Starting phenix.real_space_refine on Fri May 23 07:05:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrx_60408/05_2025/8zrx_60408_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrx_60408/05_2025/8zrx_60408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zrx_60408/05_2025/8zrx_60408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrx_60408/05_2025/8zrx_60408.map" model { file = "/net/cci-nas-00/data/ceres_data/8zrx_60408/05_2025/8zrx_60408_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrx_60408/05_2025/8zrx_60408_trim.cif" } resolution = 2.27 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= 0.002 sd= 0.147 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 18 5.49 5 Mg 2 5.21 5 S 90 5.16 5 C 7602 2.51 5 N 2040 2.21 5 O 2400 1.98 5 H 11982 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 24134 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 3966 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "B" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 3966 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "C" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 3966 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "D" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 3966 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "E" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 3966 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "F" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 3966 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {' MG': 1, 'CAA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'CAA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'CAA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {' MG': 1, 'CAA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'CAA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'CAA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 11.61, per 1000 atoms: 0.48 Number of scatterers: 24134 At special positions: 0 Unit cell: (93.936, 98.88, 93.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 90 16.00 P 18 15.00 Mg 2 11.99 O 2400 8.00 N 2040 7.00 C 7602 6.00 H 11982 1.00 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: 6.24 Conformation dependent library (CDL) restraints added in 2.1 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 15 sheets defined 58.4% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 62 through 78 Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.733A pdb=" N GLN A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 126 " --> pdb=" O HIS A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 126' Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 162 through 168 removed outlier: 4.173A pdb=" N ILE A 165 " --> pdb=" O GLN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 195 removed outlier: 8.198A pdb=" N LYS A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N SER A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 251 through 266 Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.210A pdb=" N LYS A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 58 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 117 through 126 removed outlier: 3.593A pdb=" N LEU B 123 " --> pdb=" O TRP B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 162 through 168 removed outlier: 4.157A pdb=" N ILE B 165 " --> pdb=" O GLN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 195 removed outlier: 7.226A pdb=" N LYS B 185 " --> pdb=" O ARG B 181 " (cutoff:3.500A) removed outlier: 9.140A pdb=" N SER B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 207 Processing helix chain 'B' and resid 217 through 231 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 251 through 267 removed outlier: 3.838A pdb=" N PHE B 267 " --> pdb=" O PHE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 282 removed outlier: 4.088A pdb=" N LYS B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 45 Processing helix chain 'C' and resid 62 through 78 Processing helix chain 'C' and resid 99 through 104 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 116 through 119 removed outlier: 4.235A pdb=" N HIS C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 116 through 119' Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.501A pdb=" N CYS C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 removed outlier: 4.103A pdb=" N ILE C 165 " --> pdb=" O GLN C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 200 through 206 Processing helix chain 'C' and resid 217 through 231 Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 251 through 267 removed outlier: 3.809A pdb=" N PHE C 267 " --> pdb=" O PHE C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 281 removed outlier: 4.006A pdb=" N LYS C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 54 through 58 Processing helix chain 'D' and resid 62 through 79 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 117 through 126 removed outlier: 3.651A pdb=" N HIS D 122 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 123 " --> pdb=" O TRP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 149 Processing helix chain 'D' and resid 162 through 168 removed outlier: 4.193A pdb=" N ILE D 165 " --> pdb=" O GLN D 162 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY D 168 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 184 through 195 removed outlier: 3.617A pdb=" N GLU D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 217 through 231 Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 251 through 267 removed outlier: 3.805A pdb=" N PHE D 267 " --> pdb=" O PHE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 removed outlier: 4.171A pdb=" N LYS D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 45 Processing helix chain 'E' and resid 54 through 58 removed outlier: 3.620A pdb=" N LEU E 58 " --> pdb=" O PRO E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 79 Processing helix chain 'E' and resid 107 through 115 Processing helix chain 'E' and resid 117 through 120 Processing helix chain 'E' and resid 121 through 126 removed outlier: 3.694A pdb=" N GLN E 125 " --> pdb=" O ASP E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 149 Processing helix chain 'E' and resid 162 through 168 removed outlier: 4.146A pdb=" N ILE E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 184 through 195 Processing helix chain 'E' and resid 200 through 207 Processing helix chain 'E' and resid 217 through 231 Processing helix chain 'E' and resid 233 through 246 Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 251 through 267 removed outlier: 3.849A pdb=" N PHE E 267 " --> pdb=" O PHE E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 281 removed outlier: 4.284A pdb=" N LYS E 273 " --> pdb=" O THR E 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 45 Processing helix chain 'F' and resid 62 through 78 Processing helix chain 'F' and resid 107 through 115 Processing helix chain 'F' and resid 116 through 126 removed outlier: 4.452A pdb=" N HIS F 119 " --> pdb=" O PHE F 116 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TRP F 120 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU F 123 " --> pdb=" O TRP F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 149 Processing helix chain 'F' and resid 162 through 168 removed outlier: 4.159A pdb=" N ILE F 165 " --> pdb=" O GLN F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 184 Processing helix chain 'F' and resid 184 through 195 Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 217 through 231 Processing helix chain 'F' and resid 233 through 246 Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 251 through 267 removed outlier: 3.786A pdb=" N PHE F 267 " --> pdb=" O PHE F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 281 removed outlier: 4.247A pdb=" N LYS F 273 " --> pdb=" O THR F 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 41 removed outlier: 6.211A pdb=" N GLY A 48 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N THR A 88 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ILE A 50 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 130 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR A 153 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ALA A 132 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N GLY A 155 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL A 134 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LYS A 211 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 95 removed outlier: 7.718A pdb=" N PHE A 139 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 36 through 41 removed outlier: 6.240A pdb=" N GLY B 48 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR B 88 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE B 50 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE B 85 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ALA B 133 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 87 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 130 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N TYR B 153 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA B 132 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N GLY B 155 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL B 134 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 211 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'B' and resid 93 through 95 removed outlier: 7.698A pdb=" N PHE B 139 " --> pdb=" O PHE B 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 41 removed outlier: 6.232A pdb=" N GLY C 48 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR C 88 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE C 50 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 130 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N TYR C 153 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ALA C 132 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N GLY C 155 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL C 134 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE C 152 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N CYS C 213 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA C 154 " --> pdb=" O CYS C 213 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 93 through 95 removed outlier: 7.680A pdb=" N PHE C 139 " --> pdb=" O PHE C 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 36 through 41 removed outlier: 6.161A pdb=" N GLY D 48 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR D 88 " --> pdb=" O GLY D 48 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE D 50 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE D 85 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA D 133 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU D 87 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS D 211 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 93 through 95 removed outlier: 7.814A pdb=" N PHE D 139 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 36 through 41 removed outlier: 6.206A pdb=" N GLY E 48 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR E 88 " --> pdb=" O GLY E 48 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE E 50 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL E 130 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N TYR E 153 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ALA E 132 " --> pdb=" O TYR E 153 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY E 155 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL E 134 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS E 211 " --> pdb=" O ILE E 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AB4, first strand: chain 'E' and resid 93 through 95 removed outlier: 7.719A pdb=" N PHE E 139 " --> pdb=" O PHE E 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 36 through 41 removed outlier: 6.366A pdb=" N GLY F 48 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR F 88 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE F 50 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE F 85 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N ALA F 133 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU F 87 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE F 152 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N CYS F 213 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA F 154 " --> pdb=" O CYS F 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 93 through 95 removed outlier: 7.701A pdb=" N PHE F 139 " --> pdb=" O PHE F 94 " (cutoff:3.500A) 633 hydrogen bonds defined for protein. 1722 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: 8.74 Time building geometry restraints manager: 7.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11946 1.03 - 1.23: 63 1.23 - 1.42: 4839 1.42 - 1.62: 7263 1.62 - 1.81: 177 Bond restraints: 24288 Sorted by residual: bond pdb=" C2B CAA E 301 " pdb=" C3B CAA E 301 " ideal model delta sigma weight residual 1.527 1.278 0.249 1.20e-02 6.94e+03 4.31e+02 bond pdb=" C2B CAA F 301 " pdb=" C3B CAA F 301 " ideal model delta sigma weight residual 1.527 1.278 0.249 1.20e-02 6.94e+03 4.29e+02 bond pdb=" C2B CAA A 301 " pdb=" C3B CAA A 301 " ideal model delta sigma weight residual 1.527 1.281 0.246 1.20e-02 6.94e+03 4.20e+02 bond pdb=" C2B CAA C 301 " pdb=" C3B CAA C 301 " ideal model delta sigma weight residual 1.527 1.282 0.245 1.20e-02 6.94e+03 4.16e+02 bond pdb=" C2B CAA D 301 " pdb=" C3B CAA D 301 " ideal model delta sigma weight residual 1.527 1.283 0.244 1.20e-02 6.94e+03 4.13e+02 ... (remaining 24283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 43512 3.41 - 6.81: 388 6.81 - 10.22: 37 10.22 - 13.63: 16 13.63 - 17.04: 9 Bond angle restraints: 43962 Sorted by residual: angle pdb=" CAP CAA D 301 " pdb=" C9P CAA D 301 " pdb=" N8P CAA D 301 " ideal model delta sigma weight residual 117.51 133.95 -16.44 1.00e+00 1.00e+00 2.70e+02 angle pdb=" CAP CAA B 301 " pdb=" C9P CAA B 301 " pdb=" N8P CAA B 301 " ideal model delta sigma weight residual 117.51 133.74 -16.23 1.00e+00 1.00e+00 2.63e+02 angle pdb=" CAP CAA F 301 " pdb=" C9P CAA F 301 " pdb=" N8P CAA F 301 " ideal model delta sigma weight residual 117.51 133.06 -15.55 1.00e+00 1.00e+00 2.42e+02 angle pdb=" CAP CAA A 301 " pdb=" C9P CAA A 301 " pdb=" N8P CAA A 301 " ideal model delta sigma weight residual 117.51 132.71 -15.20 1.00e+00 1.00e+00 2.31e+02 angle pdb=" C1 CAA D 301 " pdb=" S1P CAA D 301 " pdb=" C2P CAA D 301 " ideal model delta sigma weight residual 101.66 116.09 -14.43 1.00e+00 1.00e+00 2.08e+02 ... (remaining 43957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.76: 11039 30.76 - 61.52: 411 61.52 - 92.28: 23 92.28 - 123.04: 1 123.04 - 153.80: 4 Dihedral angle restraints: 11478 sinusoidal: 6474 harmonic: 5004 Sorted by residual: dihedral pdb=" C4B CAA E 301 " pdb=" C3B CAA E 301 " pdb=" O3B CAA E 301 " pdb=" P3B CAA E 301 " ideal model delta sinusoidal sigma weight residual -123.81 29.99 -153.80 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" CDP CAA E 301 " pdb=" CBP CAA E 301 " pdb=" CCP CAA E 301 " pdb=" O6A CAA E 301 " ideal model delta sinusoidal sigma weight residual 60.00 -163.09 -136.91 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" CDP CAA A 301 " pdb=" CBP CAA A 301 " pdb=" CCP CAA A 301 " pdb=" O6A CAA A 301 " ideal model delta sinusoidal sigma weight residual 60.00 -166.49 -133.51 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 11475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 1845 0.243 - 0.486: 13 0.486 - 0.729: 6 0.729 - 0.971: 0 0.971 - 1.214: 2 Chirality restraints: 1866 Sorted by residual: chirality pdb=" CAP CAA C 301 " pdb=" C9P CAA C 301 " pdb=" CBP CAA C 301 " pdb=" OAP CAA C 301 " both_signs ideal model delta sigma weight residual False -2.31 -1.10 -1.21 2.00e-01 2.50e+01 3.69e+01 chirality pdb=" C3B CAA E 301 " pdb=" C2B CAA E 301 " pdb=" C4B CAA E 301 " pdb=" O3B CAA E 301 " both_signs ideal model delta sigma weight residual False -2.76 -1.66 -1.10 2.00e-01 2.50e+01 3.02e+01 chirality pdb=" C2B CAA E 301 " pdb=" C1B CAA E 301 " pdb=" C3B CAA E 301 " pdb=" O2B CAA E 301 " both_signs ideal model delta sigma weight residual False -2.72 -2.08 -0.64 2.00e-01 2.50e+01 1.02e+01 ... (remaining 1863 not shown) Planarity restraints: 3642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 112 " 0.009 2.00e-02 2.50e+03 1.38e-02 5.71e+00 pdb=" CG TYR B 112 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 112 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 112 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 112 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 112 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 112 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 112 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR B 112 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 TYR B 112 " -0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR B 112 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR B 112 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P CAA B 301 " 0.021 2.00e-02 2.50e+03 1.81e-02 4.08e+00 pdb=" C5P CAA B 301 " -0.018 2.00e-02 2.50e+03 pdb=" C6P CAA B 301 " 0.019 2.00e-02 2.50e+03 pdb=" N4P CAA B 301 " -0.022 2.00e-02 2.50e+03 pdb=" O5P CAA B 301 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P CAA C 301 " -0.003 2.00e-02 2.50e+03 1.49e-02 2.79e+00 pdb=" C5P CAA C 301 " 0.029 2.00e-02 2.50e+03 pdb=" C6P CAA C 301 " -0.010 2.00e-02 2.50e+03 pdb=" N4P CAA C 301 " -0.006 2.00e-02 2.50e+03 pdb=" O5P CAA C 301 " -0.011 2.00e-02 2.50e+03 ... (remaining 3639 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1099 2.19 - 2.79: 49386 2.79 - 3.39: 68144 3.39 - 4.00: 91526 4.00 - 4.60: 143556 Nonbonded interactions: 353711 Sorted by model distance: nonbonded pdb=" OG SER D 243 " pdb=" HG1 THR E 176 " model vdw 1.584 2.450 nonbonded pdb=" HG SER D 243 " pdb=" HG1 THR E 176 " model vdw 1.593 2.100 nonbonded pdb=" O GLN C 125 " pdb=" HZ2 LYS C 127 " model vdw 1.604 2.450 nonbonded pdb=" O VAL B 82 " pdb=" HZ3 LYS B 128 " model vdw 1.627 2.450 nonbonded pdb=" HZ1 LYS F 211 " pdb=" OE1 GLU F 221 " model vdw 1.631 2.450 ... (remaining 353706 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' and (resid 31 through 290 or resid 301)) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and (resid 31 through 290 or resid 301)) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.400 Extract box with map and model: 0.830 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 49.900 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 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:12.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 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 : 0.010 0.249 12306 Z= 0.796 Angle : 0.919 17.036 16596 Z= 0.653 Chirality : 0.070 1.214 1866 Planarity : 0.002 0.018 2124 Dihedral : 15.049 153.805 4788 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % 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: -0.53 (0.21), residues: 1548 helix: 0.09 (0.19), residues: 744 sheet: -1.21 (0.43), residues: 162 loop : -0.46 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 120 HIS 0.005 0.001 HIS B 119 PHE 0.005 0.000 PHE F 116 TYR 0.020 0.001 TYR B 112 ARG 0.001 0.000 ARG D 41 Details of bonding type rmsd hydrogen bonds : bond 0.15590 ( 633) hydrogen bonds : angle 6.87138 ( 1722) covalent geometry : bond 0.00998 (12306) covalent geometry : angle 0.91869 (16596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.5936 (m-30) cc_final: 0.5588 (t70) REVERT: A 107 SER cc_start: 0.6812 (t) cc_final: 0.6541 (p) REVERT: A 122 HIS cc_start: 0.5808 (m170) cc_final: 0.5603 (t-90) REVERT: A 127 LYS cc_start: 0.6762 (mmtt) cc_final: 0.6539 (mmtm) REVERT: A 191 MET cc_start: 0.7256 (mtp) cc_final: 0.7010 (mtp) REVERT: A 205 GLN cc_start: 0.6525 (mt0) cc_final: 0.5030 (tm130) REVERT: A 211 LYS cc_start: 0.7556 (mtpt) cc_final: 0.7249 (tttm) REVERT: A 216 GLU cc_start: 0.7171 (mp0) cc_final: 0.6727 (mp0) REVERT: A 260 LYS cc_start: 0.6331 (ttmm) cc_final: 0.6047 (tttt) REVERT: A 273 LYS cc_start: 0.6582 (tttm) cc_final: 0.6289 (tptm) REVERT: A 290 GLN cc_start: 0.5849 (pt0) cc_final: 0.5587 (pt0) REVERT: B 46 THR cc_start: 0.7818 (p) cc_final: 0.7561 (p) REVERT: B 67 ASP cc_start: 0.6530 (m-30) cc_final: 0.5764 (t70) REVERT: B 205 GLN cc_start: 0.6369 (mt0) cc_final: 0.4708 (tm130) REVERT: B 216 GLU cc_start: 0.7305 (mp0) cc_final: 0.7024 (mp0) REVERT: B 239 MET cc_start: 0.7065 (mtt) cc_final: 0.6815 (mtp) REVERT: B 273 LYS cc_start: 0.6483 (tptp) cc_final: 0.6247 (tptm) REVERT: B 286 ASN cc_start: 0.7608 (m-40) cc_final: 0.7271 (m-40) REVERT: C 35 TYR cc_start: 0.7524 (m-80) cc_final: 0.7303 (m-80) REVERT: C 51 GLN cc_start: 0.7177 (tt0) cc_final: 0.6976 (tt0) REVERT: C 67 ASP cc_start: 0.6329 (m-30) cc_final: 0.6046 (t70) REVERT: C 122 HIS cc_start: 0.6134 (m170) cc_final: 0.5359 (t-90) REVERT: C 205 GLN cc_start: 0.6539 (mt0) cc_final: 0.5500 (tm130) REVERT: C 211 LYS cc_start: 0.7819 (tttt) cc_final: 0.7541 (tttm) REVERT: C 216 GLU cc_start: 0.7540 (pm20) cc_final: 0.7035 (mp0) REVERT: C 239 MET cc_start: 0.7249 (mtt) cc_final: 0.6938 (mtp) REVERT: D 51 GLN cc_start: 0.7108 (tt0) cc_final: 0.6851 (tt0) REVERT: D 67 ASP cc_start: 0.6651 (m-30) cc_final: 0.5773 (t70) REVERT: D 117 LEU cc_start: 0.6222 (mt) cc_final: 0.5939 (mt) REVERT: D 122 HIS cc_start: 0.6260 (m170) cc_final: 0.5992 (t70) REVERT: D 205 GLN cc_start: 0.6333 (mt0) cc_final: 0.5086 (tm130) REVERT: D 211 LYS cc_start: 0.7815 (tttt) cc_final: 0.7537 (tttm) REVERT: D 216 GLU cc_start: 0.7460 (pm20) cc_final: 0.7049 (mp0) REVERT: D 239 MET cc_start: 0.7198 (mtt) cc_final: 0.6769 (mtp) REVERT: D 286 ASN cc_start: 0.7484 (m110) cc_final: 0.7090 (m-40) REVERT: D 288 LYS cc_start: 0.6009 (mmtm) cc_final: 0.5158 (mppt) REVERT: E 39 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7277 (mt-10) REVERT: E 67 ASP cc_start: 0.6109 (m-30) cc_final: 0.5600 (t70) REVERT: E 122 HIS cc_start: 0.6002 (m170) cc_final: 0.5234 (t-90) REVERT: E 127 LYS cc_start: 0.6200 (mttp) cc_final: 0.5837 (mmtm) REVERT: E 156 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6657 (mm-30) REVERT: E 205 GLN cc_start: 0.6364 (mt0) cc_final: 0.5270 (tm130) REVERT: E 211 LYS cc_start: 0.7721 (ttmm) cc_final: 0.7147 (tttp) REVERT: E 260 LYS cc_start: 0.6573 (ttmt) cc_final: 0.6272 (tttt) REVERT: F 39 GLU cc_start: 0.8119 (pt0) cc_final: 0.7861 (pt0) REVERT: F 67 ASP cc_start: 0.6292 (m-30) cc_final: 0.5598 (t70) REVERT: F 99 ASP cc_start: 0.6766 (t0) cc_final: 0.6415 (t70) REVERT: F 121 ASP cc_start: 0.6757 (m-30) cc_final: 0.6448 (m-30) REVERT: F 122 HIS cc_start: 0.6091 (m170) cc_final: 0.5302 (t-90) REVERT: F 124 THR cc_start: 0.6953 (m) cc_final: 0.6624 (p) REVERT: F 125 GLN cc_start: 0.6409 (mm110) cc_final: 0.6155 (mp-120) REVERT: F 127 LYS cc_start: 0.7432 (mmpt) cc_final: 0.6925 (mmtm) REVERT: F 191 MET cc_start: 0.7277 (mtp) cc_final: 0.6892 (mtp) REVERT: F 205 GLN cc_start: 0.6659 (mt0) cc_final: 0.5149 (tm130) REVERT: F 216 GLU cc_start: 0.7439 (pm20) cc_final: 0.6700 (mp0) REVERT: F 242 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6012 (mt-10) outliers start: 0 outliers final: 0 residues processed: 366 average time/residue: 2.9059 time to fit residues: 1149.5768 Evaluate side-chains 200 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 162 GLN B 44 ASN B 104 GLN C 44 ASN C 162 GLN C 286 ASN D 162 GLN E 44 ASN E 162 GLN E 286 ASN F 44 ASN F 162 GLN F 205 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.136778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118488 restraints weight = 31894.525| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.07 r_work: 0.3207 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12306 Z= 0.103 Angle : 0.469 4.688 16596 Z= 0.251 Chirality : 0.040 0.151 1866 Planarity : 0.003 0.026 2124 Dihedral : 11.973 135.033 1956 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.30 % Allowed : 11.22 % Favored : 87.48 % 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: 1.10 (0.22), residues: 1548 helix: 1.57 (0.20), residues: 744 sheet: -0.64 (0.44), residues: 156 loop : 0.23 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 120 HIS 0.003 0.001 HIS B 119 PHE 0.009 0.001 PHE D 279 TYR 0.012 0.001 TYR B 35 ARG 0.002 0.000 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 633) hydrogen bonds : angle 4.65598 ( 1722) covalent geometry : bond 0.00221 (12306) covalent geometry : angle 0.46887 (16596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 207 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7467 (m-30) cc_final: 0.7260 (t70) REVERT: A 156 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7821 (mt-10) REVERT: A 191 MET cc_start: 0.8992 (mtp) cc_final: 0.8712 (mtp) REVERT: A 205 GLN cc_start: 0.8536 (mt0) cc_final: 0.8145 (tm130) REVERT: A 216 GLU cc_start: 0.7831 (mp0) cc_final: 0.7601 (mp0) REVERT: A 290 GLN cc_start: 0.7362 (pt0) cc_final: 0.7133 (pt0) REVERT: B 34 GLU cc_start: 0.7712 (pt0) cc_final: 0.7421 (pt0) REVERT: B 156 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: B 205 GLN cc_start: 0.8504 (mt0) cc_final: 0.8064 (tm130) REVERT: C 122 HIS cc_start: 0.7514 (m170) cc_final: 0.7052 (t-90) REVERT: C 216 GLU cc_start: 0.8011 (pm20) cc_final: 0.7745 (mp0) REVERT: C 288 LYS cc_start: 0.7587 (mmtm) cc_final: 0.6977 (mppt) REVERT: D 67 ASP cc_start: 0.7894 (m-30) cc_final: 0.7526 (t70) REVERT: D 117 LEU cc_start: 0.7426 (mt) cc_final: 0.7211 (mt) REVERT: D 156 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: D 286 ASN cc_start: 0.8329 (m110) cc_final: 0.8107 (m-40) REVERT: D 288 LYS cc_start: 0.7806 (mmtm) cc_final: 0.6730 (mppt) REVERT: E 67 ASP cc_start: 0.7558 (m-30) cc_final: 0.7323 (t70) REVERT: E 122 HIS cc_start: 0.7643 (m170) cc_final: 0.6883 (t-170) REVERT: E 288 LYS cc_start: 0.7981 (mttm) cc_final: 0.7502 (mtmt) REVERT: F 67 ASP cc_start: 0.7799 (m-30) cc_final: 0.7532 (t70) REVERT: F 122 HIS cc_start: 0.7640 (m170) cc_final: 0.7361 (t-90) REVERT: F 191 MET cc_start: 0.9001 (mtp) cc_final: 0.8464 (mtp) REVERT: F 205 GLN cc_start: 0.8512 (mt0) cc_final: 0.8115 (tm130) REVERT: F 216 GLU cc_start: 0.7889 (pm20) cc_final: 0.7471 (mp0) REVERT: F 242 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8023 (mt-10) outliers start: 16 outliers final: 8 residues processed: 218 average time/residue: 2.9951 time to fit residues: 703.7654 Evaluate side-chains 186 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 6.9990 chunk 149 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN B 44 ASN B 105 ASN C 32 ASN D 44 ASN D 286 ASN E 44 ASN E 104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.123885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104898 restraints weight = 31235.606| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.06 r_work: 0.3003 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12306 Z= 0.216 Angle : 0.605 5.200 16596 Z= 0.336 Chirality : 0.044 0.179 1866 Planarity : 0.005 0.047 2124 Dihedral : 13.557 118.800 1956 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.60 % Allowed : 10.65 % Favored : 86.75 % 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: 0.96 (0.21), residues: 1548 helix: 1.21 (0.18), residues: 744 sheet: -0.02 (0.45), residues: 156 loop : 0.31 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 120 HIS 0.005 0.001 HIS A 119 PHE 0.018 0.003 PHE C 279 TYR 0.011 0.002 TYR F 112 ARG 0.007 0.001 ARG F 197 Details of bonding type rmsd hydrogen bonds : bond 0.05669 ( 633) hydrogen bonds : angle 4.93885 ( 1722) covalent geometry : bond 0.00472 (12306) covalent geometry : angle 0.60464 (16596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7928 (m-30) cc_final: 0.7657 (t70) REVERT: A 106 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8247 (mp) REVERT: A 156 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: A 205 GLN cc_start: 0.8618 (mt0) cc_final: 0.8268 (tm130) REVERT: A 288 LYS cc_start: 0.8251 (mptt) cc_final: 0.7882 (mptt) REVERT: B 34 GLU cc_start: 0.7786 (pt0) cc_final: 0.7532 (pt0) REVERT: B 67 ASP cc_start: 0.7902 (m-30) cc_final: 0.7610 (t70) REVERT: B 156 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: B 205 GLN cc_start: 0.8604 (mt0) cc_final: 0.8175 (tm130) REVERT: C 122 HIS cc_start: 0.7928 (m170) cc_final: 0.7166 (t-90) REVERT: C 125 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7626 (mp-120) REVERT: C 216 GLU cc_start: 0.8039 (pm20) cc_final: 0.7824 (mp0) REVERT: D 67 ASP cc_start: 0.7992 (m-30) cc_final: 0.7633 (t70) REVERT: D 77 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: D 156 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: D 276 MET cc_start: 0.9045 (mtt) cc_final: 0.8669 (mtt) REVERT: D 288 LYS cc_start: 0.8008 (mmtm) cc_final: 0.7015 (mppt) REVERT: E 122 HIS cc_start: 0.7925 (m170) cc_final: 0.7104 (t-170) REVERT: F 67 ASP cc_start: 0.7912 (m-30) cc_final: 0.7607 (t70) REVERT: F 77 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7009 (tp30) REVERT: F 122 HIS cc_start: 0.7887 (m170) cc_final: 0.7362 (t-90) REVERT: F 205 GLN cc_start: 0.8648 (mt0) cc_final: 0.8299 (tm130) REVERT: F 216 GLU cc_start: 0.8036 (pm20) cc_final: 0.7642 (mp0) outliers start: 32 outliers final: 14 residues processed: 214 average time/residue: 2.9369 time to fit residues: 678.8735 Evaluate side-chains 181 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 260 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 84 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 138 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 104 GLN A 105 ASN B 44 ASN C 44 ASN D 44 ASN D 104 GLN D 105 ASN D 224 GLN E 44 ASN F 71 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.121761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.102777 restraints weight = 31580.920| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.06 r_work: 0.2963 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 12306 Z= 0.269 Angle : 0.656 6.197 16596 Z= 0.364 Chirality : 0.046 0.199 1866 Planarity : 0.005 0.050 2124 Dihedral : 13.640 121.904 1956 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.09 % Allowed : 9.76 % Favored : 87.15 % 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: 0.67 (0.21), residues: 1548 helix: 0.83 (0.18), residues: 738 sheet: 0.39 (0.47), residues: 156 loop : 0.18 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 120 HIS 0.006 0.002 HIS B 119 PHE 0.019 0.003 PHE F 279 TYR 0.016 0.002 TYR D 137 ARG 0.007 0.002 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.06208 ( 633) hydrogen bonds : angle 5.03226 ( 1722) covalent geometry : bond 0.00594 (12306) covalent geometry : angle 0.65622 (16596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7877 (m-30) cc_final: 0.7579 (t70) REVERT: A 106 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8312 (mp) REVERT: A 156 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: A 205 GLN cc_start: 0.8700 (mt0) cc_final: 0.8331 (tm130) REVERT: A 220 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7788 (mm-30) REVERT: B 34 GLU cc_start: 0.7855 (pt0) cc_final: 0.7638 (pt0) REVERT: B 67 ASP cc_start: 0.7907 (m-30) cc_final: 0.7629 (t70) REVERT: B 156 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: B 205 GLN cc_start: 0.8617 (mt0) cc_final: 0.8178 (tm130) REVERT: C 122 HIS cc_start: 0.7905 (m170) cc_final: 0.7211 (t-90) REVERT: C 125 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7614 (mp-120) REVERT: C 216 GLU cc_start: 0.8049 (pm20) cc_final: 0.7796 (mp0) REVERT: C 221 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: D 67 ASP cc_start: 0.7989 (m-30) cc_final: 0.7626 (t70) REVERT: D 77 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: D 156 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: D 216 GLU cc_start: 0.8018 (mp0) cc_final: 0.7768 (mp0) REVERT: D 288 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7243 (mppt) REVERT: E 122 HIS cc_start: 0.8006 (m170) cc_final: 0.7191 (t-170) REVERT: F 67 ASP cc_start: 0.7884 (m-30) cc_final: 0.7660 (t70) REVERT: F 122 HIS cc_start: 0.7964 (m170) cc_final: 0.7400 (t-90) REVERT: F 125 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8107 (mp-120) REVERT: F 156 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: F 205 GLN cc_start: 0.8643 (mt0) cc_final: 0.8290 (tm130) REVERT: F 216 GLU cc_start: 0.8070 (pm20) cc_final: 0.7709 (mp0) outliers start: 38 outliers final: 15 residues processed: 188 average time/residue: 2.9004 time to fit residues: 590.2560 Evaluate side-chains 169 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 260 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 260 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 71 GLN B 44 ASN B 224 GLN D 44 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104807 restraints weight = 31528.678| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.05 r_work: 0.3000 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12306 Z= 0.152 Angle : 0.511 4.695 16596 Z= 0.285 Chirality : 0.041 0.152 1866 Planarity : 0.003 0.034 2124 Dihedral : 12.698 117.867 1956 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.44 % Allowed : 10.16 % Favored : 87.40 % 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 (0.21), residues: 1548 helix: 1.13 (0.18), residues: 756 sheet: 0.39 (0.47), residues: 156 loop : 0.22 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 120 HIS 0.004 0.001 HIS B 119 PHE 0.015 0.002 PHE F 279 TYR 0.008 0.001 TYR D 137 ARG 0.003 0.001 ARG B 181 Details of bonding type rmsd hydrogen bonds : bond 0.04862 ( 633) hydrogen bonds : angle 4.78007 ( 1722) covalent geometry : bond 0.00322 (12306) covalent geometry : angle 0.51069 (16596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7821 (m-30) cc_final: 0.7585 (t70) REVERT: A 77 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7563 (tp30) REVERT: A 156 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: A 205 GLN cc_start: 0.8704 (mt0) cc_final: 0.8359 (tm130) REVERT: A 220 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7706 (mm-30) REVERT: B 34 GLU cc_start: 0.7816 (pt0) cc_final: 0.7599 (pt0) REVERT: B 67 ASP cc_start: 0.7877 (m-30) cc_final: 0.7607 (t70) REVERT: B 77 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: B 156 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: B 205 GLN cc_start: 0.8621 (mt0) cc_final: 0.8185 (tm130) REVERT: C 122 HIS cc_start: 0.7866 (m170) cc_final: 0.7187 (t-90) REVERT: C 125 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7580 (mp-120) REVERT: C 216 GLU cc_start: 0.8076 (pm20) cc_final: 0.7823 (mp0) REVERT: C 221 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: D 67 ASP cc_start: 0.7942 (m-30) cc_final: 0.7623 (t70) REVERT: D 156 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: D 216 GLU cc_start: 0.8010 (mp0) cc_final: 0.7725 (mp0) REVERT: D 288 LYS cc_start: 0.8149 (mmtm) cc_final: 0.7271 (mppt) REVERT: E 122 HIS cc_start: 0.7944 (m170) cc_final: 0.7103 (t-170) REVERT: F 67 ASP cc_start: 0.7865 (m-30) cc_final: 0.7640 (t70) REVERT: F 77 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: F 122 HIS cc_start: 0.7897 (m170) cc_final: 0.7425 (t-90) REVERT: F 125 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8027 (mp-120) REVERT: F 205 GLN cc_start: 0.8673 (mt0) cc_final: 0.8309 (tm130) REVERT: F 216 GLU cc_start: 0.8020 (pm20) cc_final: 0.7635 (mp0) outliers start: 30 outliers final: 13 residues processed: 181 average time/residue: 2.8821 time to fit residues: 566.4481 Evaluate side-chains 171 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain B residue 260 LYS Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 288 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 147 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN B 44 ASN C 44 ASN D 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.102732 restraints weight = 32133.338| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.13 r_work: 0.2950 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12306 Z= 0.213 Angle : 0.583 5.586 16596 Z= 0.325 Chirality : 0.043 0.175 1866 Planarity : 0.004 0.044 2124 Dihedral : 13.376 120.047 1956 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.36 % Allowed : 10.41 % Favored : 87.24 % 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: 0.79 (0.21), residues: 1548 helix: 1.00 (0.18), residues: 738 sheet: 0.45 (0.48), residues: 156 loop : 0.15 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 120 HIS 0.005 0.001 HIS B 119 PHE 0.017 0.002 PHE D 279 TYR 0.010 0.002 TYR D 137 ARG 0.005 0.001 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.05678 ( 633) hydrogen bonds : angle 4.92106 ( 1722) covalent geometry : bond 0.00464 (12306) covalent geometry : angle 0.58324 (16596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7806 (m-30) cc_final: 0.7536 (t70) REVERT: A 77 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7569 (tp30) REVERT: A 106 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8253 (mp) REVERT: A 156 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: A 205 GLN cc_start: 0.8694 (mt0) cc_final: 0.8272 (tm130) REVERT: A 220 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7739 (mm-30) REVERT: B 67 ASP cc_start: 0.7871 (m-30) cc_final: 0.7539 (t70) REVERT: B 125 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7908 (mp-120) REVERT: B 156 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: B 205 GLN cc_start: 0.8633 (mt0) cc_final: 0.8141 (tm130) REVERT: C 122 HIS cc_start: 0.7849 (m170) cc_final: 0.7138 (t-90) REVERT: C 125 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7561 (mp-120) REVERT: C 216 GLU cc_start: 0.8053 (pm20) cc_final: 0.7766 (mp0) REVERT: C 221 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: D 67 ASP cc_start: 0.7886 (m-30) cc_final: 0.7531 (t70) REVERT: D 77 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: D 125 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7927 (mp-120) REVERT: D 156 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: D 288 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7207 (mppt) REVERT: E 122 HIS cc_start: 0.7925 (m170) cc_final: 0.7070 (t-170) REVERT: F 67 ASP cc_start: 0.7864 (m-30) cc_final: 0.7591 (t70) REVERT: F 122 HIS cc_start: 0.7901 (m170) cc_final: 0.7330 (t-90) REVERT: F 125 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8103 (mp-120) REVERT: F 156 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: F 205 GLN cc_start: 0.8631 (mt0) cc_final: 0.8150 (tm130) REVERT: F 216 GLU cc_start: 0.8012 (pm20) cc_final: 0.7628 (mp0) outliers start: 29 outliers final: 13 residues processed: 176 average time/residue: 2.9005 time to fit residues: 551.8492 Evaluate side-chains 174 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 288 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN B 44 ASN C 44 ASN D 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.101680 restraints weight = 32025.214| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.15 r_work: 0.2966 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12306 Z= 0.222 Angle : 0.591 5.642 16596 Z= 0.329 Chirality : 0.044 0.181 1866 Planarity : 0.004 0.043 2124 Dihedral : 13.311 119.714 1956 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.36 % Allowed : 10.57 % Favored : 87.07 % 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: 0.76 (0.21), residues: 1548 helix: 0.98 (0.18), residues: 750 sheet: 0.47 (0.48), residues: 156 loop : 0.11 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 120 HIS 0.005 0.001 HIS B 119 PHE 0.017 0.002 PHE B 279 TYR 0.010 0.002 TYR D 137 ARG 0.005 0.001 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.05709 ( 633) hydrogen bonds : angle 4.93615 ( 1722) covalent geometry : bond 0.00490 (12306) covalent geometry : angle 0.59136 (16596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7727 (m-30) cc_final: 0.7465 (t70) REVERT: A 77 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7607 (tp30) REVERT: A 106 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8215 (mp) REVERT: A 156 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: A 205 GLN cc_start: 0.8701 (mt0) cc_final: 0.8277 (tm130) REVERT: A 220 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7727 (mm-30) REVERT: B 67 ASP cc_start: 0.7921 (m-30) cc_final: 0.7566 (t70) REVERT: B 125 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7891 (mp-120) REVERT: B 156 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: B 205 GLN cc_start: 0.8634 (mt0) cc_final: 0.8135 (tm130) REVERT: C 122 HIS cc_start: 0.7873 (m170) cc_final: 0.7155 (t-90) REVERT: C 125 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7582 (mp-120) REVERT: C 216 GLU cc_start: 0.8078 (pm20) cc_final: 0.7779 (mp0) REVERT: C 221 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: D 67 ASP cc_start: 0.7927 (m-30) cc_final: 0.7554 (t70) REVERT: D 77 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7538 (tt0) REVERT: D 156 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: E 122 HIS cc_start: 0.7997 (m170) cc_final: 0.7108 (t-170) REVERT: F 67 ASP cc_start: 0.7812 (m-30) cc_final: 0.7563 (t70) REVERT: F 122 HIS cc_start: 0.7890 (m170) cc_final: 0.7309 (t-90) REVERT: F 125 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8078 (mp-120) REVERT: F 156 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: F 205 GLN cc_start: 0.8646 (mt0) cc_final: 0.8208 (tm130) REVERT: F 216 GLU cc_start: 0.8046 (pm20) cc_final: 0.7663 (mp0) outliers start: 29 outliers final: 13 residues processed: 174 average time/residue: 2.8428 time to fit residues: 536.4351 Evaluate side-chains 171 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 288 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN B 44 ASN C 44 ASN C 104 GLN D 44 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.103306 restraints weight = 32101.082| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.12 r_work: 0.2964 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12306 Z= 0.160 Angle : 0.514 4.922 16596 Z= 0.288 Chirality : 0.042 0.156 1866 Planarity : 0.003 0.033 2124 Dihedral : 12.760 117.668 1956 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.20 % Allowed : 10.73 % Favored : 87.07 % 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: 0.94 (0.21), residues: 1548 helix: 1.18 (0.18), residues: 756 sheet: 0.46 (0.48), residues: 156 loop : 0.13 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 120 HIS 0.003 0.001 HIS B 119 PHE 0.015 0.002 PHE A 279 TYR 0.008 0.001 TYR F 112 ARG 0.003 0.001 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.04967 ( 633) hydrogen bonds : angle 4.78280 ( 1722) covalent geometry : bond 0.00346 (12306) covalent geometry : angle 0.51404 (16596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7807 (m-30) cc_final: 0.7570 (t70) REVERT: A 77 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7611 (tp30) REVERT: A 106 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8232 (mp) REVERT: A 156 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: A 205 GLN cc_start: 0.8725 (mt0) cc_final: 0.8372 (tm130) REVERT: A 220 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 56 LYS cc_start: 0.8033 (mttm) cc_final: 0.7778 (mmpt) REVERT: B 67 ASP cc_start: 0.7844 (m-30) cc_final: 0.7592 (t70) REVERT: B 77 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: B 125 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7955 (mp-120) REVERT: B 156 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8053 (mt-10) REVERT: B 205 GLN cc_start: 0.8639 (mt0) cc_final: 0.8182 (tm130) REVERT: C 122 HIS cc_start: 0.7805 (m170) cc_final: 0.7095 (t-90) REVERT: C 125 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7612 (mp-120) REVERT: C 216 GLU cc_start: 0.8069 (pm20) cc_final: 0.7780 (mp0) REVERT: C 221 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8236 (mt-10) REVERT: D 56 LYS cc_start: 0.8068 (mttm) cc_final: 0.7782 (mmpt) REVERT: D 67 ASP cc_start: 0.7900 (m-30) cc_final: 0.7576 (t70) REVERT: D 156 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: E 122 HIS cc_start: 0.7916 (m170) cc_final: 0.7055 (t-170) REVERT: F 67 ASP cc_start: 0.7743 (m-30) cc_final: 0.7536 (t70) REVERT: F 77 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: F 122 HIS cc_start: 0.7882 (m170) cc_final: 0.7373 (t-90) REVERT: F 125 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8099 (mp-120) REVERT: F 156 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: F 205 GLN cc_start: 0.8671 (mt0) cc_final: 0.8293 (tm130) REVERT: F 216 GLU cc_start: 0.8003 (pm20) cc_final: 0.7649 (mp0) outliers start: 27 outliers final: 13 residues processed: 172 average time/residue: 2.9408 time to fit residues: 546.7878 Evaluate side-chains 171 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 288 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 77 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 28 optimal weight: 0.0970 chunk 41 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN B 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.122421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.103652 restraints weight = 32289.297| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.11 r_work: 0.2964 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.42 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12306 Z= 0.196 Angle : 0.561 5.228 16596 Z= 0.314 Chirality : 0.043 0.172 1866 Planarity : 0.004 0.039 2124 Dihedral : 13.230 119.384 1956 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.11 % Allowed : 11.06 % Favored : 86.83 % 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: 0.88 (0.21), residues: 1548 helix: 1.10 (0.18), residues: 750 sheet: 0.50 (0.48), residues: 156 loop : 0.13 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 120 HIS 0.004 0.001 HIS B 119 PHE 0.016 0.002 PHE D 279 TYR 0.009 0.002 TYR D 137 ARG 0.004 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.05490 ( 633) hydrogen bonds : angle 4.87665 ( 1722) covalent geometry : bond 0.00427 (12306) covalent geometry : angle 0.56123 (16596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.914 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7609 (tp30) REVERT: A 106 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8232 (mp) REVERT: A 156 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: A 205 GLN cc_start: 0.8704 (mt0) cc_final: 0.8353 (tm130) REVERT: A 220 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7742 (mm-30) REVERT: B 67 ASP cc_start: 0.7855 (m-30) cc_final: 0.7616 (t70) REVERT: B 77 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7711 (tt0) REVERT: B 125 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7931 (mp-120) REVERT: B 156 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8043 (mt-10) REVERT: B 205 GLN cc_start: 0.8629 (mt0) cc_final: 0.8202 (tm130) REVERT: C 122 HIS cc_start: 0.7847 (m170) cc_final: 0.7172 (t-90) REVERT: C 125 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7587 (mp-120) REVERT: C 216 GLU cc_start: 0.8042 (pm20) cc_final: 0.7779 (mp0) REVERT: C 221 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: D 56 LYS cc_start: 0.8080 (mttm) cc_final: 0.7772 (mmmm) REVERT: D 67 ASP cc_start: 0.7881 (m-30) cc_final: 0.7582 (t70) REVERT: D 77 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: D 156 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: E 122 HIS cc_start: 0.7941 (m170) cc_final: 0.7114 (t-170) REVERT: F 77 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7402 (tp30) REVERT: F 122 HIS cc_start: 0.7917 (m170) cc_final: 0.7415 (t-90) REVERT: F 125 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8135 (mp-120) REVERT: F 156 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: F 205 GLN cc_start: 0.8657 (mt0) cc_final: 0.8279 (tm130) REVERT: F 216 GLU cc_start: 0.7997 (pm20) cc_final: 0.7652 (mp0) outliers start: 26 outliers final: 12 residues processed: 169 average time/residue: 2.9697 time to fit residues: 547.9316 Evaluate side-chains 169 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 288 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 70 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN B 44 ASN C 44 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.122829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.104120 restraints weight = 32299.594| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.11 r_work: 0.2953 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12306 Z= 0.177 Angle : 0.535 5.003 16596 Z= 0.299 Chirality : 0.042 0.161 1866 Planarity : 0.004 0.035 2124 Dihedral : 12.960 118.818 1956 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.11 % Allowed : 11.06 % Favored : 86.83 % 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: 0.88 (0.21), residues: 1548 helix: 1.12 (0.18), residues: 756 sheet: 0.45 (0.48), residues: 156 loop : 0.11 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 120 HIS 0.003 0.001 HIS B 119 PHE 0.015 0.002 PHE D 279 TYR 0.009 0.001 TYR D 35 ARG 0.003 0.001 ARG C 181 Details of bonding type rmsd hydrogen bonds : bond 0.05170 ( 633) hydrogen bonds : angle 4.82602 ( 1722) covalent geometry : bond 0.00383 (12306) covalent geometry : angle 0.53522 (16596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.909 Fit side-chains revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: A 106 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8210 (mp) REVERT: A 156 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: A 205 GLN cc_start: 0.8722 (mt0) cc_final: 0.8389 (tm130) REVERT: A 220 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7744 (mm-30) REVERT: B 56 LYS cc_start: 0.8042 (mttm) cc_final: 0.7810 (mmpt) REVERT: B 67 ASP cc_start: 0.7842 (m-30) cc_final: 0.7615 (t70) REVERT: B 77 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7707 (tt0) REVERT: B 125 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7996 (mp-120) REVERT: B 156 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: B 205 GLN cc_start: 0.8622 (mt0) cc_final: 0.8208 (tm130) REVERT: C 122 HIS cc_start: 0.7815 (m170) cc_final: 0.7121 (t-90) REVERT: C 125 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7619 (mp-120) REVERT: C 216 GLU cc_start: 0.8056 (pm20) cc_final: 0.7784 (mp0) REVERT: C 221 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: D 56 LYS cc_start: 0.8062 (mttm) cc_final: 0.7801 (mmpt) REVERT: D 67 ASP cc_start: 0.7884 (m-30) cc_final: 0.7601 (t70) REVERT: D 77 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: D 156 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8088 (mt-10) REVERT: E 122 HIS cc_start: 0.7918 (m170) cc_final: 0.7084 (t-170) REVERT: F 77 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: F 122 HIS cc_start: 0.7893 (m170) cc_final: 0.7413 (t-90) REVERT: F 125 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8107 (mp-120) REVERT: F 156 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7999 (mt-10) REVERT: F 205 GLN cc_start: 0.8681 (mt0) cc_final: 0.8313 (tm130) REVERT: F 216 GLU cc_start: 0.8004 (pm20) cc_final: 0.7656 (mp0) outliers start: 26 outliers final: 12 residues processed: 169 average time/residue: 2.9479 time to fit residues: 540.3736 Evaluate side-chains 169 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 125 GLN Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 243 SER Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 125 GLN Chi-restraints excluded: chain C residue 221 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 260 LYS Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 125 GLN Chi-restraints excluded: chain F residue 156 GLU Chi-restraints excluded: chain F residue 288 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 32 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN B 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.122553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.103843 restraints weight = 32282.867| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.10 r_work: 0.2976 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12306 Z= 0.186 Angle : 0.549 5.006 16596 Z= 0.306 Chirality : 0.042 0.164 1866 Planarity : 0.004 0.036 2124 Dihedral : 13.067 118.991 1956 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.03 % Allowed : 11.14 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1548 helix: 1.09 (0.18), residues: 756 sheet: 0.49 (0.48), residues: 156 loop : 0.10 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 120 HIS 0.004 0.001 HIS B 119 PHE 0.016 0.002 PHE D 279 TYR 0.009 0.002 TYR D 137 ARG 0.004 0.001 ARG A 181 Details of bonding type rmsd hydrogen bonds : bond 0.05311 ( 633) hydrogen bonds : angle 4.84785 ( 1722) covalent geometry : bond 0.00405 (12306) covalent geometry : angle 0.54871 (16596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16758.53 seconds wall clock time: 287 minutes 8.73 seconds (17228.73 seconds total)