Starting phenix.real_space_refine on Fri Jun 5 02:05:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqr_61740/06_2026/9jqr_61740_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqr_61740/06_2026/9jqr_61740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jqr_61740/06_2026/9jqr_61740_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqr_61740/06_2026/9jqr_61740_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jqr_61740/06_2026/9jqr_61740.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqr_61740/06_2026/9jqr_61740.map" } resolution = 3.0 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= -0.021 sd= 0.336 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 P 2 5.49 5 S 86 5.16 5 C 10971 2.51 5 N 2954 2.21 5 O 3282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17295 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3767 Classifications: {'peptide': 475} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 449} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2260 Classifications: {'peptide': 294} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 281} Chain: "D" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1598 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 11, 'TRANS': 191} Chain breaks: 1 Chain: "E" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3821 Classifications: {'peptide': 475} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 445} Chain breaks: 5 Chain: "F" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3815 Classifications: {'peptide': 475} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 445} Chain breaks: 3 Chain: "G" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1815 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 12, 'TRANS': 215} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'H6P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.53, per 1000 atoms: 0.26 Number of scatterers: 17295 At special positions: 0 Unit cell: (142.5, 152, 292.6, 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) S 86 16.00 P 2 15.00 O 3282 8.00 N 2954 7.00 C 10971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 97 " distance=2.02 Simple disulfide: pdb=" SG CYS A 137 " - pdb=" SG CYS A 191 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 97 " distance=1.99 Simple disulfide: pdb=" SG CYS B 137 " - pdb=" SG CYS B 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 137 " - pdb=" SG CYS E 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 237 " - pdb=" SG CYS F 237 " distance=1.84 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 97 " distance=2.04 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 210 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG B 401 " - " ASN B 86 " " NAG C 1 " - " ASN D 134 " " NAG E 601 " - " ASN E 18 " " NAG E 602 " - " ASN E 86 " " NAG E 603 " - " ASN E 194 " " NAG F 601 " - " ASN F 18 " " NAG F 602 " - " ASN F 86 " " NAG F 603 " - " ASN F 92 " " NAG F 604 " - " ASN F 188 " " NAG F 605 " - " ASN F 194 " " NAG H 1 " - " ASN E 92 " Time building additional restraints: 1.73 Conformation dependent library (CDL) restraints added in 760.1 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 40 sheets defined 18.2% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 219 through 291 removed outlier: 3.888A pdb=" N LEU A 223 " --> pdb=" O TRP A 219 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 297 through 308 removed outlier: 3.922A pdb=" N LEU A 307 " --> pdb=" O TRP A 303 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 60 Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 74 through 77 Processing helix chain 'B' and resid 209 through 215 removed outlier: 4.019A pdb=" N PHE B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 294 Proline residue: B 228 - end of helix removed outlier: 3.665A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY B 294 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.819A pdb=" N GLU D 87 " --> pdb=" O GLU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 189 removed outlier: 4.083A pdb=" N VAL D 189 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.661A pdb=" N ARG E 65 " --> pdb=" O GLU E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.946A pdb=" N ASN E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 296 Proline residue: E 233 - end of helix removed outlier: 3.608A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TRP E 292 " --> pdb=" O GLU E 288 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ARG E 293 " --> pdb=" O GLU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 Processing helix chain 'F' and resid 56 through 60 removed outlier: 3.740A pdb=" N GLN F 60 " --> pdb=" O THR F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 Processing helix chain 'F' and resid 88 through 92 removed outlier: 3.964A pdb=" N GLU F 91 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN F 92 " --> pdb=" O ALA F 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 88 through 92' Processing helix chain 'F' and resid 228 through 295 Proline residue: F 233 - end of helix removed outlier: 3.554A pdb=" N LYS F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU F 278 " --> pdb=" O VAL F 274 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N THR F 295 " --> pdb=" O ARG F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 309 Processing helix chain 'G' and resid 88 through 92 removed outlier: 4.044A pdb=" N ILE G 92 " --> pdb=" O LYS G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 146 removed outlier: 3.575A pdb=" N THR G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 221 removed outlier: 3.548A pdb=" N VAL G 221 " --> pdb=" O LYS G 218 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 14 removed outlier: 6.034A pdb=" N ILE A 11 " --> pdb=" O LYS A 113 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ALA A 115 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 13 " --> pdb=" O ALA A 115 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 56 removed outlier: 4.541A pdb=" N VAL A 49 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 162 removed outlier: 6.903A pdb=" N GLY A 132 " --> pdb=" O TYR A 128 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N TYR A 128 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N HIS A 134 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N TRP B 150 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 147 through 151 removed outlier: 9.135A pdb=" N VAL B 123 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER A 205 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL B 125 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER A 207 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY B 127 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS B 134 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS B 134 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET B 181 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU B 136 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 179 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG B 138 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ALA B 177 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N THR B 140 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 175 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 147 through 151 removed outlier: 9.135A pdb=" N VAL B 123 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER A 205 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL B 125 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER A 207 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLY B 127 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N HIS B 134 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N HIS B 134 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N MET B 181 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLU B 136 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N VAL B 179 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG B 138 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ALA B 177 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N THR B 140 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 175 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL B 166 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 309 through 310 removed outlier: 3.605A pdb=" N LYS A 309 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR A 367 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS A 454 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 315 through 320 removed outlier: 3.661A pdb=" N ASP A 316 " --> pdb=" O LEU A 356 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU A 356 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 9.529A pdb=" N LYS A 318 " --> pdb=" O CYS A 354 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N CYS A 354 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY A 405 " --> pdb=" O ARG A 413 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG A 413 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 414 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR A 420 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.588A pdb=" N LEU A 479 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 5 Processing sheet with id=AB2, first strand: chain 'B' and resid 11 through 14 removed outlier: 6.149A pdb=" N ILE B 11 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA B 115 " --> pdb=" O ILE B 11 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA B 13 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N SER B 40 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL B 46 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 51 " --> pdb=" O LYS B 54 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AB4, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.598A pdb=" N THR D 116 " --> pdb=" O VAL D 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 55 through 56 removed outlier: 3.625A pdb=" N ILE D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP D 37 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG D 51 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE D 35 " --> pdb=" O ARG D 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 129 through 134 removed outlier: 3.808A pdb=" N GLU D 144 " --> pdb=" O TYR D 175 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR D 175 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR D 161 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 129 through 134 removed outlier: 3.808A pdb=" N GLU D 144 " --> pdb=" O TYR D 175 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR D 175 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 152 through 155 Processing sheet with id=AB9, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.676A pdb=" N ALA E 81 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 11 through 14 Processing sheet with id=AC2, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AC3, first strand: chain 'E' and resid 122 through 128 removed outlier: 5.631A pdb=" N ARG E 134 " --> pdb=" O ARG E 126 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE E 173 " --> pdb=" O GLY E 141 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS E 162 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.598A pdb=" N MET E 189 " --> pdb=" O ILE E 206 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 297 through 298 removed outlier: 3.962A pdb=" N LEU E 297 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 299 " --> pdb=" O LEU E 297 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 304 through 305 removed outlier: 4.571A pdb=" N LEU E 348 " --> pdb=" O ASP E 305 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 347 " --> pdb=" O PHE E 460 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE E 460 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY E 349 " --> pdb=" O PRO E 458 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLU E 397 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ARG E 404 " --> pdb=" O GLU E 397 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN E 402 " --> pdb=" O HIS E 399 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 313 through 315 Processing sheet with id=AC8, first strand: chain 'E' and resid 357 through 363 removed outlier: 7.418A pdb=" N PHE E 435 " --> pdb=" O ILE E 444 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 4 through 5 removed outlier: 4.203A pdb=" N HIS F 24 " --> pdb=" O VAL F 5 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 11 through 14 removed outlier: 6.176A pdb=" N ILE F 11 " --> pdb=" O VAL F 113 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA F 115 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA F 13 " --> pdb=" O ALA F 115 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 122 through 127 removed outlier: 3.518A pdb=" N SER F 124 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ARG F 134 " --> pdb=" O ARG F 126 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE F 173 " --> pdb=" O GLY F 141 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR F 176 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL F 164 " --> pdb=" O THR F 176 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 147 through 149 Processing sheet with id=AD4, first strand: chain 'F' and resid 357 through 358 Processing sheet with id=AD5, first strand: chain 'F' and resid 361 through 363 Processing sheet with id=AD6, first strand: chain 'F' and resid 402 through 405 Processing sheet with id=AD7, first strand: chain 'F' and resid 435 through 437 removed outlier: 3.810A pdb=" N TYR F 445 " --> pdb=" O PHE F 435 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASN F 437 " --> pdb=" O HIS F 443 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS F 443 " --> pdb=" O ASN F 437 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.570A pdb=" N THR G 79 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 14 removed outlier: 5.988A pdb=" N SER G 11 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR G 122 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS G 13 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA G 93 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL G 35 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER G 51 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 14 removed outlier: 5.988A pdb=" N SER G 11 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR G 122 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LYS G 13 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA G 93 " --> pdb=" O LEU G 119 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 133 through 136 removed outlier: 4.470A pdb=" N SER G 195 " --> pdb=" O CYS G 154 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 133 through 136 removed outlier: 4.976A pdb=" N TYR G 191 " --> pdb=" O LYS G 158 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 164 through 170 removed outlier: 3.602A pdb=" N HIS G 208 " --> pdb=" O PHE G 227 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2871 1.31 - 1.44: 4642 1.44 - 1.57: 10027 1.57 - 1.69: 3 1.69 - 1.82: 126 Bond restraints: 17669 Sorted by residual: bond pdb=" CA CYS B 23 " pdb=" CB CYS B 23 " ideal model delta sigma weight residual 1.532 1.459 0.073 1.58e-02 4.01e+03 2.14e+01 bond pdb=" N LEU A 82 " pdb=" CA LEU A 82 " ideal model delta sigma weight residual 1.457 1.510 -0.053 1.29e-02 6.01e+03 1.69e+01 bond pdb=" CA SER A 90 " pdb=" C SER A 90 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.25e-02 6.40e+03 1.60e+01 bond pdb=" O16 H6P A 601 " pdb=" P17 H6P A 601 " ideal model delta sigma weight residual 1.697 1.619 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C ALA A 204 " pdb=" O ALA A 204 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.29e-02 6.01e+03 1.39e+01 ... (remaining 17664 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 23238 2.12 - 4.25: 555 4.25 - 6.37: 97 6.37 - 8.50: 15 8.50 - 10.62: 8 Bond angle restraints: 23913 Sorted by residual: angle pdb=" N GLY B 131 " pdb=" CA GLY B 131 " pdb=" C GLY B 131 " ideal model delta sigma weight residual 115.40 104.99 10.41 1.32e+00 5.74e-01 6.22e+01 angle pdb=" C LEU A 227 " pdb=" N PRO A 228 " pdb=" CA PRO A 228 " ideal model delta sigma weight residual 119.32 111.13 8.19 1.14e+00 7.69e-01 5.16e+01 angle pdb=" C LEU A 96 " pdb=" CA LEU A 96 " pdb=" CB LEU A 96 " ideal model delta sigma weight residual 111.17 101.37 9.80 1.54e+00 4.22e-01 4.05e+01 angle pdb=" N ASN A 48 " pdb=" CA ASN A 48 " pdb=" C ASN A 48 " ideal model delta sigma weight residual 108.79 118.09 -9.30 1.53e+00 4.27e-01 3.70e+01 angle pdb=" N TYR A 95 " pdb=" CA TYR A 95 " pdb=" C TYR A 95 " ideal model delta sigma weight residual 108.14 116.67 -8.53 1.52e+00 4.33e-01 3.15e+01 ... (remaining 23908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.23: 10517 29.23 - 58.45: 362 58.45 - 87.68: 30 87.68 - 116.91: 8 116.91 - 146.13: 2 Dihedral angle restraints: 10919 sinusoidal: 4708 harmonic: 6211 Sorted by residual: dihedral pdb=" CB CYS E 237 " pdb=" SG CYS E 237 " pdb=" SG CYS F 237 " pdb=" CB CYS F 237 " ideal model delta sinusoidal sigma weight residual -86.00 -27.69 -58.31 1 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" CB CYS A 137 " pdb=" SG CYS A 137 " pdb=" SG CYS A 191 " pdb=" CB CYS A 191 " ideal model delta sinusoidal sigma weight residual 93.00 142.99 -49.99 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 97 " pdb=" CB CYS F 97 " ideal model delta sinusoidal sigma weight residual 93.00 132.42 -39.42 1 1.00e+01 1.00e-02 2.18e+01 ... (remaining 10916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2382 0.085 - 0.170: 281 0.170 - 0.256: 12 0.256 - 0.341: 1 0.341 - 0.426: 1 Chirality restraints: 2677 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-02 2.50e+03 1.01e+02 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.34e+01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.55e+01 ... (remaining 2674 not shown) Planarity restraints: 3063 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 601 " 0.271 2.00e-02 2.50e+03 2.28e-01 6.50e+02 pdb=" C7 NAG E 601 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG E 601 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG E 601 " -0.386 2.00e-02 2.50e+03 pdb=" O7 NAG E 601 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " -0.228 2.00e-02 2.50e+03 1.91e-01 4.54e+02 pdb=" C7 NAG C 1 " 0.062 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " -0.160 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " 0.317 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.188 2.00e-02 2.50e+03 1.57e-01 3.09e+02 pdb=" C7 NAG H 1 " -0.048 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.135 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.260 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " -0.015 2.00e-02 2.50e+03 ... (remaining 3060 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2268 2.76 - 3.29: 16490 3.29 - 3.83: 27303 3.83 - 4.36: 31088 4.36 - 4.90: 54274 Nonbonded interactions: 131423 Sorted by model distance: nonbonded pdb=" O GLU F 365 " pdb=" OG SER F 467 " model vdw 2.221 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG SER A 139 " model vdw 2.222 3.040 nonbonded pdb=" O PRO E 121 " pdb=" OG SER E 204 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP A 436 " pdb=" OG1 THR A 439 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR G 38 " pdb=" NZ LYS G 111 " model vdw 2.248 3.120 ... (remaining 131418 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: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 2 through 130 or resid 133 through 326 or resid 334 throug \ h 492 or resid 601 through 603)) selection = (chain 'F' and (resid 2 through 406 or resid 409 through 462 or resid 465 throug \ h 481 or resid 483 through 492 or resid 602 through 604)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.310 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.980 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 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 : 0.005 0.193 17697 Z= 0.263 Angle : 0.864 43.957 23984 Z= 0.475 Chirality : 0.050 0.426 2677 Planarity : 0.009 0.228 3052 Dihedral : 14.450 146.134 6872 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.64 % Allowed : 1.17 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.29 (0.18), residues: 2112 helix: 1.73 (0.29), residues: 289 sheet: 0.24 (0.20), residues: 675 loop : -0.97 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 138 TYR 0.022 0.002 TYR B 266 PHE 0.019 0.001 PHE F 459 TRP 0.038 0.002 TRP B 242 HIS 0.005 0.001 HIS E 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.25 (17669) covalent geometry : angle 0.79600 / 0.45 (23913) SS BOND : bond 0.05488 / 2.63 ( 13) SS BOND : angle 9.64820 / 5.91 ( 26) hydrogen bonds : bond 0.13655 / 8.82 ( 684) hydrogen bonds : angle 6.45962 / 4.47 ( 1893) link_BETA1-4 : bond 0.00706 / 0.35 ( 4) link_BETA1-4 : angle 2.79794 / 1.71 ( 12) link_NAG-ASN : bond 0.00533 / 0.32 ( 11) link_NAG-ASN : angle 2.63283 / 1.72 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 452 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 462 average time/residue: 0.7331 time to fit residues: 370.0849 Evaluate side-chains 334 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 327 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 220 ILE Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 300 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** B 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN E 310 HIS E 391 ASN ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN G 147 GLN G 174 ASN ** G 214 HIS ** 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 = 0.3751 r_free = 0.3751 target = 0.081284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.053166 restraints weight = 64147.234| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.01 r_work: 0.2804 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 17697 Z= 0.230 Angle : 0.876 12.011 23984 Z= 0.442 Chirality : 0.051 0.310 2677 Planarity : 0.006 0.076 3052 Dihedral : 8.720 109.242 2674 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.30 % Allowed : 15.15 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.26 (0.18), residues: 2112 helix: 0.90 (0.26), residues: 303 sheet: 0.44 (0.19), residues: 726 loop : -0.90 (0.18), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 262 TYR 0.059 0.003 TYR A 290 PHE 0.026 0.002 PHE E 296 TRP 0.020 0.002 TRP B 242 HIS 0.012 0.002 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (17669) covalent geometry : angle 0.86637 / 0.44 (23913) SS BOND : bond 0.01151 / 0.70 ( 13) SS BOND : angle 1.73082 / 1.23 ( 26) hydrogen bonds : bond 0.05112 / 3.47 ( 684) hydrogen bonds : angle 5.73559 / 3.94 ( 1893) link_BETA1-4 : bond 0.00525 / 0.27 ( 4) link_BETA1-4 : angle 2.97913 / 1.73 ( 12) link_NAG-ASN : bond 0.00532 / 0.35 ( 11) link_NAG-ASN : angle 2.81696 / 1.79 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 339 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 HIS cc_start: 0.8077 (m90) cc_final: 0.7861 (m90) REVERT: A 417 GLU cc_start: 0.8433 (pm20) cc_final: 0.8117 (pm20) REVERT: A 441 ASP cc_start: 0.8517 (m-30) cc_final: 0.7982 (m-30) REVERT: B 14 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.8816 (mmt) REVERT: B 152 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7381 (p0) REVERT: B 201 GLU cc_start: 0.8824 (pm20) cc_final: 0.8613 (pp20) REVERT: B 242 TRP cc_start: 0.8775 (t60) cc_final: 0.8562 (t60) REVERT: D 138 VAL cc_start: 0.8990 (t) cc_final: 0.8761 (m) REVERT: D 159 LYS cc_start: 0.8564 (pmtt) cc_final: 0.8034 (ptpp) REVERT: E 275 GLN cc_start: 0.9113 (pp30) cc_final: 0.8817 (pp30) REVERT: E 281 GLN cc_start: 0.8963 (pp30) cc_final: 0.8226 (pp30) REVERT: E 289 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7908 (tm-30) REVERT: E 295 THR cc_start: 0.9146 (p) cc_final: 0.8873 (p) REVERT: E 357 LYS cc_start: 0.8553 (pmtt) cc_final: 0.8189 (pmtt) REVERT: E 402 GLN cc_start: 0.9197 (pp30) cc_final: 0.8882 (pp30) REVERT: E 459 PHE cc_start: 0.8959 (t80) cc_final: 0.8676 (t80) REVERT: E 485 GLU cc_start: 0.8969 (pm20) cc_final: 0.8636 (pp20) REVERT: F 152 ASP cc_start: 0.8319 (m-30) cc_final: 0.8015 (m-30) REVERT: F 272 GLU cc_start: 0.9221 (tp30) cc_final: 0.8864 (mm-30) REVERT: F 281 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8870 (pp30) REVERT: F 283 LYS cc_start: 0.9078 (tptm) cc_final: 0.8435 (tppt) REVERT: F 287 GLN cc_start: 0.8983 (mt0) cc_final: 0.8418 (mp10) REVERT: F 437 ASN cc_start: 0.9254 (t0) cc_final: 0.8916 (t0) REVERT: G 124 LYS cc_start: 0.9221 (tppp) cc_final: 0.8910 (pptt) REVERT: G 148 LYS cc_start: 0.9269 (mmmm) cc_final: 0.8882 (mmmt) outliers start: 62 outliers final: 24 residues processed: 369 average time/residue: 0.7294 time to fit residues: 294.0929 Evaluate side-chains 322 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 296 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 202 SER Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 339 GLU Chi-restraints excluded: chain F residue 366 ASN Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 152 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 162 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 chunk 153 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 197 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN F 100 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN G 174 ASN ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.080841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052908 restraints weight = 64992.894| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.03 r_work: 0.2797 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17697 Z= 0.177 Angle : 0.818 13.295 23984 Z= 0.408 Chirality : 0.049 0.238 2677 Planarity : 0.006 0.067 3052 Dihedral : 7.408 98.463 2665 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.08 % Allowed : 18.87 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.21 (0.18), residues: 2112 helix: 0.94 (0.27), residues: 303 sheet: 0.46 (0.19), residues: 733 loop : -0.87 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 457 TYR 0.036 0.002 TYR F 239 PHE 0.017 0.002 PHE E 425 TRP 0.022 0.002 TRP E 292 HIS 0.008 0.001 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (17669) covalent geometry : angle 0.81064 / 0.41 (23913) SS BOND : bond 0.01057 / 0.61 ( 13) SS BOND : angle 1.24245 / 0.87 ( 26) hydrogen bonds : bond 0.04812 / 3.30 ( 684) hydrogen bonds : angle 5.57497 / 3.81 ( 1893) link_BETA1-4 : bond 0.00401 / 0.20 ( 4) link_BETA1-4 : angle 2.80139 / 1.62 ( 12) link_NAG-ASN : bond 0.00260 / 0.19 ( 11) link_NAG-ASN : angle 2.44329 / 1.60 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 321 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 HIS cc_start: 0.8025 (m90) cc_final: 0.7764 (OUTLIER) REVERT: A 181 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.4929 (mpt) REVERT: A 262 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.7924 (tpp80) REVERT: A 264 MET cc_start: 0.9227 (tmm) cc_final: 0.8992 (tmm) REVERT: A 417 GLU cc_start: 0.8230 (pm20) cc_final: 0.7914 (pm20) REVERT: A 441 ASP cc_start: 0.8359 (m-30) cc_final: 0.7830 (m-30) REVERT: B 14 MET cc_start: 0.9285 (mmm) cc_final: 0.8862 (mmt) REVERT: B 152 ASN cc_start: 0.7481 (OUTLIER) cc_final: 0.7209 (p0) REVERT: D 159 LYS cc_start: 0.8358 (pmtt) cc_final: 0.8008 (ptpp) REVERT: E 275 GLN cc_start: 0.9062 (pp30) cc_final: 0.8728 (pp30) REVERT: E 292 TRP cc_start: 0.8511 (p-90) cc_final: 0.8071 (p-90) REVERT: E 294 ARG cc_start: 0.8558 (ptt-90) cc_final: 0.8253 (mtm110) REVERT: E 295 THR cc_start: 0.9071 (p) cc_final: 0.8859 (p) REVERT: E 357 LYS cc_start: 0.8327 (pmtt) cc_final: 0.7675 (pmtt) REVERT: F 152 ASP cc_start: 0.8025 (m-30) cc_final: 0.7776 (m-30) REVERT: F 262 ARG cc_start: 0.9142 (ttp80) cc_final: 0.8929 (ttp80) REVERT: F 283 LYS cc_start: 0.9019 (tptm) cc_final: 0.8809 (tppt) REVERT: F 288 GLU cc_start: 0.9047 (pp20) cc_final: 0.8824 (pp20) REVERT: F 336 ASP cc_start: 0.9120 (p0) cc_final: 0.8896 (p0) REVERT: F 359 TYR cc_start: 0.9179 (t80) cc_final: 0.8500 (t80) REVERT: F 385 VAL cc_start: 0.8115 (OUTLIER) cc_final: 0.7856 (m) REVERT: F 386 LEU cc_start: 0.8822 (mm) cc_final: 0.8120 (pp) REVERT: F 433 VAL cc_start: 0.9086 (t) cc_final: 0.8768 (t) REVERT: F 462 LEU cc_start: 0.7923 (tp) cc_final: 0.7619 (tp) REVERT: G 148 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8888 (mmmt) outliers start: 58 outliers final: 24 residues processed: 353 average time/residue: 0.7117 time to fit residues: 275.4671 Evaluate side-chains 317 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 291 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 303 VAL Chi-restraints excluded: chain E residue 445 TYR Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 170 ASP Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 152 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 73 optimal weight: 2.9990 chunk 64 optimal weight: 0.0270 chunk 112 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 95 optimal weight: 0.1980 chunk 59 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 194 optimal weight: 0.0570 chunk 169 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS B 289 GLN D 137 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 ASN F 100 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN G 174 ASN ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.081609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.054174 restraints weight = 64765.232| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.24 r_work: 0.2820 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17697 Z= 0.143 Angle : 0.801 16.925 23984 Z= 0.391 Chirality : 0.049 0.230 2677 Planarity : 0.005 0.061 3052 Dihedral : 6.735 89.748 2665 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.82 % Allowed : 21.05 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.11 (0.18), residues: 2112 helix: 0.94 (0.27), residues: 297 sheet: 0.57 (0.19), residues: 731 loop : -0.79 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 259 TYR 0.036 0.002 TYR F 239 PHE 0.018 0.001 PHE E 425 TRP 0.022 0.001 TRP E 292 HIS 0.005 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (17669) covalent geometry : angle 0.79609 / 0.39 (23913) SS BOND : bond 0.00848 / 0.52 ( 13) SS BOND : angle 1.01660 / 0.67 ( 26) hydrogen bonds : bond 0.04458 / 3.07 ( 684) hydrogen bonds : angle 5.40599 / 3.69 ( 1893) link_BETA1-4 : bond 0.00491 / 0.24 ( 4) link_BETA1-4 : angle 2.54356 / 1.47 ( 12) link_NAG-ASN : bond 0.00261 / 0.18 ( 11) link_NAG-ASN : angle 2.08463 / 1.39 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 307 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 HIS cc_start: 0.8085 (m90) cc_final: 0.7799 (m90) REVERT: A 181 MET cc_start: 0.6075 (OUTLIER) cc_final: 0.4906 (mpt) REVERT: A 257 ARG cc_start: 0.9303 (ptm-80) cc_final: 0.8978 (tmm-80) REVERT: A 262 ARG cc_start: 0.8276 (tpp-160) cc_final: 0.7967 (tpp80) REVERT: A 264 MET cc_start: 0.9281 (tmm) cc_final: 0.9038 (tmm) REVERT: A 417 GLU cc_start: 0.8252 (pm20) cc_final: 0.7928 (pm20) REVERT: A 441 ASP cc_start: 0.8286 (m-30) cc_final: 0.7721 (m-30) REVERT: B 14 MET cc_start: 0.9294 (mmm) cc_final: 0.8775 (mmt) REVERT: B 152 ASN cc_start: 0.7456 (OUTLIER) cc_final: 0.7244 (p0) REVERT: B 242 TRP cc_start: 0.9233 (t-100) cc_final: 0.8718 (t60) REVERT: B 243 ARG cc_start: 0.8870 (ptp-170) cc_final: 0.8635 (ptt-90) REVERT: B 280 GLN cc_start: 0.9419 (mm-40) cc_final: 0.9149 (mm-40) REVERT: D 159 LYS cc_start: 0.8468 (pmtt) cc_final: 0.8132 (ptpp) REVERT: E 259 ARG cc_start: 0.9267 (ptm-80) cc_final: 0.9032 (tmm-80) REVERT: E 275 GLN cc_start: 0.9103 (pp30) cc_final: 0.8511 (pp30) REVERT: E 276 LYS cc_start: 0.9218 (pptt) cc_final: 0.8956 (pptt) REVERT: E 281 GLN cc_start: 0.8709 (pp30) cc_final: 0.8468 (pp30) REVERT: E 295 THR cc_start: 0.9091 (p) cc_final: 0.8787 (p) REVERT: E 357 LYS cc_start: 0.8215 (pmtt) cc_final: 0.7506 (pmtt) REVERT: E 398 MET cc_start: 0.7581 (tpp) cc_final: 0.7351 (tpp) REVERT: E 485 GLU cc_start: 0.8784 (pm20) cc_final: 0.8332 (pp20) REVERT: F 61 MET cc_start: 0.4509 (mpm) cc_final: 0.4306 (mpm) REVERT: F 152 ASP cc_start: 0.7974 (m-30) cc_final: 0.7715 (m-30) REVERT: F 262 ARG cc_start: 0.9146 (ttp80) cc_final: 0.8916 (ttp80) REVERT: F 283 LYS cc_start: 0.9058 (tptm) cc_final: 0.8827 (tppt) REVERT: F 290 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7909 (tp) REVERT: F 336 ASP cc_start: 0.9158 (p0) cc_final: 0.8851 (p0) REVERT: F 386 LEU cc_start: 0.8784 (mm) cc_final: 0.8018 (pp) REVERT: F 433 VAL cc_start: 0.9083 (t) cc_final: 0.8762 (t) REVERT: F 462 LEU cc_start: 0.7953 (tp) cc_final: 0.7645 (tp) REVERT: F 470 PHE cc_start: 0.8918 (m-10) cc_final: 0.8651 (m-10) REVERT: G 104 GLN cc_start: 0.8899 (mp10) cc_final: 0.8657 (mm-40) REVERT: G 125 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8931 (mm-40) REVERT: G 148 LYS cc_start: 0.9186 (mmmm) cc_final: 0.8906 (mmmt) outliers start: 53 outliers final: 22 residues processed: 333 average time/residue: 0.7198 time to fit residues: 263.2782 Evaluate side-chains 306 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 281 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 358 CYS Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 445 TYR Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain G residue 152 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 88 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 chunk 207 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN B 289 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN G 174 ASN ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.080867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052929 restraints weight = 63931.891| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.03 r_work: 0.2801 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17697 Z= 0.164 Angle : 0.826 20.175 23984 Z= 0.405 Chirality : 0.049 0.236 2677 Planarity : 0.005 0.060 3052 Dihedral : 6.469 84.434 2665 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.08 % Allowed : 22.06 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.12 (0.18), residues: 2112 helix: 0.93 (0.28), residues: 299 sheet: 0.67 (0.19), residues: 738 loop : -0.91 (0.19), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 276 TYR 0.035 0.002 TYR F 239 PHE 0.047 0.002 PHE F 257 TRP 0.033 0.002 TRP E 292 HIS 0.007 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (17669) covalent geometry : angle 0.82057 / 0.40 (23913) SS BOND : bond 0.00883 / 0.53 ( 13) SS BOND : angle 1.18862 / 0.81 ( 26) hydrogen bonds : bond 0.04599 / 3.16 ( 684) hydrogen bonds : angle 5.35536 / 3.66 ( 1893) link_BETA1-4 : bond 0.00206 / 0.11 ( 4) link_BETA1-4 : angle 2.45826 / 1.45 ( 12) link_NAG-ASN : bond 0.00239 / 0.18 ( 11) link_NAG-ASN : angle 2.16145 / 1.42 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 293 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 HIS cc_start: 0.8278 (m90) cc_final: 0.8056 (m90) REVERT: A 181 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.5023 (mpt) REVERT: A 257 ARG cc_start: 0.9356 (ptm-80) cc_final: 0.9045 (tmm-80) REVERT: A 262 ARG cc_start: 0.8382 (tpp-160) cc_final: 0.8117 (tpp80) REVERT: A 264 MET cc_start: 0.9359 (tmm) cc_final: 0.9100 (tmm) REVERT: A 417 GLU cc_start: 0.8481 (pm20) cc_final: 0.8136 (pm20) REVERT: A 441 ASP cc_start: 0.8449 (m-30) cc_final: 0.7891 (m-30) REVERT: B 14 MET cc_start: 0.9346 (mmm) cc_final: 0.8936 (mmt) REVERT: B 152 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7519 (p0) REVERT: B 242 TRP cc_start: 0.9308 (t-100) cc_final: 0.8803 (t60) REVERT: D 159 LYS cc_start: 0.8663 (pmtt) cc_final: 0.8299 (ptpp) REVERT: E 259 ARG cc_start: 0.9307 (ptm-80) cc_final: 0.9022 (tmm160) REVERT: E 263 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8853 (mm-30) REVERT: E 295 THR cc_start: 0.9150 (p) cc_final: 0.8936 (p) REVERT: E 357 LYS cc_start: 0.8296 (pmtt) cc_final: 0.7552 (pmtt) REVERT: F 56 ARG cc_start: 0.8514 (mpp80) cc_final: 0.8037 (mpp-170) REVERT: F 61 MET cc_start: 0.4712 (mpm) cc_final: 0.4395 (mpm) REVERT: F 133 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7653 (mm) REVERT: F 152 ASP cc_start: 0.8277 (m-30) cc_final: 0.8040 (m-30) REVERT: F 260 GLU cc_start: 0.9419 (pt0) cc_final: 0.9154 (pt0) REVERT: F 290 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8085 (tp) REVERT: F 336 ASP cc_start: 0.9236 (p0) cc_final: 0.8909 (p0) REVERT: F 341 PHE cc_start: 0.8108 (m-10) cc_final: 0.6936 (m-10) REVERT: F 404 ARG cc_start: 0.8761 (mtm180) cc_final: 0.8438 (mmm-85) REVERT: F 462 LEU cc_start: 0.8127 (tp) cc_final: 0.7817 (tp) REVERT: F 470 PHE cc_start: 0.8912 (m-10) cc_final: 0.8627 (m-10) REVERT: G 125 GLN cc_start: 0.9259 (mm-40) cc_final: 0.9043 (mm-40) REVERT: G 148 LYS cc_start: 0.9317 (mmmm) cc_final: 0.9091 (mppt) outliers start: 58 outliers final: 24 residues processed: 325 average time/residue: 0.7083 time to fit residues: 252.9719 Evaluate side-chains 306 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 278 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 334 GLN Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 445 TYR Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 433 VAL Chi-restraints excluded: chain F residue 438 MET Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain G residue 3 HIS Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 152 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 31 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 188 optimal weight: 0.0070 chunk 48 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 HIS ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN G 174 ASN ** G 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.079712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051743 restraints weight = 63946.748| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.02 r_work: 0.2769 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17697 Z= 0.195 Angle : 0.879 20.352 23984 Z= 0.430 Chirality : 0.050 0.235 2677 Planarity : 0.005 0.062 3052 Dihedral : 6.493 78.967 2663 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.98 % Allowed : 23.34 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.20 (0.18), residues: 2112 helix: 0.69 (0.28), residues: 298 sheet: 0.67 (0.19), residues: 732 loop : -0.93 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 340 TYR 0.034 0.002 TYR F 239 PHE 0.022 0.002 PHE E 425 TRP 0.036 0.002 TRP E 292 HIS 0.008 0.002 HIS D 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (17669) covalent geometry : angle 0.87316 / 0.43 (23913) SS BOND : bond 0.00949 / 0.58 ( 13) SS BOND : angle 1.55367 / 1.02 ( 26) hydrogen bonds : bond 0.04837 / 3.32 ( 684) hydrogen bonds : angle 5.44173 / 3.72 ( 1893) link_BETA1-4 : bond 0.00342 / 0.18 ( 4) link_BETA1-4 : angle 2.24407 / 1.33 ( 12) link_NAG-ASN : bond 0.00308 / 0.23 ( 11) link_NAG-ASN : angle 2.33023 / 1.51 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 290 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 HIS cc_start: 0.8291 (m90) cc_final: 0.8083 (m90) REVERT: A 181 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.5100 (mpt) REVERT: A 264 MET cc_start: 0.9357 (tmm) cc_final: 0.9095 (tmm) REVERT: A 441 ASP cc_start: 0.8415 (m-30) cc_final: 0.8127 (m-30) REVERT: B 14 MET cc_start: 0.9342 (OUTLIER) cc_final: 0.9050 (mmm) REVERT: B 170 VAL cc_start: 0.9147 (OUTLIER) cc_final: 0.8872 (t) REVERT: B 242 TRP cc_start: 0.9293 (t-100) cc_final: 0.8575 (t60) REVERT: D 159 LYS cc_start: 0.8696 (pmtt) cc_final: 0.8348 (ptpp) REVERT: E 63 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8889 (mt-10) REVERT: E 259 ARG cc_start: 0.9307 (ptm-80) cc_final: 0.9007 (tmm160) REVERT: E 262 ARG cc_start: 0.9136 (mmt90) cc_final: 0.8916 (mmt90) REVERT: E 263 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8883 (mm-30) REVERT: E 295 THR cc_start: 0.9162 (p) cc_final: 0.8941 (p) REVERT: E 357 LYS cc_start: 0.8355 (pmtt) cc_final: 0.7591 (pmtt) REVERT: F 56 ARG cc_start: 0.8588 (mpp80) cc_final: 0.8136 (mpp-170) REVERT: F 61 MET cc_start: 0.4810 (mpm) cc_final: 0.4540 (mpm) REVERT: F 133 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7835 (mm) REVERT: F 152 ASP cc_start: 0.8318 (m-30) cc_final: 0.8071 (m-30) REVERT: F 242 ASN cc_start: 0.8900 (m-40) cc_final: 0.8417 (m-40) REVERT: F 262 ARG cc_start: 0.9079 (ttp80) cc_final: 0.8817 (ttp80) REVERT: F 290 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8159 (tp) REVERT: F 386 LEU cc_start: 0.8925 (mm) cc_final: 0.8210 (pp) REVERT: F 393 PHE cc_start: 0.7759 (m-80) cc_final: 0.7522 (m-80) REVERT: F 411 ARG cc_start: 0.8453 (mtm180) cc_final: 0.7671 (ttm-80) REVERT: F 462 LEU cc_start: 0.8254 (tp) cc_final: 0.7932 (tp) REVERT: F 470 PHE cc_start: 0.8938 (m-10) cc_final: 0.8678 (m-10) REVERT: G 146 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9116 (mt) outliers start: 56 outliers final: 24 residues processed: 321 average time/residue: 0.6667 time to fit residues: 235.7844 Evaluate side-chains 294 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 391 ASN Chi-restraints excluded: chain E residue 445 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain G residue 3 HIS Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 152 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 162 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 21 optimal weight: 0.0470 chunk 11 optimal weight: 4.9990 overall best weight: 1.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN G 174 ASN ** G 214 HIS ** 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 = 0.3706 r_free = 0.3706 target = 0.079170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.051256 restraints weight = 64001.104| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 3.00 r_work: 0.2753 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 17697 Z= 0.208 Angle : 0.913 20.328 23984 Z= 0.448 Chirality : 0.050 0.238 2677 Planarity : 0.006 0.062 3052 Dihedral : 6.385 74.426 2660 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.82 % Allowed : 24.56 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.26 (0.18), residues: 2112 helix: 0.48 (0.28), residues: 301 sheet: 0.71 (0.19), residues: 724 loop : -0.98 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 259 TYR 0.051 0.002 TYR B 239 PHE 0.047 0.002 PHE F 257 TRP 0.038 0.002 TRP B 219 HIS 0.008 0.002 HIS D 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (17669) covalent geometry : angle 0.90657 / 0.45 (23913) SS BOND : bond 0.00920 / 0.57 ( 13) SS BOND : angle 1.67373 / 1.09 ( 26) hydrogen bonds : bond 0.04953 / 3.39 ( 684) hydrogen bonds : angle 5.52402 / 3.77 ( 1893) link_BETA1-4 : bond 0.00565 / 0.28 ( 4) link_BETA1-4 : angle 2.08611 / 1.24 ( 12) link_NAG-ASN : bond 0.00333 / 0.25 ( 11) link_NAG-ASN : angle 2.41764 / 1.56 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 286 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.5199 (mpt) REVERT: A 257 ARG cc_start: 0.9307 (ptm-80) cc_final: 0.9015 (tmm-80) REVERT: A 264 MET cc_start: 0.9355 (tmm) cc_final: 0.9075 (tmm) REVERT: A 398 GLU cc_start: 0.8736 (mp0) cc_final: 0.8519 (mp0) REVERT: A 441 ASP cc_start: 0.8546 (m-30) cc_final: 0.8198 (m-30) REVERT: B 14 MET cc_start: 0.9340 (OUTLIER) cc_final: 0.9050 (mmm) REVERT: B 170 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8871 (t) REVERT: B 242 TRP cc_start: 0.9286 (t-100) cc_final: 0.8608 (t60) REVERT: B 246 LYS cc_start: 0.9265 (ptpp) cc_final: 0.8679 (ptpt) REVERT: D 159 LYS cc_start: 0.8743 (pmtt) cc_final: 0.8418 (ptpp) REVERT: E 259 ARG cc_start: 0.9313 (ptm-80) cc_final: 0.9054 (tmm160) REVERT: E 263 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8875 (mm-30) REVERT: E 275 GLN cc_start: 0.9085 (pp30) cc_final: 0.8432 (pp30) REVERT: E 276 LYS cc_start: 0.9279 (pptt) cc_final: 0.9009 (pptt) REVERT: E 357 LYS cc_start: 0.8348 (pmtt) cc_final: 0.7606 (pmtt) REVERT: E 459 PHE cc_start: 0.8798 (t80) cc_final: 0.8491 (t80) REVERT: F 56 ARG cc_start: 0.8606 (mpp80) cc_final: 0.8186 (mpp-170) REVERT: F 61 MET cc_start: 0.4845 (mpm) cc_final: 0.4604 (mpm) REVERT: F 133 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7892 (mm) REVERT: F 152 ASP cc_start: 0.8342 (m-30) cc_final: 0.8093 (m-30) REVERT: F 283 LYS cc_start: 0.9503 (tppt) cc_final: 0.8926 (tttt) REVERT: F 287 GLN cc_start: 0.9302 (mm-40) cc_final: 0.8977 (mt0) REVERT: F 290 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8294 (tp) REVERT: F 336 ASP cc_start: 0.9300 (p0) cc_final: 0.8701 (p0) REVERT: F 462 LEU cc_start: 0.8362 (tp) cc_final: 0.8025 (tp) REVERT: F 470 PHE cc_start: 0.8846 (m-10) cc_final: 0.8557 (m-10) outliers start: 53 outliers final: 28 residues processed: 316 average time/residue: 0.6728 time to fit residues: 234.2883 Evaluate side-chains 304 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 14 MET Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 403 TYR Chi-restraints excluded: chain E residue 445 TYR Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 252 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 432 ASP Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain G residue 3 HIS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 152 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 101 optimal weight: 0.0070 chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 204 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** G 214 HIS ** 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 = 0.3718 r_free = 0.3718 target = 0.079703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.051824 restraints weight = 64059.787| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.99 r_work: 0.2772 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.4888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17697 Z= 0.173 Angle : 0.927 20.609 23984 Z= 0.451 Chirality : 0.050 0.232 2677 Planarity : 0.005 0.061 3052 Dihedral : 6.259 69.975 2660 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.97 % Allowed : 26.37 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.31 (0.18), residues: 2112 helix: 0.36 (0.28), residues: 298 sheet: 0.70 (0.19), residues: 727 loop : -1.00 (0.18), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 259 TYR 0.039 0.002 TYR F 239 PHE 0.024 0.002 PHE E 425 TRP 0.040 0.002 TRP B 219 HIS 0.008 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.17 (17669) covalent geometry : angle 0.92209 / 0.45 (23913) SS BOND : bond 0.00786 / 0.48 ( 13) SS BOND : angle 1.40904 / 0.91 ( 26) hydrogen bonds : bond 0.04828 / 3.31 ( 684) hydrogen bonds : angle 5.48901 / 3.75 ( 1893) link_BETA1-4 : bond 0.00287 / 0.15 ( 4) link_BETA1-4 : angle 1.86422 / 1.13 ( 12) link_NAG-ASN : bond 0.00251 / 0.18 ( 11) link_NAG-ASN : angle 2.27941 / 1.48 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7061 (mpp) cc_final: 0.6787 (pmm) REVERT: A 181 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.5065 (mpt) REVERT: A 257 ARG cc_start: 0.9310 (ptm-80) cc_final: 0.9007 (tmm-80) REVERT: A 264 MET cc_start: 0.9351 (tmm) cc_final: 0.9109 (tmm) REVERT: A 398 GLU cc_start: 0.8716 (mp0) cc_final: 0.8397 (mp0) REVERT: A 441 ASP cc_start: 0.8561 (m-30) cc_final: 0.8206 (m-30) REVERT: B 14 MET cc_start: 0.9328 (mmm) cc_final: 0.9026 (mmm) REVERT: B 170 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8842 (t) REVERT: B 242 TRP cc_start: 0.9312 (t-100) cc_final: 0.8495 (t60) REVERT: B 246 LYS cc_start: 0.9275 (ptpp) cc_final: 0.8289 (pttm) REVERT: D 159 LYS cc_start: 0.8777 (pmtt) cc_final: 0.8422 (ptpp) REVERT: E 63 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8868 (mt-10) REVERT: E 259 ARG cc_start: 0.9320 (ptm-80) cc_final: 0.8991 (tmm160) REVERT: E 263 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8856 (mm-30) REVERT: E 276 LYS cc_start: 0.9230 (pptt) cc_final: 0.8961 (pptt) REVERT: E 283 LYS cc_start: 0.9458 (tptp) cc_final: 0.9112 (tppt) REVERT: E 357 LYS cc_start: 0.8344 (pmtt) cc_final: 0.7630 (pmtt) REVERT: E 459 PHE cc_start: 0.8846 (t80) cc_final: 0.8538 (t80) REVERT: F 39 PHE cc_start: 0.6964 (p90) cc_final: 0.6760 (p90) REVERT: F 56 ARG cc_start: 0.8611 (mpp80) cc_final: 0.8177 (mpp-170) REVERT: F 61 MET cc_start: 0.4851 (mpm) cc_final: 0.4634 (mpm) REVERT: F 133 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7839 (mm) REVERT: F 152 ASP cc_start: 0.8301 (m-30) cc_final: 0.8027 (m-30) REVERT: F 242 ASN cc_start: 0.8902 (m-40) cc_final: 0.8541 (m-40) REVERT: F 246 LYS cc_start: 0.9454 (mmtt) cc_final: 0.9201 (mptp) REVERT: F 260 GLU cc_start: 0.9135 (pt0) cc_final: 0.8903 (pt0) REVERT: F 283 LYS cc_start: 0.9472 (tppt) cc_final: 0.8803 (tppp) REVERT: F 287 GLN cc_start: 0.9312 (mm-40) cc_final: 0.8962 (mt0) REVERT: F 290 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8292 (tp) REVERT: F 339 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8729 (pp20) REVERT: F 404 ARG cc_start: 0.8819 (mtm180) cc_final: 0.8410 (mmm-85) REVERT: F 432 ASP cc_start: 0.8051 (t0) cc_final: 0.7408 (OUTLIER) REVERT: F 462 LEU cc_start: 0.8387 (tp) cc_final: 0.8041 (tp) REVERT: F 470 PHE cc_start: 0.8865 (m-10) cc_final: 0.8574 (m-10) outliers start: 37 outliers final: 23 residues processed: 304 average time/residue: 0.6723 time to fit residues: 225.4089 Evaluate side-chains 298 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 273 ARG Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 445 TYR Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain G residue 3 HIS Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 152 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 200 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 147 GLN ** G 214 HIS ** 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 = 0.3708 r_free = 0.3708 target = 0.079203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.051325 restraints weight = 64084.141| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.02 r_work: 0.2758 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17697 Z= 0.189 Angle : 0.959 20.691 23984 Z= 0.469 Chirality : 0.051 0.249 2677 Planarity : 0.006 0.061 3052 Dihedral : 6.284 62.427 2660 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 1.54 % Allowed : 27.17 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.36 (0.18), residues: 2112 helix: 0.15 (0.28), residues: 298 sheet: 0.74 (0.19), residues: 725 loop : -1.03 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG E 291 TYR 0.041 0.002 TYR F 239 PHE 0.033 0.002 PHE E 296 TRP 0.042 0.002 TRP E 292 HIS 0.007 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.19 (17669) covalent geometry : angle 0.95403 / 0.47 (23913) SS BOND : bond 0.00855 / 0.53 ( 13) SS BOND : angle 1.52554 / 1.00 ( 26) hydrogen bonds : bond 0.05043 / 3.45 ( 684) hydrogen bonds : angle 5.50844 / 3.78 ( 1893) link_BETA1-4 : bond 0.00318 / 0.16 ( 4) link_BETA1-4 : angle 1.87412 / 1.12 ( 12) link_NAG-ASN : bond 0.00293 / 0.22 ( 11) link_NAG-ASN : angle 2.31740 / 1.50 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 280 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7167 (mpp) cc_final: 0.6962 (pmm) REVERT: A 181 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.5170 (mpt) REVERT: A 257 ARG cc_start: 0.9328 (ptm-80) cc_final: 0.9024 (tmm-80) REVERT: A 264 MET cc_start: 0.9362 (tmm) cc_final: 0.9089 (tmm) REVERT: A 398 GLU cc_start: 0.8740 (mp0) cc_final: 0.8413 (mp0) REVERT: A 441 ASP cc_start: 0.8533 (m-30) cc_final: 0.8161 (m-30) REVERT: B 170 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8844 (t) REVERT: B 242 TRP cc_start: 0.9312 (t-100) cc_final: 0.8541 (t60) REVERT: B 246 LYS cc_start: 0.9335 (ptpp) cc_final: 0.8388 (ptpp) REVERT: D 159 LYS cc_start: 0.8791 (pmtt) cc_final: 0.8441 (ptpp) REVERT: E 259 ARG cc_start: 0.9325 (ptm-80) cc_final: 0.9067 (tmm160) REVERT: E 263 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8922 (mm-30) REVERT: E 275 GLN cc_start: 0.8985 (pp30) cc_final: 0.8456 (pp30) REVERT: E 276 LYS cc_start: 0.9287 (pptt) cc_final: 0.8998 (pptt) REVERT: E 357 LYS cc_start: 0.8326 (pmtt) cc_final: 0.7520 (pmtt) REVERT: E 459 PHE cc_start: 0.8897 (t80) cc_final: 0.8655 (t80) REVERT: F 33 ASP cc_start: 0.8740 (p0) cc_final: 0.8478 (p0) REVERT: F 56 ARG cc_start: 0.8641 (mpp80) cc_final: 0.8219 (mpp-170) REVERT: F 61 MET cc_start: 0.4907 (mpm) cc_final: 0.4630 (mpm) REVERT: F 152 ASP cc_start: 0.8336 (m-30) cc_final: 0.8075 (m-30) REVERT: F 242 ASN cc_start: 0.8913 (m-40) cc_final: 0.8618 (m-40) REVERT: F 283 LYS cc_start: 0.9523 (tppt) cc_final: 0.8987 (tttt) REVERT: F 287 GLN cc_start: 0.9314 (mm-40) cc_final: 0.8944 (mt0) REVERT: F 290 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8349 (tp) REVERT: F 336 ASP cc_start: 0.9287 (p0) cc_final: 0.8711 (p0) REVERT: F 359 TYR cc_start: 0.9224 (t80) cc_final: 0.8688 (t80) REVERT: F 432 ASP cc_start: 0.8241 (t0) cc_final: 0.7486 (t0) REVERT: F 462 LEU cc_start: 0.8442 (tp) cc_final: 0.8098 (tp) REVERT: F 470 PHE cc_start: 0.8852 (m-10) cc_final: 0.8567 (m-10) REVERT: G 105 GLU cc_start: 0.9098 (mm-30) cc_final: 0.8869 (mp0) outliers start: 29 outliers final: 23 residues processed: 296 average time/residue: 0.6865 time to fit residues: 224.4729 Evaluate side-chains 298 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 445 TYR Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain G residue 3 HIS Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 152 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 24 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 115 optimal weight: 0.0870 chunk 194 optimal weight: 0.7980 chunk 117 optimal weight: 0.0040 chunk 9 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.4770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 HIS ** 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 = 0.3728 r_free = 0.3728 target = 0.080040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.052304 restraints weight = 64029.917| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.04 r_work: 0.2788 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17697 Z= 0.164 Angle : 0.994 20.868 23984 Z= 0.482 Chirality : 0.051 0.341 2677 Planarity : 0.005 0.061 3052 Dihedral : 6.118 56.283 2660 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.54 % Allowed : 27.59 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.33 (0.18), residues: 2112 helix: 0.16 (0.28), residues: 292 sheet: 0.75 (0.19), residues: 742 loop : -1.04 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 291 TYR 0.049 0.002 TYR A 95 PHE 0.071 0.002 PHE F 257 TRP 0.045 0.002 TRP B 219 HIS 0.014 0.001 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (17669) covalent geometry : angle 0.99026 / 0.48 (23913) SS BOND : bond 0.00659 / 0.41 ( 13) SS BOND : angle 1.31630 / 0.83 ( 26) hydrogen bonds : bond 0.04844 / 3.31 ( 684) hydrogen bonds : angle 5.47369 / 3.76 ( 1893) link_BETA1-4 : bond 0.00360 / 0.18 ( 4) link_BETA1-4 : angle 1.59173 / 0.97 ( 12) link_NAG-ASN : bond 0.00250 / 0.17 ( 11) link_NAG-ASN : angle 2.13634 / 1.40 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 273 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 MET cc_start: 0.7206 (mpp) cc_final: 0.6948 (pmm) REVERT: A 181 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.5141 (mpt) REVERT: A 257 ARG cc_start: 0.9311 (ptm-80) cc_final: 0.9009 (tmm-80) REVERT: A 264 MET cc_start: 0.9350 (tmm) cc_final: 0.9113 (tmm) REVERT: A 398 GLU cc_start: 0.8725 (mp0) cc_final: 0.8431 (mp0) REVERT: A 441 ASP cc_start: 0.8493 (m-30) cc_final: 0.8062 (m-30) REVERT: B 170 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8869 (t) REVERT: B 242 TRP cc_start: 0.9304 (t-100) cc_final: 0.8560 (t60) REVERT: B 246 LYS cc_start: 0.9342 (ptpp) cc_final: 0.8616 (ptpt) REVERT: B 283 LEU cc_start: 0.9203 (pp) cc_final: 0.8963 (pt) REVERT: D 159 LYS cc_start: 0.8723 (pmtt) cc_final: 0.8408 (ptpp) REVERT: E 63 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8855 (mt-10) REVERT: E 259 ARG cc_start: 0.9334 (ptm-80) cc_final: 0.9087 (tmm160) REVERT: E 263 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8884 (mm-30) REVERT: E 276 LYS cc_start: 0.9274 (pptt) cc_final: 0.9032 (pptt) REVERT: E 283 LYS cc_start: 0.9450 (tppt) cc_final: 0.9235 (tppt) REVERT: E 357 LYS cc_start: 0.8314 (pmtt) cc_final: 0.7545 (pmtt) REVERT: F 56 ARG cc_start: 0.8648 (mpp80) cc_final: 0.8216 (mpp-170) REVERT: F 152 ASP cc_start: 0.8257 (m-30) cc_final: 0.7999 (m-30) REVERT: F 283 LYS cc_start: 0.9468 (tppt) cc_final: 0.8800 (tppp) REVERT: F 287 GLN cc_start: 0.9311 (mm-40) cc_final: 0.8907 (mt0) REVERT: F 290 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8315 (tp) REVERT: F 336 ASP cc_start: 0.9260 (p0) cc_final: 0.8656 (p0) REVERT: F 359 TYR cc_start: 0.9201 (t80) cc_final: 0.8705 (t80) REVERT: F 462 LEU cc_start: 0.8399 (tp) cc_final: 0.8062 (tp) REVERT: F 470 PHE cc_start: 0.8802 (m-10) cc_final: 0.8527 (m-10) outliers start: 29 outliers final: 22 residues processed: 292 average time/residue: 0.6492 time to fit residues: 209.6634 Evaluate side-chains 298 residues out of total 1881 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 273 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 MET Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain D residue 7 GLU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain E residue 267 LYS Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 445 TYR Chi-restraints excluded: chain E residue 471 ILE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 436 TYR Chi-restraints excluded: chain F residue 491 HIS Chi-restraints excluded: chain G residue 3 HIS Chi-restraints excluded: chain G residue 152 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 92 optimal weight: 0.8980 chunk 166 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 ASN ** G 214 HIS ** 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 = 0.3714 r_free = 0.3714 target = 0.079462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.051736 restraints weight = 64467.324| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.03 r_work: 0.2770 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 17697 Z= 0.190 Angle : 1.032 20.552 23984 Z= 0.497 Chirality : 0.052 0.366 2677 Planarity : 0.006 0.084 3052 Dihedral : 6.166 54.494 2660 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.79 % Rotamer: Outliers : 1.49 % Allowed : 28.02 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.39 (0.18), residues: 2112 helix: 0.07 (0.28), residues: 292 sheet: 0.73 (0.19), residues: 740 loop : -1.07 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 291 TYR 0.042 0.002 TYR F 239 PHE 0.067 0.002 PHE F 257 TRP 0.043 0.002 TRP B 219 HIS 0.008 0.001 HIS F 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (17669) covalent geometry : angle 1.02848 / 0.50 (23913) SS BOND : bond 0.00788 / 0.50 ( 13) SS BOND : angle 1.48899 / 0.97 ( 26) hydrogen bonds : bond 0.05002 / 3.40 ( 684) hydrogen bonds : angle 5.50562 / 3.79 ( 1893) link_BETA1-4 : bond 0.00323 / 0.16 ( 4) link_BETA1-4 : angle 1.73420 / 1.04 ( 12) link_NAG-ASN : bond 0.00272 / 0.20 ( 11) link_NAG-ASN : angle 2.20450 / 1.43 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9595.08 seconds wall clock time: 163 minutes 24.52 seconds (9804.52 seconds total)