Starting phenix.real_space_refine on Wed Feb 4 11:18:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6e_28881/02_2026/8f6e_28881.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6e_28881/02_2026/8f6e_28881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6e_28881/02_2026/8f6e_28881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6e_28881/02_2026/8f6e_28881.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6e_28881/02_2026/8f6e_28881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6e_28881/02_2026/8f6e_28881.cif" } resolution = 3.8 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= 0.001 sd= 0.056 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 28 5.16 5 C 6678 2.51 5 N 1760 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10478 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2172 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "C" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2172 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 6, 'TRANS': 275} Chain: "E" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1474 Classifications: {'peptide': 192} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1589 Classifications: {'peptide': 209} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.11, per 1000 atoms: 0.20 Number of scatterers: 10478 At special positions: 0 Unit cell: (67.284, 156.996, 144.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 28 16.00 O 2004 8.00 N 1760 7.00 C 6678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 99 " distance=2.03 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: 0.56 Conformation dependent library (CDL) restraints added in 387.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 250 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 234 " pdb=" ZN A 302 " pdb="ZN ZN A 302 " - pdb=" ND1 HIS A 73 " pdb="ZN ZN A 302 " - pdb=" NE2 HIS A 77 " pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 155 " pdb=" ZN A 304 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS B 263 " pdb="ZN ZN A 304 " - pdb=" NE2 HIS A 285 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS A 263 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 285 " pdb=" ZN B 302 " pdb="ZN ZN B 302 " - pdb=" ND1 HIS B 250 " pdb="ZN ZN B 302 " - pdb=" NE2 HIS B 234 " pdb=" ZN B 303 " pdb="ZN ZN B 303 " - pdb=" ND1 HIS B 73 " pdb="ZN ZN B 303 " - pdb=" NE2 HIS B 77 " pdb=" ZN B 304 " pdb="ZN ZN B 304 " - pdb=" NE2 HIS B 155 " 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 23 sheets defined 31.8% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 removed outlier: 3.565A pdb=" N SER A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 67 removed outlier: 4.067A pdb=" N LEU A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 109 removed outlier: 3.613A pdb=" N ALA A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 101 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 142 removed outlier: 3.723A pdb=" N VAL A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 132 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 175 removed outlier: 3.529A pdb=" N SER A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N PHE A 161 " --> pdb=" O LYS A 157 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 167 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 208 removed outlier: 3.600A pdb=" N TYR A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 222 removed outlier: 3.758A pdb=" N ARG A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 222 " --> pdb=" O GLN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 277 removed outlier: 3.655A pdb=" N SER A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 130 removed outlier: 4.200A pdb=" N LYS C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 124 through 130' Processing helix chain 'C' and resid 184 through 190 removed outlier: 3.641A pdb=" N GLU C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.983A pdb=" N THR D 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 34 removed outlier: 3.507A pdb=" N SER B 18 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 26 " --> pdb=" O ALA B 22 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 67 removed outlier: 3.954A pdb=" N ALA B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 109 removed outlier: 3.668A pdb=" N ALA B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE B 92 " --> pdb=" O GLN B 88 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 142 removed outlier: 3.561A pdb=" N GLY B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA B 132 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS B 138 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 175 removed outlier: 3.667A pdb=" N LEU B 154 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS B 155 " --> pdb=" O ALA B 151 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B 160 " --> pdb=" O TYR B 156 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 167 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 208 removed outlier: 4.061A pdb=" N ASP B 181 " --> pdb=" O TRP B 177 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU B 183 " --> pdb=" O TRP B 179 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.798A pdb=" N ARG B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 221 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 277 removed outlier: 3.650A pdb=" N SER B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU B 271 " --> pdb=" O ASP B 267 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 130 removed outlier: 4.234A pdb=" N LYS E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER E 129 " --> pdb=" O SER E 125 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY E 130 " --> pdb=" O GLN E 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 130' Processing helix chain 'E' and resid 184 through 190 removed outlier: 3.654A pdb=" N GLU E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.975A pdb=" N THR F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.808A pdb=" N GLY A 232 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 252 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 234 " --> pdb=" O HIS A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 234 removed outlier: 3.808A pdb=" N GLY A 232 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 252 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 234 " --> pdb=" O HIS A 250 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 249 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.977A pdb=" N GLU C 107 " --> pdb=" O LEU C 12 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU C 47 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 20 through 25 removed outlier: 3.801A pdb=" N VAL C 20 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 76 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 73 " --> pdb=" O SER C 66 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 90 through 91 removed outlier: 3.879A pdb=" N THR C 99 " --> pdb=" O GLN C 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 116 through 119 Processing sheet with id=AA7, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.508A pdb=" N VAL D 8 " --> pdb=" O ALA D 26 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 48 through 54 removed outlier: 7.062A pdb=" N TRP D 39 " --> pdb=" O VAL D 51 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N SER D 53 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ILE D 37 " --> pdb=" O SER D 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 76 removed outlier: 3.879A pdb=" N THR D 81 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 106 through 107 Processing sheet with id=AB2, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.537A pdb=" N LYS D 160 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 137 through 141 removed outlier: 3.537A pdb=" N LYS D 160 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY D 156 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 161 " --> pdb=" O TYR D 193 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TYR D 193 " --> pdb=" O ASP D 161 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER D 194 " --> pdb=" O VAL D 186 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 170 through 171 removed outlier: 3.810A pdb=" N ASN D 214 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS D 213 " --> pdb=" O LYS D 226 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS D 226 " --> pdb=" O CYS D 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 232 through 241 removed outlier: 6.152A pdb=" N LEU B 233 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU B 252 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ASP B 235 " --> pdb=" O HIS B 250 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N HIS B 250 " --> pdb=" O ASP B 235 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE B 249 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.868A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE E 76 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR E 73 " --> pdb=" O SER E 66 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 11 through 13 removed outlier: 3.982A pdb=" N GLU E 107 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.769A pdb=" N THR E 99 " --> pdb=" O GLN E 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.861A pdb=" N ASN E 140 " --> pdb=" O TYR E 175 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR E 175 " --> pdb=" O ASN E 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 6 through 10 removed outlier: 3.602A pdb=" N VAL F 8 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU F 23 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR F 81 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 48 through 53 removed outlier: 7.073A pdb=" N TRP F 39 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 106 through 107 Processing sheet with id=AC4, first strand: chain 'F' and resid 137 through 141 removed outlier: 3.540A pdb=" N LYS F 160 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY F 156 " --> pdb=" O LEU F 141 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 167 through 171 removed outlier: 3.823A pdb=" N ASN F 214 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS F 213 " --> pdb=" O LYS F 226 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS F 226 " --> pdb=" O CYS F 213 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1170 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: 1.07 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3352 1.34 - 1.46: 2439 1.46 - 1.58: 4869 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 10698 Sorted by residual: bond pdb=" N THR B 147 " pdb=" CA THR B 147 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.65e+00 bond pdb=" N THR A 147 " pdb=" CA THR A 147 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.35e+00 bond pdb=" CG PRO E 96 " pdb=" CD PRO E 96 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.26e+00 bond pdb=" CB TRP D 50 " pdb=" CG TRP D 50 " ideal model delta sigma weight residual 1.498 1.466 0.032 3.10e-02 1.04e+03 1.04e+00 bond pdb=" CB TRP C 95 " pdb=" CG TRP C 95 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 9.70e-01 ... (remaining 10693 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 14165 1.37 - 2.75: 292 2.75 - 4.12: 77 4.12 - 5.49: 23 5.49 - 6.87: 5 Bond angle restraints: 14562 Sorted by residual: angle pdb=" C GLN F 132 " pdb=" N ILE F 133 " pdb=" CA ILE F 133 " ideal model delta sigma weight residual 121.97 128.84 -6.87 1.80e+00 3.09e-01 1.46e+01 angle pdb=" C GLN D 132 " pdb=" N ILE D 133 " pdb=" CA ILE D 133 " ideal model delta sigma weight residual 121.97 127.64 -5.67 1.80e+00 3.09e-01 9.92e+00 angle pdb=" C PHE D 163 " pdb=" N PRO D 164 " pdb=" CD PRO D 164 " ideal model delta sigma weight residual 120.60 126.49 -5.89 2.20e+00 2.07e-01 7.16e+00 angle pdb=" C PHE D 163 " pdb=" N PRO D 164 " pdb=" CA PRO D 164 " ideal model delta sigma weight residual 127.00 120.72 6.28 2.40e+00 1.74e-01 6.85e+00 angle pdb=" C THR B 147 " pdb=" CA THR B 147 " pdb=" CB THR B 147 " ideal model delta sigma weight residual 110.42 115.52 -5.10 1.99e+00 2.53e-01 6.57e+00 ... (remaining 14557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5752 17.84 - 35.67: 496 35.67 - 53.51: 78 53.51 - 71.35: 19 71.35 - 89.19: 7 Dihedral angle restraints: 6352 sinusoidal: 2378 harmonic: 3974 Sorted by residual: dihedral pdb=" CB CYS D 25 " pdb=" SG CYS D 25 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 170.21 -77.21 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS F 25 " pdb=" SG CYS F 25 " pdb=" SG CYS F 99 " pdb=" CB CYS F 99 " ideal model delta sinusoidal sigma weight residual 93.00 149.33 -56.33 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 148.60 -55.60 1 1.00e+01 1.00e-02 4.18e+01 ... (remaining 6349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 986 0.027 - 0.055: 470 0.055 - 0.082: 134 0.082 - 0.109: 80 0.109 - 0.137: 24 Chirality restraints: 1694 Sorted by residual: chirality pdb=" CA ILE E 49 " pdb=" N ILE E 49 " pdb=" C ILE E 49 " pdb=" CB ILE E 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE C 49 " pdb=" N ILE C 49 " pdb=" C ILE C 49 " pdb=" CB ILE C 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA VAL D 96 " pdb=" N VAL D 96 " pdb=" C VAL D 96 " pdb=" CB VAL D 96 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1691 not shown) Planarity restraints: 1834 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE F 163 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO F 164 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO F 164 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 164 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 165 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO D 166 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 166 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 166 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 165 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO F 166 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO F 166 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 166 " -0.024 5.00e-02 4.00e+02 ... (remaining 1831 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 111 2.63 - 3.20: 9498 3.20 - 3.76: 15343 3.76 - 4.33: 20423 4.33 - 4.90: 34211 Nonbonded interactions: 79586 Sorted by model distance: nonbonded pdb=" OD2 ASP B 287 " pdb="ZN ZN B 302 " model vdw 2.060 2.230 nonbonded pdb=" OD1 ASP A 287 " pdb="ZN ZN A 304 " model vdw 2.062 2.230 nonbonded pdb=" OD1 ASP B 287 " pdb="ZN ZN B 301 " model vdw 2.066 2.230 nonbonded pdb=" OD2 ASP A 287 " pdb="ZN ZN A 301 " model vdw 2.071 2.230 nonbonded pdb=" OD1 ASP A 159 " pdb="ZN ZN A 303 " model vdw 2.090 2.230 ... (remaining 79581 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' 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 group one per residue 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: 2.700 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.300 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 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 : 0.003 0.032 10718 Z= 0.124 Angle : 0.546 6.869 14574 Z= 0.278 Chirality : 0.039 0.137 1694 Planarity : 0.004 0.075 1834 Dihedral : 13.515 89.186 3774 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.44 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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 are not related in a simple way. whole: -0.77 (0.24), residues: 1342 helix: 0.28 (0.27), residues: 364 sheet: -0.84 (0.30), residues: 342 loop : -0.67 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 144 TYR 0.012 0.001 TYR A 201 PHE 0.010 0.001 PHE D 183 TRP 0.030 0.002 TRP B 179 HIS 0.002 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00275 (10698) covalent geometry : angle 0.54603 (14562) SS BOND : bond 0.00241 ( 6) SS BOND : angle 0.86826 ( 12) hydrogen bonds : bond 0.29371 ( 413) hydrogen bonds : angle 8.93983 ( 1170) metal coordination : bond 0.00097 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 139 PHE cc_start: 0.6512 (m-80) cc_final: 0.6287 (m-10) REVERT: F 223 LYS cc_start: 0.8204 (mppt) cc_final: 0.7926 (mppt) outliers start: 0 outliers final: 0 residues processed: 236 average time/residue: 0.0824 time to fit residues: 27.8743 Evaluate side-chains 203 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN A 163 ASN A 285 HIS D 38 HIS D 102 GLN B 163 ASN B 285 HIS E 90 GLN E 140 ASN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.191440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.183162 restraints weight = 12662.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.182030 restraints weight = 25475.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180749 restraints weight = 24177.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.180833 restraints weight = 23764.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.179428 restraints weight = 17640.692| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.764 10718 Z= 0.383 Angle : 0.636 9.242 14574 Z= 0.323 Chirality : 0.042 0.165 1694 Planarity : 0.004 0.059 1834 Dihedral : 4.243 15.778 1466 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.11 % Favored : 93.52 % Rotamer: Outliers : 1.05 % Allowed : 9.95 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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 are not related in a simple way. whole: -0.93 (0.23), residues: 1342 helix: 0.33 (0.26), residues: 400 sheet: -1.05 (0.28), residues: 350 loop : -0.87 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 272 TYR 0.030 0.001 TYR E 142 PHE 0.026 0.002 PHE C 141 TRP 0.025 0.002 TRP F 171 HIS 0.003 0.001 HIS B 250 Details of bonding type rmsd covalent geometry : bond 0.00372 (10698) covalent geometry : angle 0.63534 (14562) SS BOND : bond 0.01032 ( 6) SS BOND : angle 1.19959 ( 12) hydrogen bonds : bond 0.05425 ( 413) hydrogen bonds : angle 5.72899 ( 1170) metal coordination : bond 0.28639 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 233 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 139 ASN cc_start: 0.7814 (t0) cc_final: 0.7562 (t0) outliers start: 12 outliers final: 10 residues processed: 240 average time/residue: 0.0877 time to fit residues: 30.1421 Evaluate side-chains 220 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 213 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 122 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 118 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.189395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.176657 restraints weight = 12627.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.174416 restraints weight = 23085.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.172955 restraints weight = 24747.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.172261 restraints weight = 21831.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.171802 restraints weight = 21186.421| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10718 Z= 0.207 Angle : 0.652 11.055 14574 Z= 0.331 Chirality : 0.044 0.166 1694 Planarity : 0.004 0.054 1834 Dihedral : 4.413 17.290 1466 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.26 % Favored : 93.29 % Rotamer: Outliers : 1.57 % Allowed : 13.96 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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 are not related in a simple way. whole: -1.02 (0.23), residues: 1342 helix: 0.37 (0.26), residues: 400 sheet: -1.12 (0.27), residues: 366 loop : -0.99 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 144 TYR 0.027 0.002 TYR E 142 PHE 0.033 0.002 PHE B 184 TRP 0.019 0.002 TRP D 50 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd covalent geometry : bond 0.00481 (10698) covalent geometry : angle 0.65128 (14562) SS BOND : bond 0.00480 ( 6) SS BOND : angle 0.88337 ( 12) hydrogen bonds : bond 0.04595 ( 413) hydrogen bonds : angle 5.33148 ( 1170) metal coordination : bond 0.00543 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 139 ASN cc_start: 0.7667 (t0) cc_final: 0.7421 (t0) REVERT: D 92 GLU cc_start: 0.7581 (tp30) cc_final: 0.7349 (tp30) REVERT: B 58 ASN cc_start: 0.7000 (t0) cc_final: 0.6546 (t0) REVERT: E 139 ASN cc_start: 0.7784 (t0) cc_final: 0.7425 (t0) outliers start: 18 outliers final: 10 residues processed: 235 average time/residue: 0.0881 time to fit residues: 29.7407 Evaluate side-chains 214 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 127 optimal weight: 3.9990 chunk 36 optimal weight: 0.0570 chunk 3 optimal weight: 9.9990 chunk 48 optimal weight: 0.0030 chunk 59 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 107 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 6 optimal weight: 0.0060 chunk 25 optimal weight: 0.7980 overall best weight: 0.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS B 248 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.192208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.183459 restraints weight = 12544.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.182600 restraints weight = 27310.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.181376 restraints weight = 23688.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.180833 restraints weight = 26129.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.179633 restraints weight = 19880.565| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10718 Z= 0.117 Angle : 0.626 9.540 14574 Z= 0.306 Chirality : 0.042 0.158 1694 Planarity : 0.004 0.051 1834 Dihedral : 4.134 15.409 1466 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.14 % Favored : 94.34 % Rotamer: Outliers : 1.05 % Allowed : 17.63 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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 are not related in a simple way. whole: -0.97 (0.23), residues: 1342 helix: 0.39 (0.26), residues: 400 sheet: -1.04 (0.27), residues: 352 loop : -0.99 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 144 TYR 0.027 0.001 TYR E 142 PHE 0.022 0.001 PHE C 141 TRP 0.015 0.001 TRP B 179 HIS 0.003 0.001 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00251 (10698) covalent geometry : angle 0.62472 (14562) SS BOND : bond 0.00878 ( 6) SS BOND : angle 1.31231 ( 12) hydrogen bonds : bond 0.03743 ( 413) hydrogen bonds : angle 4.98675 ( 1170) metal coordination : bond 0.00065 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLN cc_start: 0.8450 (pp30) cc_final: 0.7855 (pp30) REVERT: C 139 ASN cc_start: 0.7474 (t0) cc_final: 0.7159 (t0) REVERT: B 58 ASN cc_start: 0.6844 (t0) cc_final: 0.6574 (t0) REVERT: E 139 ASN cc_start: 0.7557 (t0) cc_final: 0.7209 (t0) outliers start: 12 outliers final: 8 residues processed: 229 average time/residue: 0.0992 time to fit residues: 32.1270 Evaluate side-chains 206 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 199 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 39 optimal weight: 10.0000 chunk 87 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 74 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 overall best weight: 1.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN E 91 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.189501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.178896 restraints weight = 12659.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.177640 restraints weight = 25007.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175809 restraints weight = 26061.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.167513 restraints weight = 25097.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.162252 restraints weight = 21836.615| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 10718 Z= 0.237 Angle : 0.680 13.562 14574 Z= 0.343 Chirality : 0.044 0.158 1694 Planarity : 0.004 0.049 1834 Dihedral : 4.468 17.970 1466 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.63 % Favored : 92.85 % Rotamer: Outliers : 2.18 % Allowed : 19.28 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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 are not related in a simple way. whole: -1.16 (0.23), residues: 1342 helix: 0.36 (0.26), residues: 400 sheet: -1.29 (0.26), residues: 370 loop : -1.09 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 272 TYR 0.027 0.002 TYR E 142 PHE 0.040 0.002 PHE B 184 TRP 0.022 0.002 TRP D 50 HIS 0.004 0.001 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00557 (10698) covalent geometry : angle 0.67977 (14562) SS BOND : bond 0.00511 ( 6) SS BOND : angle 1.24110 ( 12) hydrogen bonds : bond 0.03957 ( 413) hydrogen bonds : angle 5.06544 ( 1170) metal coordination : bond 0.00195 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLN cc_start: 0.8501 (pp30) cc_final: 0.7907 (pp30) REVERT: C 139 ASN cc_start: 0.7957 (t0) cc_final: 0.7506 (t0) REVERT: D 92 GLU cc_start: 0.7710 (tp30) cc_final: 0.7473 (tp30) REVERT: D 168 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6898 (p) REVERT: B 58 ASN cc_start: 0.7856 (t0) cc_final: 0.7415 (t0) REVERT: B 93 MET cc_start: 0.7475 (mtp) cc_final: 0.7270 (ttm) REVERT: B 201 TYR cc_start: 0.6550 (t80) cc_final: 0.6314 (t80) REVERT: E 91 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8133 (pp30) REVERT: E 139 ASN cc_start: 0.7986 (t0) cc_final: 0.7555 (t0) REVERT: F 123 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7956 (mm-40) REVERT: F 162 TYR cc_start: 0.6884 (p90) cc_final: 0.6677 (p90) outliers start: 25 outliers final: 15 residues processed: 222 average time/residue: 0.0902 time to fit residues: 28.3692 Evaluate side-chains 208 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 199 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 30.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.190672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.173812 restraints weight = 12708.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.171961 restraints weight = 20149.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.169929 restraints weight = 17592.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.168596 restraints weight = 20602.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.167607 restraints weight = 20355.045| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10718 Z= 0.173 Angle : 0.667 10.816 14574 Z= 0.332 Chirality : 0.043 0.159 1694 Planarity : 0.004 0.050 1834 Dihedral : 4.407 17.512 1466 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.66 % Favored : 93.82 % Rotamer: Outliers : 2.97 % Allowed : 19.28 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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 are not related in a simple way. whole: -1.13 (0.23), residues: 1342 helix: 0.40 (0.26), residues: 400 sheet: -1.27 (0.26), residues: 354 loop : -1.11 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 144 TYR 0.040 0.002 TYR E 142 PHE 0.016 0.002 PHE C 141 TRP 0.017 0.002 TRP A 179 HIS 0.003 0.001 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00405 (10698) covalent geometry : angle 0.66686 (14562) SS BOND : bond 0.00505 ( 6) SS BOND : angle 1.02747 ( 12) hydrogen bonds : bond 0.03646 ( 413) hydrogen bonds : angle 4.94683 ( 1170) metal coordination : bond 0.00126 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6557 (mt-10) cc_final: 0.6330 (mt-10) REVERT: C 82 GLU cc_start: 0.7254 (pm20) cc_final: 0.6938 (tm-30) REVERT: C 91 GLN cc_start: 0.8428 (pp30) cc_final: 0.7837 (pp30) REVERT: C 139 ASN cc_start: 0.7611 (t0) cc_final: 0.7211 (t0) REVERT: D 92 GLU cc_start: 0.7654 (tp30) cc_final: 0.7449 (tp30) REVERT: D 104 TYR cc_start: 0.6540 (OUTLIER) cc_final: 0.6114 (m-10) REVERT: D 168 THR cc_start: 0.6807 (OUTLIER) cc_final: 0.6506 (p) REVERT: B 58 ASN cc_start: 0.7188 (t0) cc_final: 0.6770 (t0) REVERT: B 201 TYR cc_start: 0.6080 (t80) cc_final: 0.5849 (t80) REVERT: B 278 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6640 (mm-30) REVERT: E 139 ASN cc_start: 0.7721 (t0) cc_final: 0.7327 (t0) REVERT: F 123 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7723 (mm-40) outliers start: 34 outliers final: 23 residues processed: 223 average time/residue: 0.0865 time to fit residues: 27.3591 Evaluate side-chains 212 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 199 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 105 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.189279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.172482 restraints weight = 12655.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.170424 restraints weight = 18742.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.168511 restraints weight = 18230.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.167586 restraints weight = 20126.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.166689 restraints weight = 18757.361| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10718 Z= 0.206 Angle : 0.681 10.159 14574 Z= 0.342 Chirality : 0.044 0.167 1694 Planarity : 0.004 0.066 1834 Dihedral : 4.513 18.237 1466 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.63 % Favored : 92.85 % Rotamer: Outliers : 2.79 % Allowed : 20.07 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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 are not related in a simple way. whole: -1.17 (0.23), residues: 1342 helix: 0.49 (0.26), residues: 394 sheet: -1.31 (0.26), residues: 360 loop : -1.18 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 144 TYR 0.018 0.002 TYR E 50 PHE 0.014 0.002 PHE C 84 TRP 0.017 0.002 TRP F 50 HIS 0.004 0.001 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00486 (10698) covalent geometry : angle 0.67982 (14562) SS BOND : bond 0.00373 ( 6) SS BOND : angle 1.78330 ( 12) hydrogen bonds : bond 0.03642 ( 413) hydrogen bonds : angle 4.88803 ( 1170) metal coordination : bond 0.00163 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6435 (mt-10) REVERT: C 91 GLN cc_start: 0.8501 (pp30) cc_final: 0.7910 (pp30) REVERT: C 139 ASN cc_start: 0.7596 (t0) cc_final: 0.7249 (t0) REVERT: D 104 TYR cc_start: 0.6541 (OUTLIER) cc_final: 0.6139 (m-10) REVERT: E 82 GLU cc_start: 0.7187 (pm20) cc_final: 0.6845 (tm-30) REVERT: E 139 ASN cc_start: 0.7665 (t0) cc_final: 0.7365 (t0) REVERT: F 104 TYR cc_start: 0.6607 (OUTLIER) cc_final: 0.6129 (m-10) REVERT: F 123 GLN cc_start: 0.8163 (mm-40) cc_final: 0.7820 (mm-40) outliers start: 32 outliers final: 23 residues processed: 227 average time/residue: 0.0847 time to fit residues: 27.4763 Evaluate side-chains 226 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 104 TYR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 54 optimal weight: 0.1980 chunk 57 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 ASN ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.191554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.174690 restraints weight = 12711.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.172292 restraints weight = 19810.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.169903 restraints weight = 19852.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.169462 restraints weight = 20965.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.168243 restraints weight = 20879.164| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10718 Z= 0.150 Angle : 0.687 11.165 14574 Z= 0.339 Chirality : 0.043 0.158 1694 Planarity : 0.004 0.056 1834 Dihedral : 4.399 17.218 1466 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.81 % Favored : 93.74 % Rotamer: Outliers : 2.53 % Allowed : 21.47 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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 are not related in a simple way. whole: -1.05 (0.23), residues: 1342 helix: 0.60 (0.27), residues: 394 sheet: -1.19 (0.27), residues: 356 loop : -1.16 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 144 TYR 0.019 0.001 TYR B 201 PHE 0.012 0.001 PHE B 184 TRP 0.012 0.001 TRP F 50 HIS 0.002 0.001 HIS D 112 Details of bonding type rmsd covalent geometry : bond 0.00349 (10698) covalent geometry : angle 0.68596 (14562) SS BOND : bond 0.00577 ( 6) SS BOND : angle 1.71453 ( 12) hydrogen bonds : bond 0.03347 ( 413) hydrogen bonds : angle 4.72483 ( 1170) metal coordination : bond 0.00087 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6286 (mt-10) REVERT: C 82 GLU cc_start: 0.7321 (pm20) cc_final: 0.7065 (tm-30) REVERT: C 91 GLN cc_start: 0.8407 (pp30) cc_final: 0.7819 (pp30) REVERT: C 107 GLU cc_start: 0.8023 (pm20) cc_final: 0.7749 (pm20) REVERT: C 139 ASN cc_start: 0.7489 (t0) cc_final: 0.7099 (t0) REVERT: D 104 TYR cc_start: 0.6499 (OUTLIER) cc_final: 0.6128 (m-10) REVERT: D 111 ARG cc_start: 0.7435 (mmp-170) cc_final: 0.7071 (mmp-170) REVERT: B 278 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6670 (mm-30) REVERT: E 82 GLU cc_start: 0.7318 (pm20) cc_final: 0.7025 (tm-30) REVERT: E 139 ASN cc_start: 0.7770 (t0) cc_final: 0.7555 (t0) REVERT: F 104 TYR cc_start: 0.6621 (OUTLIER) cc_final: 0.6173 (m-10) REVERT: F 123 GLN cc_start: 0.7991 (mm-40) cc_final: 0.7743 (mm-40) outliers start: 29 outliers final: 21 residues processed: 230 average time/residue: 0.0860 time to fit residues: 28.2081 Evaluate side-chains 226 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 104 TYR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 168 THR Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 63 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.191196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.179339 restraints weight = 12640.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.177123 restraints weight = 26384.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.175693 restraints weight = 26736.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.174671 restraints weight = 24004.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.174271 restraints weight = 23592.209| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10718 Z= 0.167 Angle : 0.717 14.629 14574 Z= 0.350 Chirality : 0.044 0.170 1694 Planarity : 0.004 0.053 1834 Dihedral : 4.405 17.674 1466 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.33 % Favored : 93.22 % Rotamer: Outliers : 2.62 % Allowed : 22.08 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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 are not related in a simple way. whole: -1.05 (0.23), residues: 1342 helix: 0.55 (0.27), residues: 398 sheet: -1.17 (0.27), residues: 356 loop : -1.16 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 144 TYR 0.022 0.001 TYR C 142 PHE 0.012 0.001 PHE C 84 TRP 0.014 0.001 TRP F 50 HIS 0.003 0.001 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00389 (10698) covalent geometry : angle 0.71525 (14562) SS BOND : bond 0.00471 ( 6) SS BOND : angle 1.97706 ( 12) hydrogen bonds : bond 0.03369 ( 413) hydrogen bonds : angle 4.71529 ( 1170) metal coordination : bond 0.00116 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6510 (mt-10) cc_final: 0.6252 (mt-10) REVERT: C 91 GLN cc_start: 0.8441 (pp30) cc_final: 0.8047 (pp30) REVERT: C 139 ASN cc_start: 0.7392 (t0) cc_final: 0.7024 (t0) REVERT: D 104 TYR cc_start: 0.6497 (OUTLIER) cc_final: 0.6083 (m-10) REVERT: B 88 GLN cc_start: 0.7435 (mm110) cc_final: 0.7212 (mm110) REVERT: F 104 TYR cc_start: 0.6546 (OUTLIER) cc_final: 0.6061 (m-10) REVERT: F 123 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7596 (mm-40) outliers start: 30 outliers final: 24 residues processed: 226 average time/residue: 0.0865 time to fit residues: 28.2136 Evaluate side-chains 222 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 PHE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 104 TYR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 196 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 124 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 78 optimal weight: 0.0670 chunk 106 optimal weight: 7.9990 chunk 121 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.191978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.175536 restraints weight = 12599.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.172805 restraints weight = 19175.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.170647 restraints weight = 21333.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.170002 restraints weight = 21268.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168275 restraints weight = 19892.589| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10718 Z= 0.149 Angle : 0.723 14.136 14574 Z= 0.352 Chirality : 0.043 0.180 1694 Planarity : 0.005 0.072 1834 Dihedral : 4.375 17.260 1466 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.66 % Favored : 93.89 % Rotamer: Outliers : 2.09 % Allowed : 22.77 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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 are not related in a simple way. whole: -0.98 (0.23), residues: 1342 helix: 0.63 (0.27), residues: 394 sheet: -1.12 (0.27), residues: 356 loop : -1.14 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 144 TYR 0.020 0.001 TYR B 201 PHE 0.012 0.001 PHE E 141 TRP 0.013 0.001 TRP F 50 HIS 0.002 0.001 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00344 (10698) covalent geometry : angle 0.72120 (14562) SS BOND : bond 0.00521 ( 6) SS BOND : angle 1.80336 ( 12) hydrogen bonds : bond 0.03260 ( 413) hydrogen bonds : angle 4.65383 ( 1170) metal coordination : bond 0.00083 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6301 (mt-10) REVERT: C 91 GLN cc_start: 0.8361 (pp30) cc_final: 0.7979 (pp30) REVERT: D 104 TYR cc_start: 0.6539 (OUTLIER) cc_final: 0.6098 (m-10) REVERT: B 88 GLN cc_start: 0.7461 (mm110) cc_final: 0.7225 (mm110) REVERT: F 104 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.6068 (m-10) outliers start: 24 outliers final: 21 residues processed: 214 average time/residue: 0.0830 time to fit residues: 25.4816 Evaluate side-chains 217 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain C residue 95 TRP Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 104 TYR Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain F residue 33 TYR Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 104 TYR Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 196 SER Chi-restraints excluded: chain F residue 212 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 72 optimal weight: 8.9990 chunk 78 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 93 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.192108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.181826 restraints weight = 12726.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.180335 restraints weight = 22130.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.178220 restraints weight = 24032.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.168403 restraints weight = 24507.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.163648 restraints weight = 24593.795| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10718 Z= 0.158 Angle : 0.720 13.853 14574 Z= 0.353 Chirality : 0.043 0.181 1694 Planarity : 0.005 0.059 1834 Dihedral : 4.367 17.153 1466 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.18 % Favored : 93.37 % Rotamer: Outliers : 2.53 % Allowed : 22.51 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.86 % 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 are not related in a simple way. whole: -0.92 (0.23), residues: 1342 helix: 0.68 (0.27), residues: 394 sheet: -1.09 (0.27), residues: 356 loop : -1.10 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 144 TYR 0.022 0.001 TYR B 201 PHE 0.010 0.001 PHE D 130 TRP 0.013 0.001 TRP F 50 HIS 0.003 0.001 HIS F 112 Details of bonding type rmsd covalent geometry : bond 0.00368 (10698) covalent geometry : angle 0.71844 (14562) SS BOND : bond 0.00512 ( 6) SS BOND : angle 1.74967 ( 12) hydrogen bonds : bond 0.03238 ( 413) hydrogen bonds : angle 4.61208 ( 1170) metal coordination : bond 0.00093 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1386.16 seconds wall clock time: 24 minutes 49.50 seconds (1489.50 seconds total)