_start: 0.8497 (mt0) cc_final: 0.7578 (mp10) REVERT: B 97 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: B 142 ASN cc_start: 0.8127 (t0) cc_final: 0.7683 (t0) REVERT: C 78 LYS cc_start: 0.8560 (mttp) cc_final: 0.8286 (mtmt) REVERT: C 109 LYS cc_start: 0.8550 (mtmm) cc_final: 0.7757 (mttm) REVERT: C 140 SER cc_start: 0.8445 (p) cc_final: 0.8156 (p) REVERT: C 142 ASN cc_start: 0.8390 (t0) cc_final: 0.7608 (t0) REVERT: D 164 ARG cc_start: 0.7442 (ttm170) cc_final: 0.7239 (ttm170) REVERT: D 193 GLU cc_start: 0.8447 (mp0) cc_final: 0.8180 (mp0) REVERT: D 218 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8361 (m-30) REVERT: E 97 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: E 218 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8474 (m-30) REVERT: F 78 LYS cc_start: 0.8651 (mttp) cc_final: 0.8371 (mtpt) REVERT: F 142 ASN cc_start: 0.8301 (t0) cc_final: 0.7610 (t0) REVERT: F 193 GLU cc_start: 0.8419 (mp0) cc_final: 0.7877 (mp0) REVERT: G 173 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7066 (mtm110) REVERT: H 173 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7051 (mtm110) REVERT: I 78 LYS cc_start: 0.8703 (mttp) cc_final: 0.8413 (mtpt) REVERT: I 164 ARG cc_start: 0.7704 (ttm170) cc_final: 0.7441 (ttm170) REVERT: I 166 GLN cc_start: 0.8504 (mt0) cc_final: 0.7853 (mp10) REVERT: J 166 GLN cc_start: 0.8262 (mt0) cc_final: 0.7567 (mp10) REVERT: J 218 ASP cc_start: 0.8638 (OUTLIER) cc_final: 0.8402 (m-30) outliers start: 32 outliers final: 8 residues processed: 232 average time/residue: 1.9490 time to fit residues: 480.2944 Evaluate side-chains 225 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 GLU 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 95 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 E residue 218 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 J residue 95 ASP Chi-restraints excluded: chain J residue 207 ASP Chi-restraints excluded: chain J residue 218 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 154 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN D 166 GLN D 213 GLN 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 = 0.3393 r_free = 0.3393 target = 0.126128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.095812 restraints weight = 16396.647| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.86 r_work: 0.2921 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- 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 = 0.28 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 = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14500 Z= 0.211 Angle : 0.585 5.401 19670 Z= 0.309 Chirality : 0.047 0.187 2190 Planarity : 0.005 0.057 2520 Dihedral : 4.633 52.780 1924 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.32 % Allowed : 14.84 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.20), residues: 1740 helix: 1.18 (0.22), residues: 540 sheet: 0.31 (0.21), residues: 460 loop : 0.05 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I 159 HIS 0.004 0.001 HIS F 197 PHE 0.021 0.002 PHE G 114 TYR 0.019 0.002 TYR E 237 ARG 0.004 0.001 ARG D 200 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 535) hydrogen bonds : angle 3.91766 ( 1461) covalent geometry : bond 0.00536 (14500) covalent geometry : angle 0.58452 (19670) *********************** 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 256 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 220 time to evaluate : 1.579 Fit side-chains REVERT: A 140 SER cc_start: 0.8493 (p) cc_final: 0.8230 (p) REVERT: A 166 GLN cc_start: 0.8464 (mt0) cc_final: 0.7502 (mp10) REVERT: B 97 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7810 (mt-10) REVERT: B 99 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8279 (mmtm) REVERT: B 142 ASN cc_start: 0.8265 (t0) cc_final: 0.7691 (t0) REVERT: C 78 LYS cc_start: 0.8569 (mttp) cc_final: 0.8291 (mtmt) REVERT: C 109 LYS cc_start: 0.8574 (mtmm) cc_final: 0.7945 (mttm) REVERT: C 140 SER cc_start: 0.8619 (p) cc_final: 0.8344 (p) REVERT: C 213 GLN cc_start: 0.9340 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: D 166 GLN cc_start: 0.8212 (mt0) cc_final: 0.7756 (mp10) REVERT: D 193 GLU cc_start: 0.8475 (mp0) cc_final: 0.8253 (mp0) REVERT: D 218 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: E 97 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7812 (mt-10) REVERT: F 142 ASN cc_start: 0.8414 (t0) cc_final: 0.7777 (t0) REVERT: G 142 ASN cc_start: 0.8384 (t0) cc_final: 0.7584 (t0) REVERT: G 173 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7117 (mtm110) REVERT: H 173 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7109 (mtm110) REVERT: I 78 LYS cc_start: 0.8721 (mttp) cc_final: 0.8454 (mtpt) REVERT: I 95 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7973 (t0) REVERT: I 166 GLN cc_start: 0.8487 (mt0) cc_final: 0.7828 (mp10) REVERT: J 166 GLN cc_start: 0.8289 (mt0) cc_final: 0.7571 (mp10) REVERT: J 218 ASP cc_start: 0.8694 (OUTLIER) cc_final: 0.8441 (m-30) outliers start: 36 outliers final: 14 residues processed: 241 average time/residue: 1.9431 time to fit residues: 496.8166 Evaluate side-chains 239 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 216 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 194 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 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 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 194 ASP Chi-restraints excluded: chain J residue 207 ASP Chi-restraints excluded: chain J residue 218 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 102 optimal weight: 0.0060 chunk 128 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 147 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 183 GLN B 166 GLN D 213 GLN G 72 HIS H 213 GLN I 217 ASN J 213 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.100676 restraints weight = 16217.262| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.88 r_work: 0.2955 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2823 r_free = 0.2823 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2823 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14500 Z= 0.095 Angle : 0.461 5.214 19670 Z= 0.246 Chirality : 0.042 0.149 2190 Planarity : 0.004 0.054 2520 Dihedral : 4.088 45.325 1924 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.61 % Allowed : 16.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1740 helix: 1.51 (0.22), residues: 540 sheet: 0.47 (0.22), residues: 460 loop : 0.06 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 88 HIS 0.005 0.000 HIS G 72 PHE 0.013 0.001 PHE B 114 TYR 0.019 0.001 TYR A 237 ARG 0.002 0.000 ARG D 107 Details of bonding type rmsd hydrogen bonds : bond 0.02960 ( 535) hydrogen bonds : angle 3.71661 ( 1461) covalent geometry : bond 0.00215 (14500) covalent geometry : angle 0.46095 (19670) *********************** 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 242 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 1.540 Fit side-chains REVERT: A 99 LYS cc_start: 0.8466 (mttm) cc_final: 0.8216 (mttp) REVERT: A 140 SER cc_start: 0.8381 (p) cc_final: 0.8107 (p) REVERT: A 142 ASN cc_start: 0.8298 (t0) cc_final: 0.7593 (t0) REVERT: A 166 GLN cc_start: 0.8458 (mt0) cc_final: 0.7480 (mp10) REVERT: B 97 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: B 99 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8225 (mmtm) REVERT: B 100 GLU cc_start: 0.8257 (tp30) cc_final: 0.7721 (tp30) REVERT: B 142 ASN cc_start: 0.8114 (t0) cc_final: 0.7700 (t0) REVERT: C 78 LYS cc_start: 0.8581 (mttp) cc_final: 0.8333 (mtmt) REVERT: C 99 LYS cc_start: 0.8475 (mttm) cc_final: 0.8232 (mttp) REVERT: C 109 LYS cc_start: 0.8555 (mtmm) cc_final: 0.7805 (mttm) REVERT: C 140 SER cc_start: 0.8468 (p) cc_final: 0.8178 (p) REVERT: C 142 ASN cc_start: 0.8352 (t0) cc_final: 0.7657 (t0) REVERT: D 139 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.8053 (ptp-170) REVERT: D 193 GLU cc_start: 0.8479 (mp0) cc_final: 0.8256 (mp0) REVERT: E 97 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7734 (mt-10) REVERT: E 137 GLU cc_start: 0.8157 (tt0) cc_final: 0.7924 (mt-10) REVERT: F 142 ASN cc_start: 0.8217 (t0) cc_final: 0.7529 (t0) REVERT: F 193 GLU cc_start: 0.8394 (mp0) cc_final: 0.7835 (mp0) REVERT: I 78 LYS cc_start: 0.8630 (mttp) cc_final: 0.8340 (mtpt) REVERT: I 95 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7966 (t0) REVERT: I 193 GLU cc_start: 0.8427 (mp0) cc_final: 0.7787 (mp0) REVERT: J 166 GLN cc_start: 0.8267 (mt0) cc_final: 0.7546 (mp10) REVERT: J 218 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8391 (m-30) outliers start: 25 outliers final: 5 residues processed: 235 average time/residue: 2.0644 time to fit residues: 514.4244 Evaluate side-chains 214 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 82 SER Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 194 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 0.9980 chunk 165 optimal weight: 0.1980 chunk 139 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN D 166 GLN D 213 GLN F 166 GLN G 213 GLN H 213 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 = 0.3452 r_free = 0.3452 target = 0.130365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.099806 restraints weight = 16283.622| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.88 r_work: 0.2898 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14500 Z= 0.165 Angle : 0.536 5.631 19670 Z= 0.284 Chirality : 0.045 0.173 2190 Planarity : 0.005 0.054 2520 Dihedral : 4.089 16.758 1920 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.94 % Allowed : 16.77 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1740 helix: 1.44 (0.22), residues: 540 sheet: 0.40 (0.21), residues: 460 loop : 0.08 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 159 HIS 0.003 0.001 HIS A 197 PHE 0.019 0.002 PHE J 114 TYR 0.020 0.002 TYR C 237 ARG 0.007 0.000 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 535) hydrogen bonds : angle 3.79450 ( 1461) covalent geometry : bond 0.00413 (14500) covalent geometry : angle 0.53564 (19670) *********************** 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 242 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 1.619 Fit side-chains REVERT: A 99 LYS cc_start: 0.8438 (mttm) cc_final: 0.8194 (mttp) REVERT: A 140 SER cc_start: 0.8587 (p) cc_final: 0.8309 (p) REVERT: B 97 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: B 99 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8252 (mmtm) REVERT: B 142 ASN cc_start: 0.8244 (t0) cc_final: 0.7733 (t0) REVERT: C 78 LYS cc_start: 0.8603 (mttp) cc_final: 0.8322 (mtmt) REVERT: C 99 LYS cc_start: 0.8485 (mttm) cc_final: 0.8240 (mttp) REVERT: C 109 LYS cc_start: 0.8556 (mtmm) cc_final: 0.7853 (mttm) REVERT: C 140 SER cc_start: 0.8582 (p) cc_final: 0.8296 (p) REVERT: D 166 GLN cc_start: 0.8204 (mt0) cc_final: 0.7633 (mp10) REVERT: D 193 GLU cc_start: 0.8498 (mp0) cc_final: 0.8276 (mp0) REVERT: E 97 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7790 (mt-10) REVERT: F 142 ASN cc_start: 0.8296 (t0) cc_final: 0.7546 (t0) REVERT: F 193 GLU cc_start: 0.8401 (mp0) cc_final: 0.7771 (mp0) REVERT: G 173 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7140 (mtm110) REVERT: H 173 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7090 (mtm110) REVERT: I 78 LYS cc_start: 0.8652 (mttp) cc_final: 0.8346 (mtpt) REVERT: I 95 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.7993 (t0) REVERT: I 166 GLN cc_start: 0.8506 (mt0) cc_final: 0.7793 (mp10) REVERT: I 193 GLU cc_start: 0.8461 (mp0) cc_final: 0.7795 (mp0) REVERT: I 218 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: J 166 GLN cc_start: 0.8270 (mt0) cc_final: 0.8052 (mt0) REVERT: J 218 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8421 (m-30) outliers start: 30 outliers final: 10 residues processed: 233 average time/residue: 2.1131 time to fit residues: 522.5746 Evaluate side-chains 229 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 211 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 207 ASP Chi-restraints excluded: chain C residue 82 SER 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 I residue 218 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 152 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 166 GLN D 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 = 0.3432 r_free = 0.3432 target = 0.129140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.098773 restraints weight = 16349.488| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.87 r_work: 0.2909 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14500 Z= 0.134 Angle : 0.505 6.151 19670 Z= 0.268 Chirality : 0.044 0.158 2190 Planarity : 0.004 0.054 2520 Dihedral : 3.982 17.030 1920 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.94 % Allowed : 16.77 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1740 helix: 1.48 (0.22), residues: 540 sheet: 0.43 (0.22), residues: 460 loop : 0.09 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 88 HIS 0.002 0.001 HIS A 197 PHE 0.017 0.001 PHE D 114 TYR 0.019 0.002 TYR C 237 ARG 0.006 0.000 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 535) hydrogen bonds : angle 3.74372 ( 1461) covalent geometry : bond 0.00329 (14500) covalent geometry : angle 0.50450 (19670) *********************** 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 237 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.489 Fit side-chains REVERT: A 140 SER cc_start: 0.8446 (p) cc_final: 0.8166 (p) REVERT: B 97 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7714 (mt-10) REVERT: B 99 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8230 (mmtm) REVERT: B 100 GLU cc_start: 0.8252 (tp30) cc_final: 0.7660 (tp30) REVERT: B 142 ASN cc_start: 0.8245 (t0) cc_final: 0.7767 (t0) REVERT: C 78 LYS cc_start: 0.8583 (mttp) cc_final: 0.8310 (mtmt) REVERT: C 99 LYS cc_start: 0.8454 (mttm) cc_final: 0.8154 (mttp) REVERT: C 109 LYS cc_start: 0.8566 (mtmm) cc_final: 0.7873 (mttm) REVERT: C 140 SER cc_start: 0.8485 (p) cc_final: 0.8199 (p) REVERT: D 193 GLU cc_start: 0.8493 (mp0) cc_final: 0.8267 (mp0) REVERT: E 97 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7739 (mt-10) REVERT: F 142 ASN cc_start: 0.8219 (t0) cc_final: 0.7496 (t0) REVERT: F 166 GLN cc_start: 0.8374 (mt0) cc_final: 0.7820 (mp10) REVERT: F 193 GLU cc_start: 0.8386 (mp0) cc_final: 0.7743 (mp0) REVERT: F 218 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8094 (m-30) REVERT: G 164 ARG cc_start: 0.7415 (ttm170) cc_final: 0.7188 (ttm170) REVERT: G 173 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7107 (mtm110) REVERT: H 173 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7103 (mtm110) REVERT: I 78 LYS cc_start: 0.8644 (mttp) cc_final: 0.8347 (mtpt) REVERT: I 95 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8002 (t0) REVERT: I 166 GLN cc_start: 0.8509 (mt0) cc_final: 0.7750 (mp10) REVERT: I 193 GLU cc_start: 0.8426 (mp0) cc_final: 0.7790 (mp0) REVERT: I 208 LYS cc_start: 0.8934 (mmtp) cc_final: 0.8721 (mptm) REVERT: I 218 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: J 166 GLN cc_start: 0.8255 (mt0) cc_final: 0.8040 (mt0) REVERT: J 218 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8273 (m-30) outliers start: 30 outliers final: 13 residues processed: 228 average time/residue: 2.0473 time to fit residues: 494.3894 Evaluate side-chains 226 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ASP 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 82 SER 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 218 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 95 ASP Chi-restraints excluded: chain I residue 218 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 142 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 142 ASN B 166 GLN B 213 GLN D 213 GLN E 213 GLN G 213 GLN H 213 GLN I 72 HIS J 213 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099050 restraints weight = 16211.497| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.83 r_work: 0.2941 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14500 Z= 0.237 Angle : 0.611 6.646 19670 Z= 0.322 Chirality : 0.049 0.194 2190 Planarity : 0.005 0.069 2520 Dihedral : 4.414 18.761 1920 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.45 % Allowed : 16.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.20), residues: 1740 helix: 1.21 (0.22), residues: 540 sheet: 0.28 (0.21), residues: 460 loop : 0.06 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 88 HIS 0.004 0.001 HIS A 197 PHE 0.024 0.002 PHE J 114 TYR 0.022 0.003 TYR E 237 ARG 0.013 0.001 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 535) hydrogen bonds : angle 3.89046 ( 1461) covalent geometry : bond 0.00606 (14500) covalent geometry : angle 0.61084 (19670) *********************** 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 248 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 1.741 Fit side-chains REVERT: A 140 SER cc_start: 0.8612 (p) cc_final: 0.8339 (p) REVERT: A 194 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: B 97 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: B 99 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8285 (mmtm) REVERT: B 142 ASN cc_start: 0.8334 (t0) cc_final: 0.7718 (t0) REVERT: C 78 LYS cc_start: 0.8549 (mttp) cc_final: 0.8283 (mtmt) REVERT: C 99 LYS cc_start: 0.8427 (mttm) cc_final: 0.8174 (mttp) REVERT: C 109 LYS cc_start: 0.8570 (mtmm) cc_final: 0.8000 (mttm) REVERT: C 140 SER cc_start: 0.8640 (p) cc_final: 0.8377 (p) REVERT: D 166 GLN cc_start: 0.8235 (mt0) cc_final: 0.7610 (mp10) REVERT: E 97 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: F 142 ASN cc_start: 0.8445 (t0) cc_final: 0.7842 (t0) REVERT: F 164 ARG cc_start: 0.7420 (ttm170) cc_final: 0.7213 (ttm170) REVERT: F 166 GLN cc_start: 0.8427 (mt0) cc_final: 0.7849 (mp10) REVERT: F 193 GLU cc_start: 0.8461 (mp0) cc_final: 0.7802 (mp0) REVERT: G 173 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7129 (mtm110) REVERT: H 142 ASN cc_start: 0.8360 (t0) cc_final: 0.7490 (t0) REVERT: H 173 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7138 (mtm110) REVERT: I 78 LYS cc_start: 0.8721 (mttp) cc_final: 0.8442 (mtpt) REVERT: I 95 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7976 (t0) REVERT: I 166 GLN cc_start: 0.8538 (mt0) cc_final: 0.7809 (mp10) REVERT: I 193 GLU cc_start: 0.8461 (mp0) cc_final: 0.7798 (mp0) REVERT: I 200 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8389 (mtt180) REVERT: J 166 GLN cc_start: 0.8271 (mt0) cc_final: 0.7549 (mp10) REVERT: J 218 ASP cc_start: 0.8559 (OUTLIER) cc_final: 0.8262 (m-30) outliers start: 38 outliers final: 14 residues processed: 238 average time/residue: 2.0162 time to fit residues: 509.3525 Evaluate side-chains 227 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASP 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 194 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 217 ASN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 121 THR 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 194 ASP Chi-restraints excluded: chain I residue 200 ARG Chi-restraints excluded: chain J residue 81 ILE 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 163 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 154 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 149 optimal weight: 0.0060 chunk 133 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN B 166 GLN B 213 GLN D 213 GLN E 213 GLN G 213 GLN H 213 GLN I 72 HIS I 217 ASN J 213 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.131688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.101169 restraints weight = 16180.432| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.89 r_work: 0.2993 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14500 Z= 0.100 Angle : 0.471 6.758 19670 Z= 0.251 Chirality : 0.043 0.142 2190 Planarity : 0.004 0.057 2520 Dihedral : 3.881 16.725 1920 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.87 % Allowed : 17.03 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1740 helix: 1.55 (0.22), residues: 540 sheet: 0.48 (0.22), residues: 460 loop : 0.08 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 88 HIS 0.002 0.000 HIS C 197 PHE 0.012 0.001 PHE B 114 TYR 0.018 0.001 TYR J 237 ARG 0.004 0.000 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.03016 ( 535) hydrogen bonds : angle 3.70183 ( 1461) covalent geometry : bond 0.00231 (14500) covalent geometry : angle 0.47104 (19670) *********************** 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 233 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 1.554 Fit side-chains REVERT: A 99 LYS cc_start: 0.8410 (mttm) cc_final: 0.8163 (mttp) REVERT: A 140 SER cc_start: 0.8480 (p) cc_final: 0.8190 (p) REVERT: B 97 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: B 99 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8225 (mmtm) REVERT: B 100 GLU cc_start: 0.8130 (tp30) cc_final: 0.7642 (tp30) REVERT: B 142 ASN cc_start: 0.8100 (t0) cc_final: 0.7613 (t0) REVERT: C 78 LYS cc_start: 0.8531 (mttp) cc_final: 0.8243 (mtmt) REVERT: C 99 LYS cc_start: 0.8477 (mttm) cc_final: 0.8185 (mttp) REVERT: C 109 LYS cc_start: 0.8565 (mtmm) cc_final: 0.7899 (mttm) REVERT: C 140 SER cc_start: 0.8488 (p) cc_final: 0.8195 (p) REVERT: C 142 ASN cc_start: 0.8267 (t0) cc_final: 0.7578 (t0) REVERT: D 166 GLN cc_start: 0.8182 (mt0) cc_final: 0.7632 (mp10) REVERT: E 78 LYS cc_start: 0.8917 (mtpp) cc_final: 0.8386 (mtpp) REVERT: E 97 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7769 (mt-10) REVERT: F 119 ASP cc_start: 0.9245 (m-30) cc_final: 0.8997 (m-30) REVERT: F 142 ASN cc_start: 0.8196 (t0) cc_final: 0.7478 (t0) REVERT: F 166 GLN cc_start: 0.8389 (mt0) cc_final: 0.7791 (mp10) REVERT: F 193 GLU cc_start: 0.8390 (mp0) cc_final: 0.7801 (mp0) REVERT: G 173 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7097 (mtm110) REVERT: H 100 GLU cc_start: 0.8107 (tp30) cc_final: 0.7620 (tp30) REVERT: H 173 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7129 (mtm110) REVERT: I 78 LYS cc_start: 0.8599 (mttp) cc_final: 0.8306 (mtpt) REVERT: I 95 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7998 (t0) REVERT: I 166 GLN cc_start: 0.8489 (mt0) cc_final: 0.7767 (mp10) REVERT: I 193 GLU cc_start: 0.8427 (mp0) cc_final: 0.7821 (mp0) REVERT: J 166 GLN cc_start: 0.8250 (mt0) cc_final: 0.8040 (mt0) REVERT: J 218 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8282 (m-30) outliers start: 29 outliers final: 5 residues processed: 225 average time/residue: 2.0943 time to fit residues: 499.7245 Evaluate side-chains 214 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 194 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 I residue 95 ASP Chi-restraints excluded: chain J residue 121 THR 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 144 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 164 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 88 optimal weight: 0.0870 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 166 GLN B 213 GLN D 213 GLN E 213 GLN G 213 GLN H 213 GLN J 213 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097716 restraints weight = 16328.351| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.87 r_work: 0.2904 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14500 Z= 0.158 Angle : 0.535 7.088 19670 Z= 0.283 Chirality : 0.045 0.174 2190 Planarity : 0.005 0.073 2520 Dihedral : 4.078 17.305 1920 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.35 % Allowed : 17.81 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1740 helix: 1.50 (0.22), residues: 540 sheet: 0.42 (0.21), residues: 460 loop : 0.11 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 88 HIS 0.002 0.001 HIS A 197 PHE 0.020 0.001 PHE D 114 TYR 0.020 0.002 TYR E 237 ARG 0.014 0.000 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 535) hydrogen bonds : angle 3.76710 ( 1461) covalent geometry : bond 0.00396 (14500) covalent geometry : angle 0.53463 (19670) ********************** 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 220 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 1.640 Fit side-chains REVERT: A 140 SER cc_start: 0.8499 (p) cc_final: 0.8218 (p) REVERT: B 97 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7746 (mt-10) REVERT: B 99 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8243 (mmtm) REVERT: B 100 GLU cc_start: 0.8169 (tp30) cc_final: 0.7711 (tp30) REVERT: B 142 ASN cc_start: 0.8170 (t0) cc_final: 0.7660 (t0) REVERT: C 78 LYS cc_start: 0.8622 (mttp) cc_final: 0.8342 (mtmt) REVERT: C 109 LYS cc_start: 0.8568 (mtmm) cc_final: 0.7928 (mttm) REVERT: C 140 SER cc_start: 0.8496 (p) cc_final: 0.8208 (p) REVERT: D 166 GLN cc_start: 0.8220 (mt0) cc_final: 0.7603 (mp10) REVERT: E 97 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: F 142 ASN cc_start: 0.8348 (t0) cc_final: 0.7630 (t0) REVERT: F 166 GLN cc_start: 0.8369 (mt0) cc_final: 0.7748 (mp10) REVERT: F 193 GLU cc_start: 0.8437 (mp0) cc_final: 0.7846 (mp0) REVERT: G 173 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7129 (mtm110) REVERT: H 100 GLU cc_start: 0.8139 (tp30) cc_final: 0.7683 (tp30) REVERT: H 173 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7083 (mtm110) REVERT: I 78 LYS cc_start: 0.8639 (mttp) cc_final: 0.8345 (mtpt) REVERT: I 95 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8072 (t0) REVERT: I 166 GLN cc_start: 0.8516 (mt0) cc_final: 0.7750 (mp10) REVERT: I 193 GLU cc_start: 0.8456 (mp0) cc_final: 0.7817 (mp0) REVERT: I 218 ASP cc_start: 0.8509 (m-30) cc_final: 0.8244 (m-30) REVERT: J 166 GLN cc_start: 0.8240 (mt0) cc_final: 0.7504 (mp10) REVERT: J 218 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8185 (m-30) outliers start: 21 outliers final: 9 residues processed: 214 average time/residue: 2.1738 time to fit residues: 492.0054 Evaluate side-chains 213 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 81 ILE Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 207 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 190 VAL 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 60 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 111 optimal weight: 0.0070 chunk 145 optimal weight: 0.0980 chunk 165 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 162 optimal weight: 8.9990 chunk 119 optimal weight: 9.9990 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 166 GLN B 213 GLN D 213 GLN E 213 GLN H 213 GLN I 217 ASN J 213 GLN J 217 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.131100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.100419 restraints weight = 16235.504| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.90 r_work: 0.2975 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 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 = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2924 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= 0.109 Angle : 0.481 6.832 19670 Z= 0.255 Chirality : 0.043 0.154 2190 Planarity : 0.005 0.065 2520 Dihedral : 3.867 18.388 1920 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.35 % Allowed : 17.94 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.20), residues: 1740 helix: 1.62 (0.22), residues: 540 sheet: 0.52 (0.22), residues: 460 loop : 0.12 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 88 HIS 0.002 0.000 HIS A 197 PHE 0.014 0.001 PHE I 114 TYR 0.019 0.002 TYR A 237 ARG 0.013 0.000 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 535) hydrogen bonds : angle 3.70481 ( 1461) covalent geometry : bond 0.00259 (14500) covalent geometry : angle 0.48096 (19670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11509.36 seconds wall clock time: 198 minutes 12.35 seconds (11892.35 seconds total)