Starting phenix.real_space_refine on Fri Sep 19 06:42:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrx_60408/09_2025/8zrx_60408_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrx_60408/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zrx_60408/09_2025/8zrx_60408_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrx_60408/09_2025/8zrx_60408_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zrx_60408/09_2025/8zrx_60408.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrx_60408/09_2025/8zrx_60408.map" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.94, per 1000 atoms: 0.20 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: 1.94 Conformation dependent library (CDL) restraints added in 689.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.44 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: 5.67 Time building geometry restraints manager: 2.79 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 301) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 31 through 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: 1.320 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: 0.160 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.210 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (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 ARG 0.001 0.000 ARG D 41 TYR 0.020 0.001 TYR B 112 PHE 0.005 0.000 PHE F 116 TRP 0.004 0.001 TRP B 120 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00998 (12306) covalent geometry : angle 0.91869 (16596) hydrogen bonds : bond 0.15590 ( 633) hydrogen bonds : angle 6.87138 ( 1722) *********************** 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 : 0.603 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: 1.2660 time to fit residues: 498.6937 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3543 r_free = 0.3543 target = 0.135599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.116671 restraints weight = 31622.456| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.11 r_work: 0.3176 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12306 Z= 0.118 Angle : 0.484 4.603 16596 Z= 0.262 Chirality : 0.040 0.163 1866 Planarity : 0.003 0.027 2124 Dihedral : 11.937 133.952 1956 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.38 % Allowed : 11.30 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.22), residues: 1548 helix: 1.57 (0.20), residues: 744 sheet: -0.60 (0.44), residues: 156 loop : 0.27 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 54 TYR 0.013 0.001 TYR B 35 PHE 0.010 0.001 PHE D 279 TRP 0.002 0.000 TRP D 120 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00232 (12306) covalent geometry : angle 0.48353 (16596) hydrogen bonds : bond 0.03514 ( 633) hydrogen bonds : angle 4.62529 ( 1722) *********************** 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 226 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7477 (m-30) cc_final: 0.7262 (t70) REVERT: A 156 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: A 191 MET cc_start: 0.9012 (mtp) cc_final: 0.8650 (mtp) REVERT: A 205 GLN cc_start: 0.8544 (mt0) cc_final: 0.8140 (tm130) REVERT: A 220 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 290 GLN cc_start: 0.7369 (pt0) cc_final: 0.7146 (pt0) REVERT: B 34 GLU cc_start: 0.7709 (pt0) cc_final: 0.7448 (pt0) REVERT: B 156 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: B 205 GLN cc_start: 0.8536 (mt0) cc_final: 0.8094 (tm130) REVERT: B 216 GLU cc_start: 0.7908 (mp0) cc_final: 0.7706 (mp0) REVERT: C 107 SER cc_start: 0.8409 (t) cc_final: 0.8207 (p) REVERT: C 122 HIS cc_start: 0.7548 (m170) cc_final: 0.7043 (t-90) REVERT: C 216 GLU cc_start: 0.8009 (pm20) cc_final: 0.7744 (mp0) REVERT: C 288 LYS cc_start: 0.7600 (mmtm) cc_final: 0.6969 (mppt) REVERT: D 67 ASP cc_start: 0.7903 (m-30) cc_final: 0.7516 (t70) REVERT: D 156 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: D 286 ASN cc_start: 0.8356 (m110) cc_final: 0.8120 (m-40) REVERT: D 288 LYS cc_start: 0.7820 (mmtm) cc_final: 0.6754 (mppt) REVERT: E 67 ASP cc_start: 0.7615 (m-30) cc_final: 0.7382 (t70) REVERT: E 122 HIS cc_start: 0.7656 (m170) cc_final: 0.6856 (t-170) REVERT: E 288 LYS cc_start: 0.7999 (mttm) cc_final: 0.7585 (mtmt) REVERT: F 67 ASP cc_start: 0.7832 (m-30) cc_final: 0.7537 (t70) REVERT: F 122 HIS cc_start: 0.7661 (m170) cc_final: 0.7356 (t-90) REVERT: F 191 MET cc_start: 0.9023 (mtp) cc_final: 0.8666 (mtp) REVERT: F 205 GLN cc_start: 0.8569 (mt0) cc_final: 0.8224 (tm130) REVERT: F 216 GLU cc_start: 0.7903 (pm20) cc_final: 0.7483 (mp0) REVERT: F 242 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8033 (mt-10) outliers start: 17 outliers final: 8 residues processed: 221 average time/residue: 1.2986 time to fit residues: 308.8301 Evaluate side-chains 192 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 181 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 83 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 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 B 105 ASN D 44 ASN D 104 GLN 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 = 0.3404 r_free = 0.3404 target = 0.124758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.105909 restraints weight = 31389.614| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.05 r_work: 0.3011 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12306 Z= 0.182 Angle : 0.559 4.734 16596 Z= 0.311 Chirality : 0.042 0.189 1866 Planarity : 0.004 0.038 2124 Dihedral : 13.140 117.508 1956 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.44 % Allowed : 10.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.21), residues: 1548 helix: 1.39 (0.19), residues: 744 sheet: -0.12 (0.45), residues: 156 loop : 0.35 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 197 TYR 0.009 0.001 TYR F 112 PHE 0.018 0.002 PHE C 279 TRP 0.004 0.001 TRP A 120 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd covalent geometry : bond 0.00397 (12306) covalent geometry : angle 0.55882 (16596) hydrogen bonds : bond 0.05260 ( 633) hydrogen bonds : angle 4.85012 ( 1722) *********************** 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 217 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7903 (m-30) cc_final: 0.7653 (t70) REVERT: A 106 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 156 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: A 205 GLN cc_start: 0.8604 (mt0) cc_final: 0.8263 (tm130) REVERT: A 288 LYS cc_start: 0.8232 (mptt) cc_final: 0.7856 (mptt) REVERT: A 290 GLN cc_start: 0.7821 (pt0) cc_final: 0.7617 (pt0) REVERT: B 34 GLU cc_start: 0.7817 (pt0) cc_final: 0.7540 (pt0) REVERT: B 67 ASP cc_start: 0.7908 (m-30) cc_final: 0.7609 (t70) REVERT: B 156 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: B 205 GLN cc_start: 0.8583 (mt0) cc_final: 0.8171 (tm130) REVERT: B 273 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8089 (tttm) REVERT: C 122 HIS cc_start: 0.7923 (m170) cc_final: 0.7186 (t-90) REVERT: C 125 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7641 (mp-120) REVERT: C 216 GLU cc_start: 0.8011 (pm20) cc_final: 0.7799 (mp0) REVERT: D 67 ASP cc_start: 0.7997 (m-30) cc_final: 0.7611 (t70) REVERT: D 156 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: D 276 MET cc_start: 0.8981 (mtt) cc_final: 0.8576 (mtt) REVERT: D 288 LYS cc_start: 0.7984 (mmtm) cc_final: 0.6966 (mppt) REVERT: E 122 HIS cc_start: 0.7907 (m170) cc_final: 0.7087 (t-170) REVERT: E 156 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: F 67 ASP cc_start: 0.7869 (m-30) cc_final: 0.7587 (t70) REVERT: F 77 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: F 122 HIS cc_start: 0.7876 (m170) cc_final: 0.7402 (t-90) REVERT: F 205 GLN cc_start: 0.8615 (mt0) cc_final: 0.8272 (tm130) REVERT: F 216 GLU cc_start: 0.7987 (pm20) cc_final: 0.7623 (mp0) outliers start: 30 outliers final: 12 residues processed: 214 average time/residue: 1.2849 time to fit residues: 296.1003 Evaluate side-chains 183 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 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 273 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 156 GLU Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 156 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 260 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 49 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 32 ASN D 44 ASN D 105 ASN E 44 ASN F 71 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.122312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.103494 restraints weight = 31384.893| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.05 r_work: 0.2977 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 12306 Z= 0.233 Angle : 0.616 5.648 16596 Z= 0.342 Chirality : 0.044 0.185 1866 Planarity : 0.005 0.045 2124 Dihedral : 13.446 120.362 1956 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.93 % Allowed : 10.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.21), residues: 1548 helix: 0.95 (0.18), residues: 744 sheet: 0.22 (0.46), residues: 156 loop : 0.22 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 181 TYR 0.015 0.002 TYR D 137 PHE 0.016 0.003 PHE F 279 TRP 0.003 0.001 TRP D 120 HIS 0.006 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00511 (12306) covalent geometry : angle 0.61627 (16596) hydrogen bonds : bond 0.05833 ( 633) hydrogen bonds : angle 4.97085 ( 1722) *********************** 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 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7929 (m-30) cc_final: 0.7613 (t70) REVERT: A 106 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8304 (mp) REVERT: A 156 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: A 205 GLN cc_start: 0.8711 (mt0) cc_final: 0.8342 (tm130) REVERT: A 220 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7773 (mm-30) REVERT: B 34 GLU cc_start: 0.7822 (pt0) cc_final: 0.7594 (pt0) REVERT: B 67 ASP cc_start: 0.7896 (m-30) cc_final: 0.7609 (t70) REVERT: B 156 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: B 205 GLN cc_start: 0.8597 (mt0) cc_final: 0.8172 (tm130) REVERT: C 122 HIS cc_start: 0.7886 (m170) cc_final: 0.7161 (t-90) REVERT: C 125 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7598 (mp-120) REVERT: C 216 GLU cc_start: 0.8042 (pm20) cc_final: 0.7811 (mp0) REVERT: C 221 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: C 288 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7920 (mmtt) REVERT: D 67 ASP cc_start: 0.7963 (m-30) cc_final: 0.7625 (t70) REVERT: D 156 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: D 216 GLU cc_start: 0.8006 (mp0) cc_final: 0.7758 (mp0) REVERT: D 276 MET cc_start: 0.9143 (mtt) cc_final: 0.8928 (mtt) REVERT: D 288 LYS cc_start: 0.8124 (mmtm) cc_final: 0.7268 (mppt) REVERT: E 122 HIS cc_start: 0.7986 (m170) cc_final: 0.7169 (t-170) REVERT: F 67 ASP cc_start: 0.7912 (m-30) cc_final: 0.7686 (t70) REVERT: F 122 HIS cc_start: 0.7949 (m170) cc_final: 0.7414 (t-90) REVERT: F 125 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8082 (mp-120) REVERT: F 156 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8013 (mt-10) REVERT: F 205 GLN cc_start: 0.8631 (mt0) cc_final: 0.8261 (tm130) REVERT: F 216 GLU cc_start: 0.8038 (pm20) cc_final: 0.7645 (mp0) outliers start: 36 outliers final: 15 residues processed: 194 average time/residue: 1.3549 time to fit residues: 283.4487 Evaluate side-chains 174 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 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 C residue 288 LYS 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 260 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 82 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 C 44 ASN D 44 ASN D 224 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.123309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.104660 restraints weight = 31209.787| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.05 r_work: 0.2996 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12306 Z= 0.166 Angle : 0.523 5.182 16596 Z= 0.292 Chirality : 0.042 0.160 1866 Planarity : 0.004 0.033 2124 Dihedral : 12.778 117.600 1956 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.28 % Allowed : 10.49 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.21), residues: 1548 helix: 1.16 (0.18), residues: 756 sheet: 0.30 (0.47), residues: 156 loop : 0.23 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 181 TYR 0.009 0.001 TYR D 137 PHE 0.015 0.002 PHE F 279 TRP 0.001 0.000 TRP E 120 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00357 (12306) covalent geometry : angle 0.52340 (16596) hydrogen bonds : bond 0.05000 ( 633) hydrogen bonds : angle 4.78359 ( 1722) *********************** 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 184 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7845 (m-30) cc_final: 0.7605 (t70) REVERT: A 77 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7740 (tp30) REVERT: A 156 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: A 205 GLN cc_start: 0.8699 (mt0) cc_final: 0.8360 (tm130) REVERT: A 220 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7711 (mm-30) REVERT: B 34 GLU cc_start: 0.7801 (pt0) cc_final: 0.7570 (pt0) REVERT: B 67 ASP cc_start: 0.7889 (m-30) cc_final: 0.7599 (t70) REVERT: B 77 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7479 (tt0) REVERT: B 125 GLN cc_start: 0.8333 (OUTLIER) cc_final: 0.7914 (mp-120) REVERT: B 156 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: B 205 GLN cc_start: 0.8630 (mt0) cc_final: 0.8200 (tm130) REVERT: C 122 HIS cc_start: 0.7868 (m170) cc_final: 0.7195 (t-90) REVERT: C 125 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7593 (mp-120) REVERT: C 216 GLU cc_start: 0.8067 (pm20) cc_final: 0.7821 (mp0) REVERT: D 67 ASP cc_start: 0.7942 (m-30) cc_final: 0.7608 (t70) REVERT: D 156 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: D 216 GLU cc_start: 0.8003 (mp0) cc_final: 0.7747 (mp0) REVERT: D 276 MET cc_start: 0.9136 (mtt) cc_final: 0.8877 (mtt) REVERT: D 288 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7274 (mppt) REVERT: E 122 HIS cc_start: 0.7946 (m170) cc_final: 0.7114 (t-170) REVERT: F 67 ASP cc_start: 0.7854 (m-30) cc_final: 0.7633 (t70) REVERT: F 77 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7452 (tt0) REVERT: F 122 HIS cc_start: 0.7913 (m170) cc_final: 0.7426 (t-90) REVERT: F 125 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.8040 (mp-120) REVERT: F 156 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: F 205 GLN cc_start: 0.8664 (mt0) cc_final: 0.8300 (tm130) REVERT: F 216 GLU cc_start: 0.8005 (pm20) cc_final: 0.7649 (mp0) outliers start: 28 outliers final: 12 residues processed: 180 average time/residue: 1.3098 time to fit residues: 254.0183 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 : 0.602 ------------------------------------------------------------------------------- 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 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 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 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 260 LYS 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 152 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 D 44 ASN D 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103075 restraints weight = 31320.672| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.05 r_work: 0.2973 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12306 Z= 0.223 Angle : 0.595 5.735 16596 Z= 0.332 Chirality : 0.044 0.180 1866 Planarity : 0.005 0.047 2124 Dihedral : 13.479 120.567 1956 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.36 % Allowed : 10.65 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.21), residues: 1548 helix: 0.96 (0.18), residues: 738 sheet: 0.42 (0.47), residues: 156 loop : 0.14 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 181 TYR 0.011 0.002 TYR D 137 PHE 0.017 0.002 PHE B 279 TRP 0.002 0.001 TRP E 120 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00488 (12306) covalent geometry : angle 0.59506 (16596) hydrogen bonds : bond 0.05799 ( 633) hydrogen bonds : angle 4.93875 ( 1722) *********************** 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 : 0.617 Fit side-chains REVERT: A 67 ASP cc_start: 0.7827 (m-30) cc_final: 0.7573 (t70) REVERT: A 106 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8287 (mp) REVERT: A 156 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: A 205 GLN cc_start: 0.8701 (mt0) cc_final: 0.8340 (tm130) REVERT: A 220 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7726 (mm-30) REVERT: B 67 ASP cc_start: 0.7924 (m-30) cc_final: 0.7612 (t70) REVERT: B 125 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7903 (mp-120) REVERT: B 156 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: B 205 GLN cc_start: 0.8660 (mt0) cc_final: 0.8212 (tm130) REVERT: C 122 HIS cc_start: 0.7895 (m170) cc_final: 0.7158 (t-90) REVERT: C 125 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7551 (mp-120) REVERT: C 216 GLU cc_start: 0.8080 (pm20) cc_final: 0.7810 (mp0) REVERT: D 67 ASP cc_start: 0.7921 (m-30) cc_final: 0.7604 (t70) REVERT: D 77 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: D 125 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7992 (mp-120) REVERT: D 156 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: D 216 GLU cc_start: 0.8001 (mp0) cc_final: 0.7752 (mp0) REVERT: D 276 MET cc_start: 0.9172 (mtt) cc_final: 0.8928 (mtt) REVERT: D 288 LYS cc_start: 0.8118 (mmtm) cc_final: 0.7221 (mppt) REVERT: E 122 HIS cc_start: 0.7986 (m170) cc_final: 0.7143 (t-170) REVERT: F 67 ASP cc_start: 0.7858 (m-30) cc_final: 0.7635 (t70) REVERT: F 122 HIS cc_start: 0.7943 (m170) cc_final: 0.7396 (t-90) REVERT: F 125 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8097 (mp-120) REVERT: F 156 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: F 205 GLN cc_start: 0.8644 (mt0) cc_final: 0.8229 (tm130) REVERT: F 216 GLU cc_start: 0.8047 (pm20) cc_final: 0.7685 (mp0) outliers start: 29 outliers final: 15 residues processed: 177 average time/residue: 1.3142 time to fit residues: 250.8527 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 : 0.638 ------------------------------------------------------------------------------- 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 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 D residue 260 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 243 SER 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 260 LYS 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 49 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 D 224 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.122835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.104276 restraints weight = 31324.336| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.04 r_work: 0.2986 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12306 Z= 0.169 Angle : 0.524 4.892 16596 Z= 0.293 Chirality : 0.042 0.160 1866 Planarity : 0.004 0.033 2124 Dihedral : 12.787 117.948 1956 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.20 % Allowed : 11.14 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.21), residues: 1548 helix: 1.13 (0.18), residues: 756 sheet: 0.41 (0.47), residues: 156 loop : 0.15 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 181 TYR 0.008 0.001 TYR D 137 PHE 0.015 0.002 PHE A 279 TRP 0.001 0.000 TRP E 120 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00365 (12306) covalent geometry : angle 0.52444 (16596) hydrogen bonds : bond 0.05048 ( 633) hydrogen bonds : angle 4.79665 ( 1722) *********************** 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 181 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.422 Fit side-chains REVERT: A 67 ASP cc_start: 0.7763 (m-30) cc_final: 0.7528 (t70) REVERT: A 77 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7823 (tp30) REVERT: A 106 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8242 (mp) REVERT: A 156 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: A 205 GLN cc_start: 0.8710 (mt0) cc_final: 0.8370 (tm130) REVERT: A 220 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7721 (mm-30) REVERT: B 56 LYS cc_start: 0.8004 (mttm) cc_final: 0.7776 (mmpt) REVERT: B 67 ASP cc_start: 0.7888 (m-30) cc_final: 0.7623 (t70) REVERT: B 77 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7566 (tt0) REVERT: B 125 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7964 (mp-120) REVERT: B 156 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: B 205 GLN cc_start: 0.8642 (mt0) cc_final: 0.8222 (tm130) REVERT: B 276 MET cc_start: 0.9111 (mtt) cc_final: 0.8700 (mtt) REVERT: C 122 HIS cc_start: 0.7838 (m170) cc_final: 0.7119 (t-90) REVERT: C 125 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7583 (mp-120) REVERT: C 216 GLU cc_start: 0.8087 (pm20) cc_final: 0.7804 (mp0) REVERT: D 67 ASP cc_start: 0.7917 (m-30) cc_final: 0.7611 (t70) REVERT: D 125 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8040 (mp-120) REVERT: D 156 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: D 276 MET cc_start: 0.9155 (mtt) cc_final: 0.8898 (mtt) REVERT: D 288 LYS cc_start: 0.8095 (mmtm) cc_final: 0.7287 (mppt) REVERT: E 122 HIS cc_start: 0.7974 (m170) cc_final: 0.7116 (t-170) REVERT: F 67 ASP cc_start: 0.7828 (m-30) cc_final: 0.7611 (t70) REVERT: F 77 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: F 122 HIS cc_start: 0.7911 (m170) cc_final: 0.7416 (t-90) REVERT: F 125 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.8080 (mp-120) REVERT: F 156 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: F 205 GLN cc_start: 0.8688 (mt0) cc_final: 0.8305 (tm130) REVERT: F 216 GLU cc_start: 0.8043 (pm20) cc_final: 0.7683 (mp0) outliers start: 27 outliers final: 14 residues processed: 176 average time/residue: 1.2612 time to fit residues: 239.5878 Evaluate side-chains 175 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 D residue 63 ASP Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 260 LYS 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 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 260 LYS 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 125 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.122009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.102564 restraints weight = 31908.429| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.15 r_work: 0.2977 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 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 : 0.004 0.042 12306 Z= 0.176 Angle : 0.538 4.925 16596 Z= 0.300 Chirality : 0.042 0.161 1866 Planarity : 0.004 0.034 2124 Dihedral : 12.994 118.504 1956 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.36 % Allowed : 11.06 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.21), residues: 1548 helix: 1.16 (0.18), residues: 750 sheet: 0.44 (0.48), residues: 156 loop : 0.18 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 181 TYR 0.009 0.001 TYR D 137 PHE 0.016 0.002 PHE B 279 TRP 0.002 0.000 TRP E 120 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00380 (12306) covalent geometry : angle 0.53792 (16596) hydrogen bonds : bond 0.05194 ( 633) hydrogen bonds : angle 4.80843 ( 1722) *********************** 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 178 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: A 67 ASP cc_start: 0.7724 (m-30) cc_final: 0.7456 (t70) REVERT: A 77 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7846 (tp30) REVERT: A 106 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8189 (mp) REVERT: A 156 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8037 (mt-10) REVERT: A 205 GLN cc_start: 0.8721 (mt0) cc_final: 0.8296 (tm130) REVERT: A 220 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7696 (mm-30) REVERT: B 56 LYS cc_start: 0.7995 (mttm) cc_final: 0.7723 (mmpt) REVERT: B 67 ASP cc_start: 0.7881 (m-30) cc_final: 0.7518 (t70) REVERT: B 77 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: B 125 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7910 (mp-120) REVERT: B 156 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: B 189 MET cc_start: 0.9462 (mmt) cc_final: 0.9244 (mmt) REVERT: B 205 GLN cc_start: 0.8623 (mt0) cc_final: 0.8146 (tm130) REVERT: B 276 MET cc_start: 0.9086 (mtt) cc_final: 0.8677 (mtt) REVERT: C 122 HIS cc_start: 0.7847 (m170) cc_final: 0.7080 (t-90) REVERT: C 125 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7578 (mp-120) REVERT: C 216 GLU cc_start: 0.8076 (pm20) cc_final: 0.7787 (mp0) REVERT: C 221 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: D 67 ASP cc_start: 0.7887 (m-30) cc_final: 0.7503 (t70) REVERT: D 125 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7996 (mp-120) REVERT: D 156 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8113 (mt-10) REVERT: D 276 MET cc_start: 0.9126 (mtt) cc_final: 0.8861 (mtt) REVERT: D 288 LYS cc_start: 0.8089 (mmtm) cc_final: 0.7251 (mppt) REVERT: E 122 HIS cc_start: 0.7965 (m170) cc_final: 0.7066 (t-170) REVERT: F 67 ASP cc_start: 0.7721 (m-30) cc_final: 0.7488 (t70) REVERT: F 122 HIS cc_start: 0.7859 (m170) cc_final: 0.7314 (t-90) REVERT: F 125 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8057 (mp-120) REVERT: F 156 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: F 205 GLN cc_start: 0.8652 (mt0) cc_final: 0.8220 (tm130) REVERT: F 216 GLU cc_start: 0.8044 (pm20) cc_final: 0.7676 (mp0) outliers start: 29 outliers final: 15 residues processed: 173 average time/residue: 1.2596 time to fit residues: 235.7067 Evaluate side-chains 175 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 125 GLN Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain D residue 260 LYS 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 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 260 LYS 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 61 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.121705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102307 restraints weight = 31704.564| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.14 r_work: 0.2973 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12306 Z= 0.196 Angle : 0.558 5.139 16596 Z= 0.311 Chirality : 0.043 0.171 1866 Planarity : 0.004 0.038 2124 Dihedral : 13.133 119.038 1956 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.36 % Allowed : 10.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.21), residues: 1548 helix: 1.09 (0.18), residues: 750 sheet: 0.45 (0.48), residues: 156 loop : 0.15 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 181 TYR 0.009 0.002 TYR D 137 PHE 0.016 0.002 PHE B 279 TRP 0.002 0.000 TRP E 120 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00427 (12306) covalent geometry : angle 0.55839 (16596) hydrogen bonds : bond 0.05430 ( 633) hydrogen bonds : angle 4.85253 ( 1722) *********************** 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 177 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.527 Fit side-chains REVERT: A 67 ASP cc_start: 0.7741 (m-30) cc_final: 0.7482 (t70) REVERT: A 106 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8187 (mp) REVERT: A 156 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: A 205 GLN cc_start: 0.8724 (mt0) cc_final: 0.8308 (tm130) REVERT: A 220 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7694 (mm-30) REVERT: B 56 LYS cc_start: 0.7996 (mttm) cc_final: 0.7727 (mmpt) REVERT: B 67 ASP cc_start: 0.7903 (m-30) cc_final: 0.7561 (t70) REVERT: B 77 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: B 125 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7917 (mp-120) REVERT: B 156 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: B 205 GLN cc_start: 0.8623 (mt0) cc_final: 0.8155 (tm130) REVERT: B 276 MET cc_start: 0.9095 (mtt) cc_final: 0.8689 (mtt) REVERT: C 122 HIS cc_start: 0.7852 (m170) cc_final: 0.7088 (t-90) REVERT: C 125 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7580 (mp-120) REVERT: C 216 GLU cc_start: 0.8074 (pm20) cc_final: 0.7785 (mp0) REVERT: C 221 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: D 67 ASP cc_start: 0.7900 (m-30) cc_final: 0.7530 (t70) REVERT: D 77 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: D 125 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7980 (mp-120) REVERT: D 156 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: D 276 MET cc_start: 0.9138 (mtt) cc_final: 0.8885 (mtt) REVERT: E 122 HIS cc_start: 0.7976 (m170) cc_final: 0.7097 (t-170) REVERT: F 67 ASP cc_start: 0.7730 (m-30) cc_final: 0.7506 (t70) REVERT: F 77 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: F 122 HIS cc_start: 0.7872 (m170) cc_final: 0.7324 (t-90) REVERT: F 125 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8080 (mp-120) REVERT: F 156 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: F 205 GLN cc_start: 0.8631 (mt0) cc_final: 0.8198 (tm130) REVERT: F 216 GLU cc_start: 0.8055 (pm20) cc_final: 0.7685 (mp0) outliers start: 29 outliers final: 13 residues processed: 172 average time/residue: 1.2825 time to fit residues: 238.0908 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 : 0.538 ------------------------------------------------------------------------------- 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 D residue 260 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 243 SER 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 260 LYS 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 57 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.101879 restraints weight = 32088.593| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.15 r_work: 0.2967 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12306 Z= 0.212 Angle : 0.575 5.398 16596 Z= 0.321 Chirality : 0.043 0.174 1866 Planarity : 0.004 0.041 2124 Dihedral : 13.250 119.598 1956 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.11 % Allowed : 11.22 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.21), residues: 1548 helix: 1.04 (0.18), residues: 750 sheet: 0.47 (0.48), residues: 156 loop : 0.12 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 181 TYR 0.009 0.002 TYR D 137 PHE 0.017 0.002 PHE B 279 TRP 0.002 0.000 TRP E 120 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00463 (12306) covalent geometry : angle 0.57515 (16596) hydrogen bonds : bond 0.05585 ( 633) hydrogen bonds : angle 4.88716 ( 1722) ********************** 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 176 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.506 Fit side-chains REVERT: A 67 ASP cc_start: 0.7743 (m-30) cc_final: 0.7482 (t70) REVERT: A 106 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8193 (mp) REVERT: A 156 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: A 205 GLN cc_start: 0.8726 (mt0) cc_final: 0.8302 (tm130) REVERT: A 220 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7699 (mm-30) REVERT: B 56 LYS cc_start: 0.7975 (mttm) cc_final: 0.7697 (mmpt) REVERT: B 67 ASP cc_start: 0.7903 (m-30) cc_final: 0.7555 (t70) REVERT: B 125 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7914 (mp-120) REVERT: B 156 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: B 205 GLN cc_start: 0.8631 (mt0) cc_final: 0.8151 (tm130) REVERT: B 276 MET cc_start: 0.9099 (mtt) cc_final: 0.8695 (mtt) REVERT: C 122 HIS cc_start: 0.7876 (m170) cc_final: 0.7106 (t-90) REVERT: C 125 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7573 (mp-120) REVERT: C 216 GLU cc_start: 0.8086 (pm20) cc_final: 0.7795 (mp0) REVERT: C 221 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8200 (mt-10) REVERT: D 67 ASP cc_start: 0.7905 (m-30) cc_final: 0.7526 (t70) REVERT: D 77 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7396 (tt0) REVERT: D 125 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8013 (mp-120) REVERT: D 156 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8156 (mt-10) REVERT: D 276 MET cc_start: 0.9138 (mtt) cc_final: 0.8886 (mtt) REVERT: E 122 HIS cc_start: 0.7989 (m170) cc_final: 0.7095 (t-170) REVERT: F 67 ASP cc_start: 0.7734 (m-30) cc_final: 0.7504 (t70) REVERT: F 122 HIS cc_start: 0.7876 (m170) cc_final: 0.7313 (t-90) REVERT: F 125 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8077 (mp-120) REVERT: F 156 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: F 205 GLN cc_start: 0.8636 (mt0) cc_final: 0.8190 (tm130) REVERT: F 216 GLU cc_start: 0.8052 (pm20) cc_final: 0.7682 (mp0) outliers start: 26 outliers final: 15 residues processed: 171 average time/residue: 1.3108 time to fit residues: 242.0204 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 : 0.531 ------------------------------------------------------------------------------- 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 D residue 260 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 243 SER 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 260 LYS 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 114 optimal weight: 5.9990 chunk 146 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 120 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 F 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.106061 restraints weight = 32093.662| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.10 r_work: 0.2985 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12306 Z= 0.142 Angle : 0.497 4.807 16596 Z= 0.277 Chirality : 0.041 0.140 1866 Planarity : 0.003 0.032 2124 Dihedral : 12.588 117.391 1956 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.11 % Allowed : 11.22 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.21), residues: 1548 helix: 1.27 (0.18), residues: 756 sheet: 0.41 (0.48), residues: 156 loop : 0.17 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 272 TYR 0.007 0.001 TYR B 35 PHE 0.014 0.001 PHE F 279 TRP 0.001 0.000 TRP E 120 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00304 (12306) covalent geometry : angle 0.49673 (16596) hydrogen bonds : bond 0.04684 ( 633) hydrogen bonds : angle 4.70932 ( 1722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8173.15 seconds wall clock time: 138 minutes 43.50 seconds (8323.50 seconds total)