Starting phenix.real_space_refine on Sat Aug 23 12:16:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zrw_60407/08_2025/8zrw_60407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zrw_60407/08_2025/8zrw_60407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zrw_60407/08_2025/8zrw_60407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zrw_60407/08_2025/8zrw_60407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zrw_60407/08_2025/8zrw_60407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zrw_60407/08_2025/8zrw_60407.map" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.137 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 2 5.21 5 S 90 5.16 5 C 7626 2.51 5 N 2040 2.21 5 O 2394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12170 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "B" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "C" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "D" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "E" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "F" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {' MG': 1, 'CO8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CO8': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CO8': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CO8': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {' MG': 1, 'CO8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'CO8': 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: 3.56, per 1000 atoms: 0.29 Number of scatterers: 12170 At special positions: 0 Unit cell: (92.288, 98.88, 93.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 18 15.00 Mg 2 11.99 O 2394 8.00 N 2040 7.00 C 7626 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 608.9 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: 90 helices and 13 sheets defined 56.8% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 62 through 78 Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.517A pdb=" N MET A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.690A pdb=" N TYR A 112 " --> pdb=" O PHE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 removed outlier: 4.102A pdb=" N LEU A 123 " --> pdb=" O TRP A 120 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 126 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 162 through 168 removed outlier: 4.217A pdb=" N ILE A 165 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 removed outlier: 3.602A pdb=" N ALA A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 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 267 removed outlier: 4.097A pdb=" N PHE A 267 " --> pdb=" O PHE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.215A pdb=" N LYS A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.833A pdb=" N TYR B 112 " --> pdb=" O PHE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 removed outlier: 4.448A pdb=" N LEU B 123 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 126 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 Processing helix chain 'B' and resid 162 through 168 removed outlier: 4.244A pdb=" N ILE B 165 " --> pdb=" O GLN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 184 Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 200 through 206 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: 3.968A pdb=" N PHE B 267 " --> pdb=" O PHE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 282 removed outlier: 4.050A 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 removed outlier: 3.512A pdb=" N MET C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 114 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.655A pdb=" N CYS C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 removed outlier: 4.185A pdb=" N ILE C 165 " --> pdb=" O GLN C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 184 Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 200 through 207 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: 4.011A pdb=" N PHE C 267 " --> pdb=" O PHE C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 281 removed outlier: 3.910A 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 62 through 79 Processing helix chain 'D' and resid 99 through 104 Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.592A pdb=" N TYR D 112 " --> pdb=" O PHE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 removed outlier: 4.193A pdb=" N LEU D 123 " --> pdb=" O TRP D 120 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 149 Processing helix chain 'D' and resid 162 through 168 removed outlier: 4.229A pdb=" N ILE D 165 " --> pdb=" O GLN D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 195 removed outlier: 7.428A pdb=" N LYS D 185 " --> pdb=" O ARG D 181 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N SER D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU D 187 " --> pdb=" O VAL D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 217 through 230 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: 3.950A pdb=" N PHE D 267 " --> pdb=" O PHE D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 282 removed outlier: 4.087A 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 62 through 79 Processing helix chain 'E' and resid 99 through 104 removed outlier: 3.602A pdb=" N MET E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 114 Processing helix chain 'E' and resid 120 through 126 removed outlier: 4.262A pdb=" N LEU E 123 " --> pdb=" O TRP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 149 removed outlier: 3.680A pdb=" N CYS E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 168 removed outlier: 4.208A pdb=" N ILE E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY E 168 " --> pdb=" O ILE E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 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: 3.862A pdb=" N PHE E 267 " --> pdb=" O PHE E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 281 removed outlier: 4.102A 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 99 through 104 removed outlier: 3.540A pdb=" N MET F 103 " --> pdb=" O ASP F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 120 through 124 removed outlier: 4.106A pdb=" N LEU F 123 " --> pdb=" O TRP F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 149 removed outlier: 3.625A pdb=" N CYS F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 168 removed outlier: 4.195A pdb=" N ILE F 165 " --> pdb=" O GLN F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 184 removed outlier: 3.613A pdb=" N ALA F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) 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 230 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: 4.039A pdb=" N PHE F 267 " --> pdb=" O PHE F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 281 removed outlier: 4.025A 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: 3.695A pdb=" N VAL A 47 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY A 48 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N THR A 88 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE A 50 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 211 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 95 removed outlier: 7.635A pdb=" N PHE A 139 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 41 removed outlier: 3.650A pdb=" N VAL B 47 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY B 48 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR B 88 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE B 50 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE B 85 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ALA B 133 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU B 87 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 151 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE B 152 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N CYS B 213 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ALA B 154 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 93 through 95 removed outlier: 7.761A pdb=" N PHE B 139 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 161 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 41 removed outlier: 6.504A pdb=" N GLY C 48 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N THR C 88 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE C 50 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE C 152 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N CYS C 213 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA C 154 " --> pdb=" O CYS C 213 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'C' and resid 93 through 95 removed outlier: 7.644A pdb=" N PHE C 139 " --> pdb=" O PHE C 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 36 through 41 removed outlier: 3.585A pdb=" N VAL D 47 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS D 211 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 93 through 95 removed outlier: 7.622A pdb=" N PHE D 139 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 36 through 41 removed outlier: 3.515A pdb=" N VAL E 47 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY E 48 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N THR E 88 " --> pdb=" O GLY E 48 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE E 50 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE E 152 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N CYS E 213 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA E 154 " --> pdb=" O CYS E 213 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 93 through 95 removed outlier: 7.586A pdb=" N PHE E 139 " --> pdb=" O PHE E 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 36 through 41 removed outlier: 3.506A pdb=" N VAL F 47 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY F 48 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR F 88 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE F 50 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE F 152 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N CYS F 213 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA F 154 " --> pdb=" O CYS F 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 93 through 95 removed outlier: 7.630A pdb=" N PHE F 139 " --> pdb=" O PHE F 94 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1728 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: 2.15 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2118 1.29 - 1.43: 2746 1.43 - 1.56: 7262 1.56 - 1.70: 54 1.70 - 1.83: 144 Bond restraints: 12324 Sorted by residual: bond pdb=" C1B CO8 A 301 " pdb=" C2B CO8 A 301 " ideal model delta sigma weight residual 1.534 1.336 0.198 2.00e-02 2.50e+03 9.83e+01 bond pdb=" C1B CO8 C 301 " pdb=" C2B CO8 C 301 " ideal model delta sigma weight residual 1.534 1.336 0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C1B CO8 F 301 " pdb=" C2B CO8 F 301 " ideal model delta sigma weight residual 1.534 1.337 0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C1B CO8 B 301 " pdb=" C2B CO8 B 301 " ideal model delta sigma weight residual 1.534 1.339 0.195 2.00e-02 2.50e+03 9.50e+01 bond pdb=" C1B CO8 E 301 " pdb=" C2B CO8 E 301 " ideal model delta sigma weight residual 1.534 1.339 0.195 2.00e-02 2.50e+03 9.48e+01 ... (remaining 12319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 16430 4.49 - 8.98: 143 8.98 - 13.47: 31 13.47 - 17.96: 2 17.96 - 22.45: 2 Bond angle restraints: 16608 Sorted by residual: angle pdb=" C7P CO8 C 301 " pdb=" N8P CO8 C 301 " pdb=" C9P CO8 C 301 " ideal model delta sigma weight residual 123.01 100.56 22.45 3.00e+00 1.11e-01 5.60e+01 angle pdb=" C7P CO8 A 301 " pdb=" N8P CO8 A 301 " pdb=" C9P CO8 A 301 " ideal model delta sigma weight residual 123.01 102.04 20.97 3.00e+00 1.11e-01 4.89e+01 angle pdb=" C3P CO8 B 301 " pdb=" N4P CO8 B 301 " pdb=" C5P CO8 B 301 " ideal model delta sigma weight residual 123.75 108.30 15.45 3.00e+00 1.11e-01 2.65e+01 angle pdb=" N TYR A 112 " pdb=" CA TYR A 112 " pdb=" C TYR A 112 " ideal model delta sigma weight residual 113.20 107.23 5.97 1.21e+00 6.83e-01 2.43e+01 angle pdb=" O1A CO8 C 301 " pdb=" P1A CO8 C 301 " pdb=" O2A CO8 C 301 " ideal model delta sigma weight residual 119.69 105.98 13.71 3.00e+00 1.11e-01 2.09e+01 ... (remaining 16603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 7213 21.85 - 43.71: 431 43.71 - 65.56: 94 65.56 - 87.41: 8 87.41 - 109.27: 6 Dihedral angle restraints: 7752 sinusoidal: 3300 harmonic: 4452 Sorted by residual: dihedral pdb=" CAP CO8 D 301 " pdb=" CBP CO8 D 301 " pdb=" CCP CO8 D 301 " pdb=" O6A CO8 D 301 " ideal model delta sinusoidal sigma weight residual 56.27 -53.00 109.27 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" CA SER D 113 " pdb=" C SER D 113 " pdb=" N SER D 114 " pdb=" CA SER D 114 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CEP CO8 D 301 " pdb=" CBP CO8 D 301 " pdb=" CCP CO8 D 301 " pdb=" O6A CO8 D 301 " ideal model delta sinusoidal sigma weight residual 175.94 69.48 106.46 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 7749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1681 0.070 - 0.139: 156 0.139 - 0.209: 18 0.209 - 0.279: 3 0.279 - 0.348: 8 Chirality restraints: 1866 Sorted by residual: chirality pdb=" CAP CO8 E 301 " pdb=" C9P CO8 E 301 " pdb=" CBP CO8 E 301 " pdb=" OAP CO8 E 301 " both_signs ideal model delta sigma weight residual False -2.45 -2.80 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" C2B CO8 C 301 " pdb=" C1B CO8 C 301 " pdb=" C3B CO8 C 301 " pdb=" O2B CO8 C 301 " both_signs ideal model delta sigma weight residual False -2.45 -2.11 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C2B CO8 B 301 " pdb=" C1B CO8 B 301 " pdb=" C3B CO8 B 301 " pdb=" O2B CO8 B 301 " both_signs ideal model delta sigma weight residual False -2.45 -2.13 -0.32 2.00e-01 2.50e+01 2.60e+00 ... (remaining 1863 not shown) Planarity restraints: 2118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 111 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C CYS A 111 " -0.064 2.00e-02 2.50e+03 pdb=" O CYS A 111 " 0.025 2.00e-02 2.50e+03 pdb=" N TYR A 112 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B CO8 E 301 " 0.023 2.00e-02 2.50e+03 1.11e-02 3.37e+00 pdb=" C2A CO8 E 301 " 0.002 2.00e-02 2.50e+03 pdb=" C4A CO8 E 301 " -0.005 2.00e-02 2.50e+03 pdb=" C5A CO8 E 301 " 0.006 2.00e-02 2.50e+03 pdb=" C6A CO8 E 301 " 0.002 2.00e-02 2.50e+03 pdb=" C8A CO8 E 301 " 0.001 2.00e-02 2.50e+03 pdb=" N1A CO8 E 301 " 0.007 2.00e-02 2.50e+03 pdb=" N3A CO8 E 301 " -0.011 2.00e-02 2.50e+03 pdb=" N6A CO8 E 301 " 0.001 2.00e-02 2.50e+03 pdb=" N7A CO8 E 301 " 0.000 2.00e-02 2.50e+03 pdb=" N9A CO8 E 301 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1B CO8 D 301 " 0.022 2.00e-02 2.50e+03 1.07e-02 3.17e+00 pdb=" C2A CO8 D 301 " 0.002 2.00e-02 2.50e+03 pdb=" C4A CO8 D 301 " -0.007 2.00e-02 2.50e+03 pdb=" C5A CO8 D 301 " 0.007 2.00e-02 2.50e+03 pdb=" C6A CO8 D 301 " 0.002 2.00e-02 2.50e+03 pdb=" C8A CO8 D 301 " -0.001 2.00e-02 2.50e+03 pdb=" N1A CO8 D 301 " 0.003 2.00e-02 2.50e+03 pdb=" N3A CO8 D 301 " -0.007 2.00e-02 2.50e+03 pdb=" N6A CO8 D 301 " 0.002 2.00e-02 2.50e+03 pdb=" N7A CO8 D 301 " 0.001 2.00e-02 2.50e+03 pdb=" N9A CO8 D 301 " -0.024 2.00e-02 2.50e+03 ... (remaining 2115 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 88 2.57 - 3.15: 10017 3.15 - 3.74: 18573 3.74 - 4.32: 28026 4.32 - 4.90: 46675 Nonbonded interactions: 103379 Sorted by model distance: nonbonded pdb=" O GLN C 162 " pdb=" O HOH C 401 " model vdw 1.988 3.040 nonbonded pdb=" O GLN F 162 " pdb=" O HOH F 401 " model vdw 2.022 3.040 nonbonded pdb=" O GLU D 190 " pdb=" OG1 THR D 194 " model vdw 2.060 3.040 nonbonded pdb=" O GLN A 162 " pdb=" O HOH A 401 " model vdw 2.068 3.040 nonbonded pdb=" O GLU A 190 " pdb=" OG1 THR A 194 " model vdw 2.069 3.040 ... (remaining 103374 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' selection = (chain 'E' and resid 31 through 301) 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: 1.160 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.530 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:7.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 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 0.198 12324 Z= 0.508 Angle : 0.967 22.453 16608 Z= 0.401 Chirality : 0.047 0.348 1866 Planarity : 0.002 0.037 2118 Dihedral : 14.588 109.267 4884 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % 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: -1.43 (0.18), residues: 1548 helix: -0.65 (0.16), residues: 726 sheet: -0.63 (0.45), residues: 144 loop : -1.22 (0.20), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 178 TYR 0.014 0.001 TYR A 112 PHE 0.007 0.000 PHE A 116 TRP 0.005 0.000 TRP F 120 HIS 0.001 0.000 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00993 (12324) covalent geometry : angle 0.96738 (16608) hydrogen bonds : bond 0.19110 ( 622) hydrogen bonds : angle 7.63239 ( 1728) *********************** 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 387 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 67 ASP cc_start: 0.6330 (m-30) cc_final: 0.5938 (t70) REVERT: A 121 ASP cc_start: 0.6155 (p0) cc_final: 0.5723 (p0) REVERT: A 124 THR cc_start: 0.7506 (m) cc_final: 0.7211 (p) REVERT: A 144 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6717 (mt-10) REVERT: A 191 MET cc_start: 0.7292 (mtp) cc_final: 0.6949 (mtp) REVERT: A 205 GLN cc_start: 0.6186 (mt0) cc_final: 0.5193 (mp10) REVERT: A 217 THR cc_start: 0.7181 (m) cc_final: 0.6913 (p) REVERT: A 242 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6230 (mt-10) REVERT: A 260 LYS cc_start: 0.6000 (mmtm) cc_final: 0.5602 (mmtt) REVERT: B 44 ASN cc_start: 0.6992 (m110) cc_final: 0.6211 (t0) REVERT: B 67 ASP cc_start: 0.6540 (m-30) cc_final: 0.5793 (t70) REVERT: B 71 GLN cc_start: 0.7305 (mt0) cc_final: 0.6938 (mt0) REVERT: B 77 GLU cc_start: 0.6900 (tt0) cc_final: 0.6690 (tp30) REVERT: B 99 ASP cc_start: 0.6961 (t0) cc_final: 0.6321 (t0) REVERT: B 127 LYS cc_start: 0.7641 (mmtm) cc_final: 0.7227 (mmtt) REVERT: B 239 MET cc_start: 0.7743 (mtt) cc_final: 0.7534 (mtt) REVERT: B 242 GLU cc_start: 0.6245 (mt-10) cc_final: 0.6022 (mt-10) REVERT: B 260 LYS cc_start: 0.5918 (tttt) cc_final: 0.5635 (ttmm) REVERT: C 67 ASP cc_start: 0.6754 (m-30) cc_final: 0.5963 (t70) REVERT: C 71 GLN cc_start: 0.7414 (mt0) cc_final: 0.6988 (mt0) REVERT: C 91 ASP cc_start: 0.6976 (m-30) cc_final: 0.6757 (m-30) REVERT: C 99 ASP cc_start: 0.6323 (t0) cc_final: 0.6085 (t0) REVERT: C 127 LYS cc_start: 0.6949 (mmtm) cc_final: 0.6725 (mmtt) REVERT: C 205 GLN cc_start: 0.6543 (mt0) cc_final: 0.5728 (tm-30) REVERT: C 228 LYS cc_start: 0.7218 (mtmm) cc_final: 0.6994 (mtpp) REVERT: C 233 SER cc_start: 0.7791 (p) cc_final: 0.7590 (t) REVERT: C 242 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6393 (mt-10) REVERT: D 67 ASP cc_start: 0.6414 (m-30) cc_final: 0.6115 (OUTLIER) REVERT: D 156 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6953 (mm-30) REVERT: D 205 GLN cc_start: 0.6586 (mt0) cc_final: 0.5417 (tm130) REVERT: D 239 MET cc_start: 0.7434 (mtt) cc_final: 0.7225 (mtt) REVERT: D 242 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6423 (mt-10) REVERT: E 44 ASN cc_start: 0.7214 (m110) cc_final: 0.6064 (t0) REVERT: E 63 ASP cc_start: 0.7120 (m-30) cc_final: 0.6724 (m-30) REVERT: E 67 ASP cc_start: 0.7144 (t0) cc_final: 0.6875 (t70) REVERT: E 71 GLN cc_start: 0.7220 (mt0) cc_final: 0.6846 (mt0) REVERT: E 99 ASP cc_start: 0.6525 (t0) cc_final: 0.6253 (t0) REVERT: E 122 HIS cc_start: 0.6648 (m170) cc_final: 0.5663 (t-90) REVERT: E 127 LYS cc_start: 0.6982 (mttp) cc_final: 0.6625 (mmtt) REVERT: E 144 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6964 (mt-10) REVERT: E 201 GLN cc_start: 0.6667 (mp10) cc_final: 0.6378 (mp-120) REVERT: E 205 GLN cc_start: 0.6426 (mt0) cc_final: 0.5590 (tm-30) REVERT: E 242 GLU cc_start: 0.6792 (mt-10) cc_final: 0.6302 (mt-10) REVERT: F 71 GLN cc_start: 0.6933 (mt0) cc_final: 0.6617 (mt0) REVERT: F 99 ASP cc_start: 0.6884 (t0) cc_final: 0.6303 (t0) REVERT: F 103 MET cc_start: 0.7735 (ptm) cc_final: 0.7481 (ptp) REVERT: F 127 LYS cc_start: 0.7540 (mmtm) cc_final: 0.7323 (mmpt) REVERT: F 191 MET cc_start: 0.7445 (mtp) cc_final: 0.7157 (mtp) REVERT: F 201 GLN cc_start: 0.6474 (mp10) cc_final: 0.6158 (mp-120) REVERT: F 205 GLN cc_start: 0.6313 (mt0) cc_final: 0.5125 (mm110) REVERT: F 228 LYS cc_start: 0.7145 (mtmt) cc_final: 0.6942 (mtpp) REVERT: F 242 GLU cc_start: 0.6492 (tt0) cc_final: 0.6016 (mt-10) REVERT: F 260 LYS cc_start: 0.6321 (ttpt) cc_final: 0.5945 (ttmm) REVERT: F 265 SER cc_start: 0.7081 (t) cc_final: 0.6871 (p) REVERT: F 281 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7338 (mt-10) REVERT: F 290 GLN cc_start: 0.5634 (pt0) cc_final: 0.5302 (pt0) outliers start: 0 outliers final: 1 residues processed: 387 average time/residue: 0.7164 time to fit residues: 296.8306 Evaluate side-chains 259 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 162 GLN A 205 GLN A 224 GLN B 162 GLN B 205 GLN B 245 ASN C 162 GLN C 205 GLN D 162 GLN D 224 GLN E 32 ASN E 162 GLN E 205 GLN E 290 GLN F 53 ASN F 104 GLN F 162 GLN F 205 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.115080 restraints weight = 10842.464| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.19 r_work: 0.3130 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 12324 Z= 0.273 Angle : 0.714 8.453 16608 Z= 0.382 Chirality : 0.052 0.166 1866 Planarity : 0.006 0.061 2118 Dihedral : 10.788 59.617 2052 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.93 % Allowed : 9.92 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.21), residues: 1548 helix: 1.23 (0.19), residues: 702 sheet: 0.33 (0.46), residues: 144 loop : -0.41 (0.22), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 54 TYR 0.009 0.002 TYR A 112 PHE 0.024 0.003 PHE B 139 TRP 0.015 0.003 TRP D 120 HIS 0.006 0.002 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00627 (12324) covalent geometry : angle 0.71398 (16608) hydrogen bonds : bond 0.05979 ( 622) hydrogen bonds : angle 5.38991 ( 1728) *********************** 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 273 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.460 Fit side-chains REVERT: A 45 ASN cc_start: 0.8624 (m-40) cc_final: 0.8383 (m-40) REVERT: A 71 GLN cc_start: 0.8729 (mt0) cc_final: 0.8518 (mt0) REVERT: A 77 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.6677 (tp30) REVERT: A 205 GLN cc_start: 0.8251 (mt0) cc_final: 0.8020 (tm-30) REVERT: B 67 ASP cc_start: 0.7933 (m-30) cc_final: 0.7546 (t70) REVERT: B 71 GLN cc_start: 0.8674 (mt0) cc_final: 0.8435 (mt0) REVERT: B 91 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7456 (t0) REVERT: B 127 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8654 (mmtt) REVERT: B 242 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8094 (mt-10) REVERT: C 54 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7564 (ttt90) REVERT: C 67 ASP cc_start: 0.7812 (m-30) cc_final: 0.7463 (t70) REVERT: C 71 GLN cc_start: 0.8679 (mt0) cc_final: 0.8409 (mt0) REVERT: C 103 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8163 (ptt) REVERT: C 124 THR cc_start: 0.8760 (m) cc_final: 0.8474 (p) REVERT: C 205 GLN cc_start: 0.8193 (mt0) cc_final: 0.7963 (tm-30) REVERT: C 290 GLN cc_start: 0.8126 (pt0) cc_final: 0.7898 (pt0) REVERT: D 54 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7747 (ttt90) REVERT: E 45 ASN cc_start: 0.8779 (m-40) cc_final: 0.8484 (m-40) REVERT: E 71 GLN cc_start: 0.8754 (mt0) cc_final: 0.8378 (mt0) REVERT: E 92 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8030 (mptt) REVERT: E 242 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8411 (mt-10) REVERT: F 67 ASP cc_start: 0.8005 (m-30) cc_final: 0.7525 (t70) REVERT: F 71 GLN cc_start: 0.8703 (mt0) cc_final: 0.8405 (mt0) REVERT: F 124 THR cc_start: 0.8743 (m) cc_final: 0.8531 (p) REVERT: F 205 GLN cc_start: 0.8149 (mt0) cc_final: 0.7844 (tm-30) REVERT: F 220 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7478 (mp0) REVERT: F 242 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: F 290 GLN cc_start: 0.8286 (pt0) cc_final: 0.8027 (pt0) outliers start: 36 outliers final: 11 residues processed: 257 average time/residue: 0.7388 time to fit residues: 203.5009 Evaluate side-chains 224 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 54 ARG Chi-restraints excluded: chain C residue 56 LYS Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 54 ARG Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain E residue 92 LYS Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 242 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 129 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN F 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.118384 restraints weight = 11015.571| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.23 r_work: 0.3194 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12324 Z= 0.124 Angle : 0.495 5.755 16608 Z= 0.269 Chirality : 0.043 0.139 1866 Planarity : 0.004 0.036 2118 Dihedral : 9.960 58.615 2052 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.60 % Allowed : 12.44 % Favored : 84.96 % 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: 0.74 (0.21), residues: 1548 helix: 1.40 (0.19), residues: 738 sheet: 1.44 (0.55), residues: 114 loop : -0.65 (0.20), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 178 TYR 0.011 0.001 TYR D 264 PHE 0.011 0.001 PHE B 139 TRP 0.006 0.001 TRP D 120 HIS 0.002 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00273 (12324) covalent geometry : angle 0.49471 (16608) hydrogen bonds : bond 0.04304 ( 622) hydrogen bonds : angle 4.94872 ( 1728) *********************** 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 263 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.489 Fit side-chains REVERT: A 45 ASN cc_start: 0.8635 (m-40) cc_final: 0.8285 (m-40) REVERT: A 71 GLN cc_start: 0.8712 (mt0) cc_final: 0.8473 (mt0) REVERT: A 205 GLN cc_start: 0.8255 (mt0) cc_final: 0.8047 (tm-30) REVERT: B 67 ASP cc_start: 0.7866 (m-30) cc_final: 0.7482 (t70) REVERT: B 91 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7556 (t0) REVERT: B 144 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8758 (mt-10) REVERT: B 242 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8065 (mt-10) REVERT: C 67 ASP cc_start: 0.7769 (m-30) cc_final: 0.7463 (t70) REVERT: C 71 GLN cc_start: 0.8690 (mt0) cc_final: 0.8416 (mt0) REVERT: C 117 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5931 (mt) REVERT: C 124 THR cc_start: 0.8767 (m) cc_final: 0.8478 (p) REVERT: C 205 GLN cc_start: 0.8273 (mt0) cc_final: 0.8019 (tm-30) REVERT: C 290 GLN cc_start: 0.8129 (pt0) cc_final: 0.7917 (pt0) REVERT: D 92 LYS cc_start: 0.8402 (mmtp) cc_final: 0.8187 (mmtt) REVERT: D 144 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8743 (mt-10) REVERT: E 45 ASN cc_start: 0.8730 (m-40) cc_final: 0.8470 (m-40) REVERT: E 71 GLN cc_start: 0.8715 (mt0) cc_final: 0.8472 (mt0) REVERT: E 242 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8384 (mt-10) REVERT: F 41 ARG cc_start: 0.8449 (mmt90) cc_final: 0.8243 (mmt90) REVERT: F 45 ASN cc_start: 0.8682 (m-40) cc_final: 0.8307 (m-40) REVERT: F 67 ASP cc_start: 0.7906 (m-30) cc_final: 0.7451 (t70) REVERT: F 71 GLN cc_start: 0.8607 (mt0) cc_final: 0.8278 (mt0) REVERT: F 205 GLN cc_start: 0.8205 (mt0) cc_final: 0.7899 (tm-30) REVERT: F 220 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7478 (mp0) REVERT: F 288 LYS cc_start: 0.7732 (mmtm) cc_final: 0.7391 (mmtp) REVERT: F 290 GLN cc_start: 0.8282 (pt0) cc_final: 0.8029 (pt0) outliers start: 32 outliers final: 8 residues processed: 250 average time/residue: 0.7036 time to fit residues: 188.9855 Evaluate side-chains 223 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 211 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118583 restraints weight = 10892.714| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.21 r_work: 0.3195 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12324 Z= 0.148 Angle : 0.515 6.194 16608 Z= 0.281 Chirality : 0.044 0.141 1866 Planarity : 0.004 0.041 2118 Dihedral : 9.629 59.993 2052 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.76 % Allowed : 12.85 % Favored : 84.39 % 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: 1.14 (0.21), residues: 1548 helix: 1.75 (0.19), residues: 702 sheet: 1.57 (0.56), residues: 114 loop : -0.34 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 54 TYR 0.015 0.001 TYR D 264 PHE 0.012 0.001 PHE B 139 TRP 0.007 0.001 TRP D 120 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00334 (12324) covalent geometry : angle 0.51524 (16608) hydrogen bonds : bond 0.04524 ( 622) hydrogen bonds : angle 4.89099 ( 1728) *********************** 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 239 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 205 time to evaluate : 0.507 Fit side-chains REVERT: A 45 ASN cc_start: 0.8665 (m-40) cc_final: 0.8335 (m-40) REVERT: B 45 ASN cc_start: 0.8698 (m-40) cc_final: 0.8323 (m-40) REVERT: B 67 ASP cc_start: 0.7862 (m-30) cc_final: 0.7560 (t70) REVERT: B 91 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7624 (t0) REVERT: B 242 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8104 (mt-10) REVERT: C 67 ASP cc_start: 0.7782 (m-30) cc_final: 0.7460 (t70) REVERT: C 71 GLN cc_start: 0.8666 (mt0) cc_final: 0.8410 (mt0) REVERT: C 103 MET cc_start: 0.8570 (ptt) cc_final: 0.8236 (ptm) REVERT: C 117 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5947 (mt) REVERT: C 124 THR cc_start: 0.8793 (m) cc_final: 0.8489 (p) REVERT: C 205 GLN cc_start: 0.8353 (mt0) cc_final: 0.8016 (tm-30) REVERT: C 284 LYS cc_start: 0.8548 (tttm) cc_final: 0.8346 (tmmt) REVERT: D 92 LYS cc_start: 0.8425 (mmtp) cc_final: 0.8218 (mmtt) REVERT: D 216 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: E 45 ASN cc_start: 0.8668 (m-40) cc_final: 0.8420 (m-40) REVERT: E 71 GLN cc_start: 0.8740 (mt0) cc_final: 0.8497 (mt0) REVERT: E 91 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7664 (t0) REVERT: E 242 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8289 (mt-10) REVERT: F 45 ASN cc_start: 0.8681 (m-40) cc_final: 0.8339 (m-40) REVERT: F 67 ASP cc_start: 0.7931 (m-30) cc_final: 0.7577 (t70) REVERT: F 92 LYS cc_start: 0.8291 (tmtp) cc_final: 0.7945 (mptt) REVERT: F 205 GLN cc_start: 0.8213 (mt0) cc_final: 0.7925 (tm-30) REVERT: F 288 LYS cc_start: 0.7694 (mmtm) cc_final: 0.7381 (mmtp) REVERT: F 290 GLN cc_start: 0.8409 (pt0) cc_final: 0.8135 (pt0) outliers start: 34 outliers final: 11 residues processed: 229 average time/residue: 0.6558 time to fit residues: 161.8417 Evaluate side-chains 218 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.142402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117360 restraints weight = 10948.172| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.23 r_work: 0.3183 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12324 Z= 0.138 Angle : 0.500 6.021 16608 Z= 0.274 Chirality : 0.043 0.139 1866 Planarity : 0.004 0.038 2118 Dihedral : 9.459 59.621 2052 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.28 % Allowed : 13.50 % Favored : 84.23 % 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: 1.17 (0.21), residues: 1548 helix: 1.80 (0.19), residues: 702 sheet: 1.60 (0.56), residues: 114 loop : -0.35 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 181 TYR 0.016 0.001 TYR D 264 PHE 0.016 0.001 PHE F 116 TRP 0.006 0.001 TRP C 120 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00309 (12324) covalent geometry : angle 0.49989 (16608) hydrogen bonds : bond 0.04337 ( 622) hydrogen bonds : angle 4.82509 ( 1728) *********************** 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 232 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.551 Fit side-chains REVERT: A 45 ASN cc_start: 0.8653 (m-40) cc_final: 0.8331 (m-40) REVERT: A 77 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.6843 (tp30) REVERT: A 91 ASP cc_start: 0.7855 (m-30) cc_final: 0.7514 (t0) REVERT: A 220 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7439 (mp0) REVERT: B 45 ASN cc_start: 0.8709 (m-40) cc_final: 0.8341 (m-40) REVERT: B 67 ASP cc_start: 0.7843 (m-30) cc_final: 0.7523 (t70) REVERT: B 91 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7605 (t0) REVERT: B 92 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7703 (tmtp) REVERT: B 242 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8076 (mt-10) REVERT: C 67 ASP cc_start: 0.7746 (m-30) cc_final: 0.7414 (t70) REVERT: C 71 GLN cc_start: 0.8705 (mt0) cc_final: 0.8436 (mt0) REVERT: C 91 ASP cc_start: 0.7888 (OUTLIER) cc_final: 0.7665 (t0) REVERT: C 117 LEU cc_start: 0.6330 (OUTLIER) cc_final: 0.5960 (mt) REVERT: C 124 THR cc_start: 0.8780 (m) cc_final: 0.8467 (p) REVERT: C 156 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8095 (mt-10) REVERT: C 205 GLN cc_start: 0.8345 (mt0) cc_final: 0.7988 (tm-30) REVERT: D 45 ASN cc_start: 0.8763 (m-40) cc_final: 0.8376 (m-40) REVERT: D 92 LYS cc_start: 0.8488 (mmtp) cc_final: 0.8260 (mmtt) REVERT: D 144 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8722 (mt-10) REVERT: E 45 ASN cc_start: 0.8681 (m-40) cc_final: 0.8456 (m-40) REVERT: E 63 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: E 71 GLN cc_start: 0.8760 (mt0) cc_final: 0.8468 (mt0) REVERT: E 91 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7726 (t0) REVERT: E 242 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8324 (mt-10) REVERT: F 45 ASN cc_start: 0.8677 (m-40) cc_final: 0.8351 (m-40) REVERT: F 67 ASP cc_start: 0.7922 (m-30) cc_final: 0.7566 (t70) REVERT: F 92 LYS cc_start: 0.8312 (tmtp) cc_final: 0.7941 (mptt) REVERT: F 205 GLN cc_start: 0.8232 (mt0) cc_final: 0.7904 (tm-30) REVERT: F 288 LYS cc_start: 0.7667 (mmtm) cc_final: 0.7362 (mmtp) REVERT: F 290 GLN cc_start: 0.8369 (pt0) cc_final: 0.8102 (pt0) outliers start: 28 outliers final: 12 residues processed: 221 average time/residue: 0.6360 time to fit residues: 151.9662 Evaluate side-chains 219 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 132 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.143444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.118590 restraints weight = 10933.737| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.22 r_work: 0.3201 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12324 Z= 0.108 Angle : 0.453 5.516 16608 Z= 0.250 Chirality : 0.042 0.138 1866 Planarity : 0.004 0.037 2118 Dihedral : 9.163 59.171 2052 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.28 % Allowed : 13.74 % Favored : 83.98 % 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: 1.35 (0.21), residues: 1548 helix: 1.95 (0.20), residues: 702 sheet: 0.94 (0.50), residues: 144 loop : -0.16 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 181 TYR 0.013 0.001 TYR D 264 PHE 0.013 0.001 PHE F 116 TRP 0.004 0.001 TRP C 120 HIS 0.002 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00237 (12324) covalent geometry : angle 0.45321 (16608) hydrogen bonds : bond 0.03828 ( 622) hydrogen bonds : angle 4.71303 ( 1728) *********************** 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 234 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 0.508 Fit side-chains REVERT: A 45 ASN cc_start: 0.8638 (m-40) cc_final: 0.8338 (m-40) REVERT: A 77 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.6851 (tp30) REVERT: A 91 ASP cc_start: 0.7874 (m-30) cc_final: 0.7532 (t0) REVERT: A 221 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8318 (mt-10) REVERT: B 45 ASN cc_start: 0.8729 (m-40) cc_final: 0.8395 (m-40) REVERT: B 67 ASP cc_start: 0.7839 (m-30) cc_final: 0.7524 (t70) REVERT: B 91 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7596 (t0) REVERT: B 92 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7739 (tttp) REVERT: B 242 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8107 (mt-10) REVERT: C 67 ASP cc_start: 0.7698 (m-30) cc_final: 0.7381 (t70) REVERT: C 71 GLN cc_start: 0.8671 (mt0) cc_final: 0.8399 (mt0) REVERT: C 112 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.6764 (t80) REVERT: C 117 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.6071 (mt) REVERT: C 124 THR cc_start: 0.8771 (m) cc_final: 0.8439 (p) REVERT: C 156 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: C 205 GLN cc_start: 0.8342 (mt0) cc_final: 0.7995 (tm-30) REVERT: D 45 ASN cc_start: 0.8739 (m-40) cc_final: 0.8370 (m-40) REVERT: D 92 LYS cc_start: 0.8386 (mmtp) cc_final: 0.8176 (mmtt) REVERT: D 144 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8713 (mt-10) REVERT: E 45 ASN cc_start: 0.8673 (m-40) cc_final: 0.8460 (m-40) REVERT: E 71 GLN cc_start: 0.8727 (mt0) cc_final: 0.8436 (mt0) REVERT: E 91 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7726 (t0) REVERT: E 144 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8311 (mt-10) REVERT: E 242 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8319 (mt-10) REVERT: F 45 ASN cc_start: 0.8651 (m-40) cc_final: 0.8337 (m-40) REVERT: F 67 ASP cc_start: 0.7916 (m-30) cc_final: 0.7561 (t70) REVERT: F 92 LYS cc_start: 0.8315 (tmtp) cc_final: 0.7925 (mptt) REVERT: F 205 GLN cc_start: 0.8276 (mt0) cc_final: 0.7948 (tm-30) REVERT: F 288 LYS cc_start: 0.7625 (mmtm) cc_final: 0.7370 (mmtp) REVERT: F 290 GLN cc_start: 0.8390 (pt0) cc_final: 0.8138 (pt0) outliers start: 28 outliers final: 13 residues processed: 222 average time/residue: 0.6334 time to fit residues: 151.3355 Evaluate side-chains 222 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 117 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 132 optimal weight: 0.0970 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.143960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119174 restraints weight = 10869.876| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.22 r_work: 0.3209 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12324 Z= 0.103 Angle : 0.445 5.157 16608 Z= 0.246 Chirality : 0.042 0.137 1866 Planarity : 0.003 0.038 2118 Dihedral : 9.012 58.959 2052 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.36 % Allowed : 13.90 % Favored : 83.74 % 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: 1.42 (0.21), residues: 1548 helix: 2.01 (0.20), residues: 702 sheet: 1.00 (0.50), residues: 144 loop : -0.14 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 178 TYR 0.014 0.001 TYR D 264 PHE 0.012 0.001 PHE F 116 TRP 0.005 0.001 TRP C 120 HIS 0.002 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00224 (12324) covalent geometry : angle 0.44475 (16608) hydrogen bonds : bond 0.03711 ( 622) hydrogen bonds : angle 4.65819 ( 1728) *********************** 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 234 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.425 Fit side-chains REVERT: A 45 ASN cc_start: 0.8626 (m-40) cc_final: 0.8425 (m-40) REVERT: A 77 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.6867 (tp30) REVERT: A 91 ASP cc_start: 0.7879 (m-30) cc_final: 0.7543 (t0) REVERT: A 220 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7486 (mp0) REVERT: A 221 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8280 (mt-10) REVERT: B 45 ASN cc_start: 0.8722 (m-40) cc_final: 0.8399 (m-40) REVERT: B 67 ASP cc_start: 0.7825 (m-30) cc_final: 0.7502 (t70) REVERT: B 91 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7597 (t0) REVERT: B 92 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7721 (tttp) REVERT: B 145 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8399 (tp) REVERT: B 242 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8108 (mt-10) REVERT: C 67 ASP cc_start: 0.7708 (m-30) cc_final: 0.7317 (t70) REVERT: C 71 GLN cc_start: 0.8679 (mt0) cc_final: 0.8312 (mt0) REVERT: C 77 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6588 (tp30) REVERT: C 112 TYR cc_start: 0.7505 (OUTLIER) cc_final: 0.6727 (t80) REVERT: C 124 THR cc_start: 0.8775 (m) cc_final: 0.8449 (p) REVERT: C 156 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: C 205 GLN cc_start: 0.8321 (mt0) cc_final: 0.7979 (tm-30) REVERT: C 284 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8080 (ttmt) REVERT: D 45 ASN cc_start: 0.8750 (m-40) cc_final: 0.8388 (m-40) REVERT: D 92 LYS cc_start: 0.8346 (mmtp) cc_final: 0.8142 (mmtt) REVERT: D 144 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8710 (mt-10) REVERT: E 45 ASN cc_start: 0.8663 (m-40) cc_final: 0.8459 (m-40) REVERT: E 71 GLN cc_start: 0.8720 (mt0) cc_final: 0.8438 (mt0) REVERT: E 112 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7324 (t80) REVERT: E 144 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8313 (mt-10) REVERT: E 242 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8333 (mt-10) REVERT: F 45 ASN cc_start: 0.8646 (m-40) cc_final: 0.8426 (m-40) REVERT: F 67 ASP cc_start: 0.7904 (m-30) cc_final: 0.7551 (t70) REVERT: F 92 LYS cc_start: 0.8317 (tmtp) cc_final: 0.7922 (mptt) REVERT: F 205 GLN cc_start: 0.8286 (mt0) cc_final: 0.7944 (tm-30) REVERT: F 288 LYS cc_start: 0.7624 (mmtm) cc_final: 0.7369 (mmtp) REVERT: F 290 GLN cc_start: 0.8392 (pt0) cc_final: 0.8158 (pt0) outliers start: 29 outliers final: 11 residues processed: 221 average time/residue: 0.5617 time to fit residues: 134.0338 Evaluate side-chains 221 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 63 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 99 optimal weight: 0.4980 chunk 13 optimal weight: 0.1980 chunk 88 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117107 restraints weight = 10942.687| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.22 r_work: 0.3179 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12324 Z= 0.143 Angle : 0.498 5.349 16608 Z= 0.274 Chirality : 0.043 0.141 1866 Planarity : 0.004 0.040 2118 Dihedral : 9.200 58.888 2052 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.11 % Allowed : 14.47 % Favored : 83.41 % 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: 1.24 (0.21), residues: 1548 helix: 1.88 (0.19), residues: 702 sheet: 1.58 (0.55), residues: 114 loop : -0.33 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 181 TYR 0.017 0.001 TYR D 264 PHE 0.013 0.001 PHE B 279 TRP 0.008 0.001 TRP C 120 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00322 (12324) covalent geometry : angle 0.49833 (16608) hydrogen bonds : bond 0.04414 ( 622) hydrogen bonds : angle 4.80523 ( 1728) *********************** 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 222 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.521 Fit side-chains REVERT: A 45 ASN cc_start: 0.8637 (m-40) cc_final: 0.8350 (m-40) REVERT: A 77 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.6843 (tp30) REVERT: A 91 ASP cc_start: 0.7896 (m-30) cc_final: 0.7566 (t0) REVERT: A 221 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8350 (mt-10) REVERT: B 45 ASN cc_start: 0.8714 (m-40) cc_final: 0.8384 (m-40) REVERT: B 67 ASP cc_start: 0.7833 (m-30) cc_final: 0.7513 (t70) REVERT: B 91 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7613 (t0) REVERT: B 92 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7717 (tmtp) REVERT: B 242 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8104 (mt-10) REVERT: C 67 ASP cc_start: 0.7710 (m-30) cc_final: 0.7380 (t70) REVERT: C 71 GLN cc_start: 0.8716 (mt0) cc_final: 0.8448 (mt0) REVERT: C 91 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7653 (t0) REVERT: C 112 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6800 (t80) REVERT: C 124 THR cc_start: 0.8775 (m) cc_final: 0.8463 (p) REVERT: C 156 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8090 (mt-10) REVERT: C 205 GLN cc_start: 0.8331 (mt0) cc_final: 0.7968 (tm-30) REVERT: D 45 ASN cc_start: 0.8749 (m-40) cc_final: 0.8387 (m-40) REVERT: D 92 LYS cc_start: 0.8477 (mmtp) cc_final: 0.8248 (mmtt) REVERT: D 144 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8753 (mt-10) REVERT: E 45 ASN cc_start: 0.8663 (m-40) cc_final: 0.8463 (m-40) REVERT: E 71 GLN cc_start: 0.8729 (mt0) cc_final: 0.8465 (mt0) REVERT: E 103 MET cc_start: 0.8553 (ptt) cc_final: 0.8330 (ptt) REVERT: E 144 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8364 (mt-10) REVERT: E 242 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8336 (mt-10) REVERT: F 45 ASN cc_start: 0.8672 (m-40) cc_final: 0.8444 (m-40) REVERT: F 67 ASP cc_start: 0.7909 (m-30) cc_final: 0.7558 (t70) REVERT: F 92 LYS cc_start: 0.8330 (tmtp) cc_final: 0.7948 (mptt) REVERT: F 205 GLN cc_start: 0.8267 (mt0) cc_final: 0.7981 (tm-30) REVERT: F 288 LYS cc_start: 0.7649 (mmtm) cc_final: 0.7399 (mmtp) REVERT: F 290 GLN cc_start: 0.8379 (pt0) cc_final: 0.8120 (pt0) outliers start: 26 outliers final: 9 residues processed: 214 average time/residue: 0.6063 time to fit residues: 139.8652 Evaluate side-chains 212 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 91 ASP Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 144 optimal weight: 0.0050 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.145358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120718 restraints weight = 10829.361| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.21 r_work: 0.3236 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12324 Z= 0.085 Angle : 0.420 4.582 16608 Z= 0.233 Chirality : 0.041 0.137 1866 Planarity : 0.003 0.041 2118 Dihedral : 8.810 59.711 2052 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.63 % Allowed : 14.63 % Favored : 83.74 % 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: 1.49 (0.21), residues: 1548 helix: 2.08 (0.20), residues: 702 sheet: 1.00 (0.50), residues: 144 loop : -0.10 (0.21), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 41 TYR 0.013 0.001 TYR B 264 PHE 0.011 0.001 PHE F 116 TRP 0.004 0.000 TRP C 120 HIS 0.001 0.000 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00178 (12324) covalent geometry : angle 0.42017 (16608) hydrogen bonds : bond 0.03333 ( 622) hydrogen bonds : angle 4.60417 ( 1728) *********************** 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 229 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 209 time to evaluate : 0.475 Fit side-chains REVERT: A 77 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.6894 (tp30) REVERT: A 91 ASP cc_start: 0.7878 (m-30) cc_final: 0.7563 (t0) REVERT: A 221 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8271 (mt-10) REVERT: B 45 ASN cc_start: 0.8700 (m-40) cc_final: 0.8396 (m-40) REVERT: B 67 ASP cc_start: 0.7792 (m-30) cc_final: 0.7447 (t70) REVERT: B 92 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7731 (tttp) REVERT: B 242 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8047 (mt-10) REVERT: C 67 ASP cc_start: 0.7689 (m-30) cc_final: 0.7367 (t70) REVERT: C 71 GLN cc_start: 0.8681 (mt0) cc_final: 0.8415 (mt0) REVERT: C 112 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6700 (t80) REVERT: C 124 THR cc_start: 0.8735 (m) cc_final: 0.8423 (p) REVERT: C 156 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: C 205 GLN cc_start: 0.8352 (mt0) cc_final: 0.7987 (tm-30) REVERT: D 45 ASN cc_start: 0.8728 (m-40) cc_final: 0.8377 (m-40) REVERT: D 92 LYS cc_start: 0.8331 (mmtp) cc_final: 0.8128 (mmtt) REVERT: D 145 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8211 (mt) REVERT: E 71 GLN cc_start: 0.8715 (mt0) cc_final: 0.8446 (mt0) REVERT: E 112 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7281 (t80) REVERT: E 144 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8300 (mt-10) REVERT: E 242 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8356 (mt-10) REVERT: F 45 ASN cc_start: 0.8637 (m-40) cc_final: 0.8414 (m-40) REVERT: F 67 ASP cc_start: 0.7869 (m-30) cc_final: 0.7504 (t70) REVERT: F 91 ASP cc_start: 0.7806 (m-30) cc_final: 0.7480 (t0) REVERT: F 92 LYS cc_start: 0.8223 (tmtp) cc_final: 0.7863 (mptt) REVERT: F 205 GLN cc_start: 0.8304 (mt0) cc_final: 0.7958 (tm-30) REVERT: F 288 LYS cc_start: 0.7601 (mmtm) cc_final: 0.7363 (mmtp) REVERT: F 290 GLN cc_start: 0.8360 (pt0) cc_final: 0.8134 (pt0) outliers start: 20 outliers final: 8 residues processed: 220 average time/residue: 0.6039 time to fit residues: 143.2679 Evaluate side-chains 213 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 156 GLU Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 10.0000 chunk 108 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 53 ASN B 44 ASN C 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.141536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.116907 restraints weight = 10883.508| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.19 r_work: 0.3175 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12324 Z= 0.213 Angle : 0.585 7.330 16608 Z= 0.319 Chirality : 0.047 0.146 1866 Planarity : 0.005 0.053 2118 Dihedral : 9.486 58.798 2052 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.30 % Allowed : 15.28 % Favored : 83.41 % 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: 1.10 (0.21), residues: 1548 helix: 1.72 (0.19), residues: 702 sheet: 0.66 (0.48), residues: 150 loop : -0.23 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 181 TYR 0.022 0.002 TYR B 264 PHE 0.017 0.002 PHE B 279 TRP 0.010 0.002 TRP C 120 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00489 (12324) covalent geometry : angle 0.58499 (16608) hydrogen bonds : bond 0.05233 ( 622) hydrogen bonds : angle 4.96175 ( 1728) ********************** 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 198 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.557 Fit side-chains REVERT: A 77 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.6914 (tp30) REVERT: A 91 ASP cc_start: 0.7930 (m-30) cc_final: 0.7617 (t0) REVERT: A 221 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8425 (mt-10) REVERT: B 45 ASN cc_start: 0.8709 (m-40) cc_final: 0.8386 (m-40) REVERT: B 67 ASP cc_start: 0.7853 (m-30) cc_final: 0.7550 (t70) REVERT: B 92 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7783 (tmtp) REVERT: B 242 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8120 (mt-10) REVERT: C 67 ASP cc_start: 0.7838 (m-30) cc_final: 0.7431 (t70) REVERT: C 71 GLN cc_start: 0.8678 (mt0) cc_final: 0.8451 (mt0) REVERT: C 112 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.6908 (t80) REVERT: C 124 THR cc_start: 0.8791 (m) cc_final: 0.8519 (p) REVERT: C 205 GLN cc_start: 0.8292 (mt0) cc_final: 0.7968 (tm-30) REVERT: D 45 ASN cc_start: 0.8773 (m-40) cc_final: 0.8422 (m-40) REVERT: D 92 LYS cc_start: 0.8513 (mmtp) cc_final: 0.8275 (mmtt) REVERT: E 71 GLN cc_start: 0.8759 (mt0) cc_final: 0.8526 (mt0) REVERT: E 103 MET cc_start: 0.8607 (ptt) cc_final: 0.8380 (ptt) REVERT: E 242 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8301 (mt-10) REVERT: F 45 ASN cc_start: 0.8672 (m-40) cc_final: 0.8441 (m-40) REVERT: F 67 ASP cc_start: 0.7939 (m-30) cc_final: 0.7646 (t70) REVERT: F 91 ASP cc_start: 0.7871 (m-30) cc_final: 0.7557 (t0) REVERT: F 92 LYS cc_start: 0.8309 (tmtp) cc_final: 0.7967 (mptt) REVERT: F 205 GLN cc_start: 0.8284 (mt0) cc_final: 0.8010 (tm-30) REVERT: F 290 GLN cc_start: 0.8455 (pt0) cc_final: 0.8252 (pt0) outliers start: 16 outliers final: 11 residues processed: 195 average time/residue: 0.6115 time to fit residues: 128.3574 Evaluate side-chains 193 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 179 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 265 SER Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 284 LYS Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain E residue 243 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 83 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN B 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.141736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116848 restraints weight = 10886.876| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.21 r_work: 0.3174 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12324 Z= 0.154 Angle : 0.516 5.358 16608 Z= 0.284 Chirality : 0.044 0.141 1866 Planarity : 0.004 0.043 2118 Dihedral : 9.303 58.859 2052 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.30 % Allowed : 15.37 % Favored : 83.33 % 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: 1.12 (0.21), residues: 1548 helix: 1.76 (0.19), residues: 702 sheet: 1.53 (0.55), residues: 114 loop : -0.38 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 197 TYR 0.018 0.001 TYR B 264 PHE 0.014 0.001 PHE B 279 TRP 0.008 0.001 TRP C 120 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00350 (12324) covalent geometry : angle 0.51645 (16608) hydrogen bonds : bond 0.04525 ( 622) hydrogen bonds : angle 4.86800 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4824.97 seconds wall clock time: 82 minutes 58.33 seconds (4978.33 seconds total)