Starting phenix.real_space_refine on Sun Jun 22 11:31:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ekw_28214/06_2025/8ekw_28214.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ekw_28214/06_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_28214/06_2025/8ekw_28214.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ekw_28214/06_2025/8ekw_28214.map" model { file = "/net/cci-nas-00/data/ceres_data/8ekw_28214/06_2025/8ekw_28214.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ekw_28214/06_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-5710/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: 8.05, per 1000 atoms: 0.55 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 2.0 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: 1.73 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: 3.94 Time building geometry restraints manager: 3.87 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.930 Find NCS groups from input model: 0.480 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: 0.010 Load rotamer database and sin/cos tables:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.500 ------------------------------------------------------------------------------- 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 : 1.688 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: 1.9135 time to fit residues: 635.9259 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 : 1.586 ------------------------------------------------------------------------------- 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 = 40)----------------| | 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: 3.90 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- 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 : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 SER cc_start: 0.8519 (p) cc_final: 0.8254 (p) REVERT: B 97 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7780 (mt-10) REVERT: B 142 ASN cc_start: 0.8322 (t0) cc_final: 0.7822 (t0) REVERT: B 218 ASP cc_start: 0.8931 (t0) cc_final: 0.8727 (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: 0.8003 (t0) REVERT: C 140 SER cc_start: 0.8513 (p) cc_final: 0.8248 (p) REVERT: D 164 ARG cc_start: 0.7434 (ttm170) cc_final: 0.7084 (ttm170) REVERT: D 166 GLN cc_start: 0.8330 (mt0) cc_final: 0.7752 (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: 0.7782 (mt-10) REVERT: E 102 LYS cc_start: 0.9042 (mttp) cc_final: 0.8842 (mtmm) REVERT: E 218 ASP cc_start: 0.8916 (t0) cc_final: 0.8697 (m-30) REVERT: F 78 LYS cc_start: 0.8635 (mttp) cc_final: 0.8427 (mtpt) REVERT: F 142 ASN cc_start: 0.8451 (t0) cc_final: 0.7746 (t0) REVERT: G 142 ASN cc_start: 0.8365 (t0) cc_final: 0.7613 (t0) REVERT: G 173 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7084 (mtm110) REVERT: H 142 ASN cc_start: 0.8364 (t0) cc_final: 0.7610 (t0) REVERT: H 173 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7100 (mtm110) REVERT: H 218 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8467 (m-30) REVERT: I 78 LYS cc_start: 0.8784 (mttp) cc_final: 0.8506 (mtpt) REVERT: I 164 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7292 (ttm170) REVERT: I 166 GLN cc_start: 0.8566 (mt0) cc_final: 0.7935 (mp10) outliers start: 32 outliers final: 8 residues processed: 252 average time/residue: 2.3355 time to fit residues: 623.9464 Evaluate side-chains 235 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 220 time to evaluate : 1.621 ------------------------------------------------------------------------------- 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: 0.4980 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: 0.9990 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: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.131016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.100835 restraints weight = 16254.374| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.87 r_work: 0.2965 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2847 r_free = 0.2847 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2318 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= 0.130 Angle : 0.501 4.787 19670 Z= 0.267 Chirality : 0.044 0.165 2190 Planarity : 0.005 0.057 2520 Dihedral : 4.330 52.353 1924 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.95 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: 0.72 (0.20), residues: 1740 helix: 1.25 (0.22), residues: 540 sheet: 0.40 (0.21), residues: 460 loop : 0.09 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 88 HIS 0.003 0.001 HIS F 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 0.03596 ( 535) hydrogen bonds : angle 3.83506 ( 1461) covalent geometry : bond 0.00314 (14500) covalent geometry : angle 0.50133 (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 248 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 1.515 Fit side-chains REVERT: A 140 SER cc_start: 0.8354 (p) cc_final: 0.8044 (p) REVERT: A 166 GLN cc_start: 0.8514 (mt0) cc_final: 0.7564 (mp10) REVERT: B 97 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: B 142 ASN cc_start: 0.8135 (t0) cc_final: 0.7685 (t0) REVERT: C 78 LYS cc_start: 0.8562 (mttp) cc_final: 0.8287 (mtmt) REVERT: C 109 LYS cc_start: 0.8558 (mtmm) cc_final: 0.7759 (mttm) REVERT: C 140 SER cc_start: 0.8440 (p) cc_final: 0.8152 (p) REVERT: C 142 ASN cc_start: 0.8397 (t0) cc_final: 0.7615 (t0) REVERT: D 164 ARG cc_start: 0.7423 (ttm170) cc_final: 0.7219 (ttm170) REVERT: D 193 GLU cc_start: 0.8451 (mp0) cc_final: 0.8184 (mp0) REVERT: D 218 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8332 (m-30) REVERT: E 97 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: E 102 LYS cc_start: 0.9045 (mttp) cc_final: 0.8843 (mtmm) REVERT: E 218 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8480 (m-30) REVERT: F 78 LYS cc_start: 0.8652 (mttp) cc_final: 0.8370 (mtpt) REVERT: F 142 ASN cc_start: 0.8307 (t0) cc_final: 0.7615 (t0) REVERT: F 193 GLU cc_start: 0.8430 (mp0) cc_final: 0.7890 (mp0) REVERT: G 173 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7075 (mtm110) REVERT: H 173 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7049 (mtm110) REVERT: I 78 LYS cc_start: 0.8709 (mttp) cc_final: 0.8374 (mtpt) REVERT: I 164 ARG cc_start: 0.7687 (ttm170) cc_final: 0.7429 (ttm170) REVERT: I 166 GLN cc_start: 0.8500 (mt0) cc_final: 0.7847 (mp10) REVERT: J 166 GLN cc_start: 0.8249 (mt0) cc_final: 0.7542 (mp10) REVERT: J 218 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8406 (m-30) outliers start: 32 outliers final: 8 residues processed: 233 average time/residue: 2.0891 time to fit residues: 517.7035 Evaluate side-chains 226 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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: 0.9990 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: 3.9990 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 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 213 GLN D 166 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 = 0.3408 r_free = 0.3408 target = 0.127024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.096769 restraints weight = 16347.715| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.87 r_work: 0.2882 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14500 Z= 0.240 Angle : 0.613 5.845 19670 Z= 0.323 Chirality : 0.049 0.191 2190 Planarity : 0.005 0.058 2520 Dihedral : 4.722 50.118 1924 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.45 % Allowed : 14.58 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.56 (0.20), residues: 1740 helix: 1.10 (0.22), residues: 540 sheet: 0.28 (0.21), residues: 460 loop : 0.03 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 88 HIS 0.003 0.001 HIS F 197 PHE 0.022 0.002 PHE G 114 TYR 0.019 0.003 TYR C 237 ARG 0.007 0.001 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 535) hydrogen bonds : angle 3.95310 ( 1461) covalent geometry : bond 0.00612 (14500) covalent geometry : angle 0.61263 (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 260 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 1.535 Fit side-chains REVERT: A 140 SER cc_start: 0.8513 (p) cc_final: 0.8250 (p) REVERT: A 166 GLN cc_start: 0.8466 (mt0) cc_final: 0.7488 (mp10) REVERT: B 97 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: B 99 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8272 (mmtm) REVERT: B 142 ASN cc_start: 0.8292 (t0) cc_final: 0.7676 (t0) REVERT: C 78 LYS cc_start: 0.8573 (mttp) cc_final: 0.8292 (mtmt) REVERT: C 109 LYS cc_start: 0.8575 (mtmm) cc_final: 0.7954 (mttm) REVERT: C 140 SER cc_start: 0.8616 (p) cc_final: 0.8346 (p) REVERT: C 213 GLN cc_start: 0.9373 (OUTLIER) cc_final: 0.8523 (tt0) REVERT: D 166 GLN cc_start: 0.8225 (mt0) cc_final: 0.7756 (mp10) REVERT: D 193 GLU cc_start: 0.8480 (mp0) cc_final: 0.8236 (mp0) REVERT: E 97 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: F 142 ASN cc_start: 0.8398 (t0) cc_final: 0.7776 (t0) REVERT: G 142 ASN cc_start: 0.8387 (t0) cc_final: 0.7591 (t0) REVERT: G 173 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7172 (mtm110) REVERT: H 173 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7174 (mtm110) REVERT: I 78 LYS cc_start: 0.8776 (mttp) cc_final: 0.8509 (mtpt) REVERT: I 95 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7974 (t0) REVERT: I 166 GLN cc_start: 0.8523 (mt0) cc_final: 0.7834 (mp10) REVERT: I 193 GLU cc_start: 0.8495 (mp0) cc_final: 0.7900 (mp0) REVERT: J 166 GLN cc_start: 0.8281 (mt0) cc_final: 0.7550 (mp10) REVERT: J 218 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8471 (m-30) outliers start: 38 outliers final: 15 residues processed: 244 average time/residue: 2.1380 time to fit residues: 551.8805 Evaluate side-chains 237 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 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 102 LYS 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: 0.9990 chunk 113 optimal weight: 0.6980 chunk 169 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 102 optimal weight: 0.0970 chunk 128 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 B 213 GLN D 213 GLN E 213 GLN G 72 HIS G 213 GLN H 213 GLN 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 = 0.3472 r_free = 0.3472 target = 0.132113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.101855 restraints weight = 16152.194| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.88 r_work: 0.2943 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14500 Z= 0.106 Angle : 0.474 5.083 19670 Z= 0.253 Chirality : 0.043 0.154 2190 Planarity : 0.004 0.054 2520 Dihedral : 4.049 44.905 1922 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.06 % Allowed : 16.00 % Favored : 81.94 % 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: 0.78 (0.20), residues: 1740 helix: 1.42 (0.22), residues: 540 sheet: 0.43 (0.21), residues: 460 loop : 0.03 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 88 HIS 0.004 0.001 HIS G 72 PHE 0.014 0.001 PHE I 114 TYR 0.018 0.002 TYR E 237 ARG 0.004 0.000 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.03129 ( 535) hydrogen bonds : angle 3.74028 ( 1461) covalent geometry : bond 0.00244 (14500) covalent geometry : angle 0.47365 (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 247 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 215 time to evaluate : 1.602 Fit side-chains REVERT: A 99 LYS cc_start: 0.8452 (mttm) cc_final: 0.8213 (mttp) REVERT: A 140 SER cc_start: 0.8440 (p) cc_final: 0.8164 (p) REVERT: B 97 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7722 (mt-10) REVERT: B 99 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8230 (mmtm) REVERT: B 100 GLU cc_start: 0.8252 (tp30) cc_final: 0.7669 (tp30) REVERT: B 142 ASN cc_start: 0.8189 (t0) cc_final: 0.7742 (t0) REVERT: C 78 LYS cc_start: 0.8540 (mttp) cc_final: 0.8272 (mtmt) REVERT: C 99 LYS cc_start: 0.8424 (mttm) cc_final: 0.8185 (mttp) REVERT: C 109 LYS cc_start: 0.8568 (mtmm) cc_final: 0.7843 (mttm) REVERT: C 140 SER cc_start: 0.8479 (p) cc_final: 0.8200 (p) REVERT: C 142 ASN cc_start: 0.8284 (t0) cc_final: 0.7582 (t0) REVERT: C 200 ARG cc_start: 0.9024 (mtp85) cc_final: 0.8820 (mtt-85) REVERT: C 213 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8425 (tt0) REVERT: D 139 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8063 (ptp-170) REVERT: D 193 GLU cc_start: 0.8470 (mp0) cc_final: 0.8257 (mp0) REVERT: E 97 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7731 (mt-10) REVERT: E 100 GLU cc_start: 0.8141 (tp30) cc_final: 0.7657 (tp30) REVERT: F 142 ASN cc_start: 0.8216 (t0) cc_final: 0.7498 (t0) REVERT: F 193 GLU cc_start: 0.8378 (mp0) cc_final: 0.7797 (mp0) REVERT: G 173 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7046 (mtm110) REVERT: H 173 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7057 (mtm110) REVERT: I 78 LYS cc_start: 0.8653 (mttp) cc_final: 0.8342 (mtpt) REVERT: I 95 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7963 (t0) REVERT: I 193 GLU cc_start: 0.8464 (mp0) cc_final: 0.7828 (mp0) REVERT: I 218 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: J 166 GLN cc_start: 0.8260 (mt0) cc_final: 0.7524 (mp10) REVERT: J 218 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8415 (m-30) outliers start: 32 outliers final: 6 residues processed: 237 average time/residue: 2.3722 time to fit residues: 595.6954 Evaluate side-chains 220 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 C residue 213 GLN Chi-restraints excluded: chain D residue 139 ARG Chi-restraints excluded: chain D residue 194 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 95 ASP Chi-restraints excluded: chain I residue 218 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: 0.8980 chunk 165 optimal weight: 0.0770 chunk 139 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 137 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.9140 ------------------------------------------------------------------------------- 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 213 GLN D 166 GLN D 213 GLN E 213 GLN F 166 GLN H 213 GLN I 217 ASN J 213 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.130751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100193 restraints weight = 16283.152| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.89 r_work: 0.2920 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14500 Z= 0.122 Angle : 0.493 5.533 19670 Z= 0.262 Chirality : 0.044 0.156 2190 Planarity : 0.004 0.054 2520 Dihedral : 3.921 15.923 1920 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.94 % Allowed : 16.58 % Favored : 81.48 % 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: 1.51 (0.22), residues: 540 sheet: 0.46 (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 A 197 PHE 0.016 0.001 PHE G 114 TYR 0.019 0.002 TYR C 237 ARG 0.005 0.000 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 535) hydrogen bonds : angle 3.73053 ( 1461) covalent geometry : bond 0.00294 (14500) covalent geometry : angle 0.49276 (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 237 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.514 Fit side-chains REVERT: A 140 SER cc_start: 0.8448 (p) cc_final: 0.8169 (p) REVERT: B 97 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: B 99 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8228 (mmtm) REVERT: B 100 GLU cc_start: 0.8269 (tp30) cc_final: 0.7724 (tp30) REVERT: B 142 ASN cc_start: 0.8193 (t0) cc_final: 0.7774 (t0) REVERT: C 78 LYS cc_start: 0.8597 (mttp) cc_final: 0.8316 (mtmt) REVERT: C 99 LYS cc_start: 0.8463 (mttm) cc_final: 0.8166 (mttp) REVERT: C 109 LYS cc_start: 0.8537 (mtmm) cc_final: 0.7821 (mttm) REVERT: C 140 SER cc_start: 0.8483 (p) cc_final: 0.8197 (p) REVERT: C 142 ASN cc_start: 0.8284 (t0) cc_final: 0.7628 (t0) REVERT: C 213 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8463 (tt0) REVERT: D 139 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8036 (ptp-170) REVERT: D 166 GLN cc_start: 0.8198 (mt0) cc_final: 0.7615 (mp10) REVERT: D 193 GLU cc_start: 0.8474 (mp0) cc_final: 0.8255 (mp0) REVERT: E 97 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: E 137 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7949 (mt-10) REVERT: F 142 ASN cc_start: 0.8201 (t0) cc_final: 0.7484 (t0) REVERT: F 193 GLU cc_start: 0.8387 (mp0) cc_final: 0.7777 (mp0) REVERT: G 173 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7123 (mtm110) REVERT: H 173 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7115 (mtm110) REVERT: I 78 LYS cc_start: 0.8630 (mttp) cc_final: 0.8334 (mtpt) REVERT: I 95 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.8017 (t0) REVERT: I 166 GLN cc_start: 0.8576 (mt0) cc_final: 0.7899 (mp10) REVERT: I 193 GLU cc_start: 0.8469 (mp0) cc_final: 0.7837 (mp0) REVERT: I 218 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: J 166 GLN cc_start: 0.8263 (mt0) cc_final: 0.7517 (mp10) REVERT: J 218 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8376 (m-30) outliers start: 30 outliers final: 10 residues processed: 229 average time/residue: 2.1994 time to fit residues: 531.8303 Evaluate side-chains 222 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 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 139 ARG 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 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: 3.9990 chunk 89 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 43 optimal weight: 0.0020 chunk 58 optimal weight: 6.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- 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 72 HIS J 213 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.129271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.098853 restraints weight = 16255.128| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.87 r_work: 0.2939 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14500 Z= 0.197 Angle : 0.567 6.277 19670 Z= 0.300 Chirality : 0.047 0.179 2190 Planarity : 0.005 0.055 2520 Dihedral : 4.251 17.690 1920 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.26 % Allowed : 16.65 % 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: 0.73 (0.20), residues: 1740 helix: 1.35 (0.22), residues: 540 sheet: 0.33 (0.21), residues: 460 loop : 0.07 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 88 HIS 0.004 0.001 HIS A 197 PHE 0.020 0.002 PHE I 114 TYR 0.020 0.002 TYR A 237 ARG 0.009 0.001 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 535) hydrogen bonds : angle 3.84624 ( 1461) covalent geometry : bond 0.00500 (14500) covalent geometry : angle 0.56692 (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 238 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 1.499 Fit side-chains REVERT: A 78 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8668 (mtmt) REVERT: A 140 SER cc_start: 0.8595 (p) cc_final: 0.8310 (p) REVERT: B 97 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7811 (mt-10) REVERT: B 99 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8256 (mmtm) REVERT: B 100 GLU cc_start: 0.8240 (tp30) cc_final: 0.7749 (tp30) REVERT: B 142 ASN cc_start: 0.8281 (t0) cc_final: 0.7723 (t0) REVERT: C 78 LYS cc_start: 0.8551 (mttp) cc_final: 0.8285 (mtmt) REVERT: C 109 LYS cc_start: 0.8564 (mtmm) cc_final: 0.7966 (mttm) REVERT: C 140 SER cc_start: 0.8618 (p) cc_final: 0.8345 (p) REVERT: C 213 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.8479 (tt0) REVERT: D 166 GLN cc_start: 0.8225 (mt0) cc_final: 0.7670 (mp10) REVERT: E 97 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: E 218 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: F 142 ASN cc_start: 0.8399 (t0) cc_final: 0.7781 (t0) REVERT: F 166 GLN cc_start: 0.8407 (mt0) cc_final: 0.7845 (mp10) REVERT: F 193 GLU cc_start: 0.8414 (mp0) cc_final: 0.7791 (mp0) REVERT: G 173 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7144 (mtm110) REVERT: H 100 GLU cc_start: 0.8149 (tp30) cc_final: 0.7625 (tp30) REVERT: H 173 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7134 (mtm110) REVERT: I 78 LYS cc_start: 0.8721 (mttp) cc_final: 0.8453 (mtpt) REVERT: I 95 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7998 (t0) REVERT: I 166 GLN cc_start: 0.8520 (mt0) cc_final: 0.7853 (mp10) REVERT: I 200 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8661 (mtt90) REVERT: J 166 GLN cc_start: 0.8263 (mt0) cc_final: 0.7530 (mp10) REVERT: J 218 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8253 (m-30) outliers start: 35 outliers final: 12 residues processed: 228 average time/residue: 2.2702 time to fit residues: 546.9591 Evaluate side-chains 222 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 1.971 ------------------------------------------------------------------------------- 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 194 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 E residue 97 GLU Chi-restraints excluded: chain E residue 207 ASP 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 I residue 95 ASP Chi-restraints excluded: chain I residue 200 ARG 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: 0.8980 chunk 56 optimal weight: 0.5980 chunk 122 optimal weight: 0.3980 chunk 150 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 37 optimal weight: 0.0570 chunk 130 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.133148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102659 restraints weight = 16090.723| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.89 r_work: 0.2956 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14500 Z= 0.099 Angle : 0.464 6.409 19670 Z= 0.248 Chirality : 0.043 0.141 2190 Planarity : 0.004 0.054 2520 Dihedral : 3.814 16.832 1920 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.87 % Allowed : 17.23 % Favored : 80.90 % 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: 0.93 (0.20), residues: 1740 helix: 1.61 (0.22), residues: 540 sheet: 0.51 (0.22), residues: 460 loop : 0.07 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 88 HIS 0.002 0.000 HIS A 197 PHE 0.012 0.001 PHE B 114 TYR 0.018 0.001 TYR C 237 ARG 0.006 0.000 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 535) hydrogen bonds : angle 3.67565 ( 1461) covalent geometry : bond 0.00228 (14500) covalent geometry : angle 0.46351 (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 233 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 1.658 Fit side-chains REVERT: A 99 LYS cc_start: 0.8427 (mttm) cc_final: 0.8194 (mttp) REVERT: A 140 SER cc_start: 0.8600 (p) cc_final: 0.8320 (p) REVERT: A 142 ASN cc_start: 0.8309 (t0) cc_final: 0.7605 (t0) REVERT: B 97 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: B 99 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8225 (mmtm) REVERT: B 100 GLU cc_start: 0.8247 (tp30) cc_final: 0.7667 (tp30) REVERT: B 142 ASN cc_start: 0.8174 (t0) cc_final: 0.7730 (t0) REVERT: C 78 LYS cc_start: 0.8555 (mttp) cc_final: 0.8301 (mtmt) REVERT: C 99 LYS cc_start: 0.8439 (mttm) cc_final: 0.8194 (mttp) REVERT: C 109 LYS cc_start: 0.8569 (mtmm) cc_final: 0.7886 (mttm) REVERT: C 140 SER cc_start: 0.8451 (p) cc_final: 0.8157 (p) REVERT: C 142 ASN cc_start: 0.8265 (t0) cc_final: 0.7617 (t0) REVERT: D 166 GLN cc_start: 0.8183 (mt0) cc_final: 0.7602 (mp10) REVERT: E 97 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7744 (mt-10) REVERT: E 100 GLU cc_start: 0.8243 (tp30) cc_final: 0.7682 (tp30) REVERT: F 95 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7959 (t0) REVERT: F 142 ASN cc_start: 0.8207 (t0) cc_final: 0.7488 (t0) REVERT: F 166 GLN cc_start: 0.8369 (mt0) cc_final: 0.7773 (mp10) REVERT: F 193 GLU cc_start: 0.8380 (mp0) cc_final: 0.7811 (mp0) REVERT: G 173 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7104 (mtm110) REVERT: H 173 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7114 (mtm110) REVERT: I 78 LYS cc_start: 0.8614 (mttp) cc_final: 0.8329 (mtpt) REVERT: I 95 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7980 (t0) REVERT: I 166 GLN cc_start: 0.8490 (mt0) cc_final: 0.7762 (mp10) REVERT: J 166 GLN cc_start: 0.8258 (mt0) cc_final: 0.8052 (mt0) REVERT: J 218 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8211 (m-30) outliers start: 29 outliers final: 8 residues processed: 222 average time/residue: 2.4210 time to fit residues: 568.5616 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 : 1.602 ------------------------------------------------------------------------------- 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 D residue 207 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain H residue 173 ARG Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 95 ASP Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 194 ASP Chi-restraints excluded: chain J residue 218 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 163 optimal weight: 0.0170 chunk 86 optimal weight: 0.3980 chunk 73 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 115 optimal weight: 0.5980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103151 restraints weight = 16235.073| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.87 r_work: 0.2970 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2795 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14500 Z= 0.090 Angle : 0.460 6.999 19670 Z= 0.243 Chirality : 0.042 0.140 2190 Planarity : 0.004 0.052 2520 Dihedral : 3.654 17.460 1920 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.68 % Allowed : 17.68 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 1740 helix: 1.67 (0.22), residues: 550 sheet: 0.80 (0.22), residues: 440 loop : 0.15 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 88 HIS 0.001 0.000 HIS E 197 PHE 0.013 0.001 PHE D 114 TYR 0.018 0.001 TYR J 237 ARG 0.006 0.000 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.02812 ( 535) hydrogen bonds : angle 3.60343 ( 1461) covalent geometry : bond 0.00203 (14500) covalent geometry : angle 0.46018 (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 238 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 1.533 Fit side-chains REVERT: A 99 LYS cc_start: 0.8448 (mttm) cc_final: 0.8223 (mttp) REVERT: A 140 SER cc_start: 0.8393 (p) cc_final: 0.8110 (p) REVERT: A 142 ASN cc_start: 0.8240 (t0) cc_final: 0.7663 (t0) REVERT: A 200 ARG cc_start: 0.8915 (mtp85) cc_final: 0.8627 (mtt-85) REVERT: B 97 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7659 (mt-10) REVERT: B 99 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8273 (mttp) REVERT: B 100 GLU cc_start: 0.8265 (tp30) cc_final: 0.7737 (tp30) REVERT: B 142 ASN cc_start: 0.8036 (t0) cc_final: 0.7788 (t0) REVERT: C 78 LYS cc_start: 0.8569 (mttp) cc_final: 0.8305 (mtmt) REVERT: C 99 LYS cc_start: 0.8450 (mttm) cc_final: 0.8207 (mttp) REVERT: C 109 LYS cc_start: 0.8470 (mtmm) cc_final: 0.7727 (mttm) REVERT: C 140 SER cc_start: 0.8418 (p) cc_final: 0.8113 (p) REVERT: C 142 ASN cc_start: 0.8262 (t0) cc_final: 0.7665 (t0) REVERT: C 166 GLN cc_start: 0.8446 (mt0) cc_final: 0.8091 (mt0) REVERT: E 78 LYS cc_start: 0.8950 (mtpp) cc_final: 0.8484 (mtpp) REVERT: E 97 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: E 100 GLU cc_start: 0.8234 (tp30) cc_final: 0.7643 (tp30) REVERT: E 213 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.7822 (tm130) REVERT: F 95 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7976 (t0) REVERT: F 142 ASN cc_start: 0.8144 (t0) cc_final: 0.7473 (t0) REVERT: F 166 GLN cc_start: 0.8269 (mt0) cc_final: 0.7685 (mp10) REVERT: F 193 GLU cc_start: 0.8369 (mp0) cc_final: 0.7737 (mp0) REVERT: G 173 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7127 (mtm110) REVERT: H 100 GLU cc_start: 0.8136 (tp30) cc_final: 0.7669 (tp30) REVERT: H 173 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7130 (mtm110) REVERT: I 78 LYS cc_start: 0.8589 (mttp) cc_final: 0.8335 (mtpt) REVERT: I 95 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.8055 (t0) REVERT: I 119 ASP cc_start: 0.9084 (m-30) cc_final: 0.8785 (m-30) REVERT: I 166 GLN cc_start: 0.8486 (mt0) cc_final: 0.7810 (mp10) REVERT: J 218 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8211 (m-30) outliers start: 26 outliers final: 11 residues processed: 231 average time/residue: 2.1498 time to fit residues: 526.8038 Evaluate side-chains 223 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS 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 D residue 207 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain F residue 95 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 95 ASP Chi-restraints excluded: chain I residue 194 ASP Chi-restraints excluded: chain J residue 121 THR Chi-restraints excluded: chain J residue 207 ASP Chi-restraints excluded: chain J residue 218 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 144 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 0.0000 chunk 153 optimal weight: 0.0970 chunk 77 optimal weight: 0.0970 chunk 164 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 165 optimal weight: 0.9980 chunk 88 optimal weight: 0.0000 overall best weight: 0.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN B 213 GLN D 166 GLN D 213 GLN D 217 ASN E 213 GLN H 213 GLN J 166 GLN J 213 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.137092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.107454 restraints weight = 15961.107| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.83 r_work: 0.3033 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14500 Z= 0.080 Angle : 0.445 7.246 19670 Z= 0.234 Chirality : 0.041 0.137 2190 Planarity : 0.004 0.055 2520 Dihedral : 3.493 17.636 1920 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.29 % Allowed : 18.19 % Favored : 80.52 % 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: 1.30 (0.21), residues: 1740 helix: 1.82 (0.22), residues: 550 sheet: 0.91 (0.23), residues: 440 loop : 0.21 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 88 HIS 0.001 0.000 HIS E 197 PHE 0.011 0.001 PHE E 114 TYR 0.019 0.001 TYR C 237 ARG 0.011 0.000 ARG J 200 Details of bonding type rmsd hydrogen bonds : bond 0.02494 ( 535) hydrogen bonds : angle 3.56995 ( 1461) covalent geometry : bond 0.00173 (14500) covalent geometry : angle 0.44492 (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 243 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 1.569 Fit side-chains REVERT: A 99 LYS cc_start: 0.8462 (mttm) cc_final: 0.8209 (mttp) REVERT: A 140 SER cc_start: 0.8439 (p) cc_final: 0.8142 (p) REVERT: A 142 ASN cc_start: 0.8156 (t0) cc_final: 0.7673 (t0) REVERT: A 200 ARG cc_start: 0.8898 (mtp85) cc_final: 0.8589 (mtt-85) REVERT: B 97 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7577 (mt-10) REVERT: B 99 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8287 (mttp) REVERT: C 99 LYS cc_start: 0.8468 (mttm) cc_final: 0.8241 (mttp) REVERT: C 140 SER cc_start: 0.8450 (p) cc_final: 0.8137 (p) REVERT: C 142 ASN cc_start: 0.8190 (t0) cc_final: 0.7677 (t0) REVERT: C 166 GLN cc_start: 0.8426 (mt0) cc_final: 0.8132 (mt0) REVERT: D 166 GLN cc_start: 0.8222 (mt0) cc_final: 0.7682 (mp10) REVERT: E 78 LYS cc_start: 0.8912 (mtpp) cc_final: 0.8436 (mtpp) REVERT: E 97 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7610 (mt-10) REVERT: E 99 LYS cc_start: 0.8559 (mmtm) cc_final: 0.8297 (mttp) REVERT: E 100 GLU cc_start: 0.8235 (tp30) cc_final: 0.7711 (tp30) REVERT: F 78 LYS cc_start: 0.9003 (mtpm) cc_final: 0.8530 (mtpt) REVERT: F 95 ASP cc_start: 0.8196 (OUTLIER) cc_final: 0.7945 (t0) REVERT: F 142 ASN cc_start: 0.8076 (t0) cc_final: 0.7446 (t0) REVERT: F 166 GLN cc_start: 0.8270 (mt0) cc_final: 0.7749 (mp10) REVERT: G 142 ASN cc_start: 0.8077 (t0) cc_final: 0.7581 (t0) REVERT: I 78 LYS cc_start: 0.8553 (mttp) cc_final: 0.8322 (mtpt) REVERT: I 95 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8073 (t0) REVERT: I 119 ASP cc_start: 0.9024 (m-30) cc_final: 0.8689 (m-30) REVERT: I 166 GLN cc_start: 0.8438 (mt0) cc_final: 0.7784 (mp10) REVERT: J 166 GLN cc_start: 0.8149 (mt0) cc_final: 0.7615 (mp10) REVERT: J 218 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8195 (m-30) outliers start: 20 outliers final: 6 residues processed: 237 average time/residue: 2.4271 time to fit residues: 608.9019 Evaluate side-chains 221 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 209 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 207 ASP Chi-restraints excluded: chain F residue 95 ASP 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 60 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 107 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 GLN B 213 GLN C 217 ASN D 213 GLN E 213 GLN F 217 ASN G 213 GLN H 213 GLN J 213 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.133346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102689 restraints weight = 16162.249| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.88 r_work: 0.2960 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14500 Z= 0.109 Angle : 0.487 6.925 19670 Z= 0.255 Chirality : 0.043 0.158 2190 Planarity : 0.004 0.055 2520 Dihedral : 3.642 14.785 1920 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.55 % Allowed : 18.32 % Favored : 80.13 % 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: 1.25 (0.21), residues: 1740 helix: 1.74 (0.22), residues: 550 sheet: 0.87 (0.22), residues: 440 loop : 0.22 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 88 HIS 0.002 0.000 HIS B 197 PHE 0.017 0.001 PHE J 114 TYR 0.018 0.001 TYR E 237 ARG 0.005 0.000 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 535) hydrogen bonds : angle 3.60845 ( 1461) covalent geometry : bond 0.00262 (14500) covalent geometry : angle 0.48660 (19670) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12715.29 seconds wall clock time: 222 minutes 3.18 seconds (13323.18 seconds total)