Starting phenix.real_space_refine on Wed Feb 12 19:11:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iw7_35763/02_2025/8iw7_35763.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iw7_35763/02_2025/8iw7_35763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iw7_35763/02_2025/8iw7_35763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iw7_35763/02_2025/8iw7_35763.map" model { file = "/net/cci-nas-00/data/ceres_data/8iw7_35763/02_2025/8iw7_35763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iw7_35763/02_2025/8iw7_35763.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5310 2.51 5 N 1415 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8305 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1971 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 147 Chain: "B" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2437 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 110 Chain: "A" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1839 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 74 Chain: "S" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1680 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ARG:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 57 Chain: "Y" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 369 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.18, per 1000 atoms: 0.62 Number of scatterers: 8305 At special positions: 0 Unit cell: (105.448, 101.144, 120.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1532 8.00 N 1415 7.00 C 5310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 190 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.0 seconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 12 sheets defined 36.8% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'R' and resid 37 through 59 removed outlier: 4.501A pdb=" N ASN R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU R 52 " --> pdb=" O PHE R 48 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL R 53 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE R 57 " --> pdb=" O VAL R 53 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 64 removed outlier: 3.627A pdb=" N LEU R 63 " --> pdb=" O PHE R 60 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS R 64 " --> pdb=" O LYS R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 60 through 64' Processing helix chain 'R' and resid 65 through 84 removed outlier: 4.017A pdb=" N LEU R 70 " --> pdb=" O PRO R 66 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 removed outlier: 4.214A pdb=" N PHE R 88 " --> pdb=" O THR R 84 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 116 removed outlier: 4.517A pdb=" N CYS R 110 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP R 112 " --> pdb=" O HIS R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 136 removed outlier: 3.826A pdb=" N PHE R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS R 122 " --> pdb=" O ALA R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 163 removed outlier: 3.696A pdb=" N ILE R 153 " --> pdb=" O SER R 149 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA R 154 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER R 160 " --> pdb=" O SER R 156 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL R 161 " --> pdb=" O TRP R 157 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR R 163 " --> pdb=" O PHE R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 169 removed outlier: 3.810A pdb=" N TYR R 169 " --> pdb=" O PHE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 185 removed outlier: 3.788A pdb=" N VAL R 182 " --> pdb=" O GLU R 178 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 232 removed outlier: 3.805A pdb=" N LEU R 200 " --> pdb=" O GLN R 196 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU R 201 " --> pdb=" O ASN R 197 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE R 206 " --> pdb=" O CYS R 202 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 208 " --> pdb=" O LEU R 204 " (cutoff:3.500A) Proline residue: R 209 - end of helix removed outlier: 4.176A pdb=" N MET R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE R 220 " --> pdb=" O LEU R 216 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA R 228 " --> pdb=" O ALA R 224 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 269 removed outlier: 3.714A pdb=" N LYS R 258 " --> pdb=" O ARG R 254 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE R 267 " --> pdb=" O ALA R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 280 removed outlier: 4.008A pdb=" N TYR R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE R 280 " --> pdb=" O ILE R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 283 No H-bonds generated for 'chain 'R' and resid 281 through 283' Processing helix chain 'R' and resid 289 through 292 Processing helix chain 'R' and resid 293 through 311 removed outlier: 4.065A pdb=" N VAL R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 323 removed outlier: 3.686A pdb=" N ARG R 319 " --> pdb=" O TYR R 315 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA R 321 " --> pdb=" O TRP R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 324 through 326 No H-bonds generated for 'chain 'R' and resid 324 through 326' Processing helix chain 'B' and resid 5 through 26 removed outlier: 4.481A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'A' and resid 6 through 39 removed outlier: 3.920A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 253 through 278 removed outlier: 4.435A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU A 268 " --> pdb=" O ASN A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.601A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.703A pdb=" N ILE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.141A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'Y' and resid 10 through 24 Processing helix chain 'Y' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.787A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.040A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.580A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.321A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 191 removed outlier: 4.578A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.010A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.582A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 315 through 320 removed outlier: 3.685A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.548A pdb=" N VAL A 217 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 9.776A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 5 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.601A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 148 through 149 removed outlier: 3.717A pdb=" N GLU S 247 " --> pdb=" O VAL S 148 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU S 246 " --> pdb=" O GLY S 226 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) 360 hydrogen bonds defined for protein. 1035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.38 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2676 1.34 - 1.46: 1598 1.46 - 1.58: 4147 1.58 - 1.70: 0 1.70 - 1.81: 64 Bond restraints: 8485 Sorted by residual: bond pdb=" N GLN A 390 " pdb=" CA GLN A 390 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.66e+00 bond pdb=" N ARG A 385 " pdb=" CA ARG A 385 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.30e-02 5.92e+03 4.27e+00 bond pdb=" CA ASN R 307 " pdb=" C ASN R 307 " ideal model delta sigma weight residual 1.524 1.545 -0.022 1.26e-02 6.30e+03 2.91e+00 bond pdb=" N PEA R 401 " pdb=" C1 PEA R 401 " ideal model delta sigma weight residual 1.486 1.452 0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" C ASP A 381 " pdb=" O ASP A 381 " ideal model delta sigma weight residual 1.237 1.218 0.019 1.19e-02 7.06e+03 2.42e+00 ... (remaining 8480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 11256 1.84 - 3.69: 250 3.69 - 5.53: 47 5.53 - 7.37: 9 7.37 - 9.22: 6 Bond angle restraints: 11568 Sorted by residual: angle pdb=" N GLN B 17 " pdb=" CA GLN B 17 " pdb=" C GLN B 17 " ideal model delta sigma weight residual 111.14 103.58 7.56 1.08e+00 8.57e-01 4.90e+01 angle pdb=" N ILE A 308 " pdb=" CA ILE A 308 " pdb=" C ILE A 308 " ideal model delta sigma weight residual 111.90 107.50 4.40 8.10e-01 1.52e+00 2.95e+01 angle pdb=" N ASP R 112 " pdb=" CA ASP R 112 " pdb=" C ASP R 112 " ideal model delta sigma weight residual 111.03 105.07 5.96 1.11e+00 8.12e-01 2.88e+01 angle pdb=" N TYR R 301 " pdb=" CA TYR R 301 " pdb=" C TYR R 301 " ideal model delta sigma weight residual 112.23 107.14 5.09 1.26e+00 6.30e-01 1.63e+01 angle pdb=" N LEU Y 50 " pdb=" CA LEU Y 50 " pdb=" C LEU Y 50 " ideal model delta sigma weight residual 114.04 109.03 5.01 1.24e+00 6.50e-01 1.63e+01 ... (remaining 11563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4396 17.73 - 35.47: 433 35.47 - 53.20: 88 53.20 - 70.94: 20 70.94 - 88.67: 5 Dihedral angle restraints: 4942 sinusoidal: 1667 harmonic: 3275 Sorted by residual: dihedral pdb=" CA PHE R 115 " pdb=" C PHE R 115 " pdb=" N CYS R 116 " pdb=" CA CYS R 116 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA LEU R 205 " pdb=" C LEU R 205 " pdb=" N PHE R 206 " pdb=" CA PHE R 206 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB CYS R 105 " pdb=" SG CYS R 105 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 124.40 -31.40 1 1.00e+01 1.00e-02 1.41e+01 ... (remaining 4939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 924 0.038 - 0.077: 308 0.077 - 0.115: 103 0.115 - 0.153: 15 0.153 - 0.191: 4 Chirality restraints: 1354 Sorted by residual: chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CG LEU Y 37 " pdb=" CB LEU Y 37 " pdb=" CD1 LEU Y 37 " pdb=" CD2 LEU Y 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA ARG A 356 " pdb=" N ARG A 356 " pdb=" C ARG A 356 " pdb=" CB ARG A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 1351 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.88e+00 pdb=" N PRO S 75 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 16 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C ASN B 16 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN B 16 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN B 17 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C THR B 87 " 0.034 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.011 2.00e-02 2.50e+03 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1205 2.75 - 3.29: 8046 3.29 - 3.83: 13179 3.83 - 4.36: 15482 4.36 - 4.90: 27059 Nonbonded interactions: 64971 Sorted by model distance: nonbonded pdb=" N GLU B 226 " pdb=" OE1 GLU B 226 " model vdw 2.214 3.120 nonbonded pdb=" N GLU Y 58 " pdb=" OE1 GLU Y 58 " model vdw 2.239 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.257 3.040 nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.258 3.040 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.265 3.040 ... (remaining 64966 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.270 Find NCS groups from input model: 0.110 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 : 0.004 0.062 8485 Z= 0.273 Angle : 0.705 9.218 11568 Z= 0.409 Chirality : 0.044 0.191 1354 Planarity : 0.004 0.070 1471 Dihedral : 15.117 88.670 2822 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.85 % Allowed : 23.24 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.24), residues: 1109 helix: -1.07 (0.26), residues: 369 sheet: -0.50 (0.34), residues: 246 loop : -1.61 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.026 0.002 PHE R 159 TYR 0.020 0.001 TYR S 228 ARG 0.005 0.000 ARG S 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 1.246 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 147 average time/residue: 0.9111 time to fit residues: 144.8994 Evaluate side-chains 126 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain S residue 146 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 307 ASN B 75 GLN B 225 HIS B 268 ASN A 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.139755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.106517 restraints weight = 12074.659| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.72 r_work: 0.3421 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8485 Z= 0.192 Angle : 0.573 9.083 11568 Z= 0.300 Chirality : 0.041 0.276 1354 Planarity : 0.004 0.054 1471 Dihedral : 5.262 55.289 1227 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.33 % Allowed : 21.63 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1109 helix: 0.21 (0.28), residues: 374 sheet: -0.34 (0.34), residues: 255 loop : -1.66 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.019 0.002 PHE R 159 TYR 0.017 0.001 TYR S 191 ARG 0.003 0.000 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.8288 (m-80) REVERT: B 75 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7687 (mp-120) REVERT: B 226 GLU cc_start: 0.8320 (pm20) cc_final: 0.7804 (pm20) outliers start: 35 outliers final: 11 residues processed: 157 average time/residue: 0.9467 time to fit residues: 161.5367 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.141277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.107982 restraints weight = 12181.799| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.73 r_work: 0.3439 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8485 Z= 0.165 Angle : 0.545 8.684 11568 Z= 0.283 Chirality : 0.041 0.295 1354 Planarity : 0.003 0.053 1471 Dihedral : 4.542 52.807 1212 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.20 % Allowed : 24.23 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.26), residues: 1109 helix: 0.69 (0.29), residues: 363 sheet: -0.27 (0.34), residues: 255 loop : -1.65 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE R 144 TYR 0.014 0.001 TYR S 191 ARG 0.005 0.000 ARG S 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 128 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: R 127 SER cc_start: 0.8156 (m) cc_final: 0.7898 (p) REVERT: B 75 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7548 (mp-120) REVERT: B 124 TYR cc_start: 0.8248 (m-80) cc_final: 0.8000 (m-80) REVERT: B 226 GLU cc_start: 0.8354 (pm20) cc_final: 0.7900 (pm20) REVERT: S 4 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7190 (pp) REVERT: S 180 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8246 (tm-30) outliers start: 34 outliers final: 13 residues processed: 154 average time/residue: 0.8671 time to fit residues: 145.1328 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 146 SER Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 105 optimal weight: 0.0010 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 68 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 overall best weight: 1.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.139909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.106885 restraints weight = 12333.219| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.76 r_work: 0.3426 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8485 Z= 0.208 Angle : 0.558 8.362 11568 Z= 0.288 Chirality : 0.041 0.292 1354 Planarity : 0.003 0.051 1471 Dihedral : 4.548 50.939 1212 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.08 % Allowed : 25.22 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.26), residues: 1109 helix: 0.81 (0.29), residues: 363 sheet: -0.18 (0.35), residues: 245 loop : -1.65 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.032 0.002 PHE R 115 TYR 0.021 0.001 TYR B 59 ARG 0.005 0.000 ARG S 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 124 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: R 106 LYS cc_start: 0.7821 (tptm) cc_final: 0.7599 (tppp) REVERT: B 124 TYR cc_start: 0.8265 (m-80) cc_final: 0.7954 (m-80) REVERT: B 226 GLU cc_start: 0.8349 (pm20) cc_final: 0.8127 (pm20) REVERT: S 4 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7131 (pp) REVERT: S 180 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8316 (tm-30) outliers start: 33 outliers final: 17 residues processed: 151 average time/residue: 0.8987 time to fit residues: 147.4189 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN A 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.136010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.102231 restraints weight = 12266.539| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.76 r_work: 0.3359 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8485 Z= 0.338 Angle : 0.622 8.673 11568 Z= 0.325 Chirality : 0.044 0.298 1354 Planarity : 0.004 0.049 1471 Dihedral : 4.903 49.709 1212 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.07 % Allowed : 24.97 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.26), residues: 1109 helix: 0.68 (0.29), residues: 362 sheet: -0.31 (0.34), residues: 251 loop : -1.69 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.024 0.002 PHE A 376 TYR 0.020 0.002 TYR B 59 ARG 0.008 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 121 time to evaluate : 1.012 Fit side-chains REVERT: R 293 TYR cc_start: 0.7344 (m-80) cc_final: 0.7127 (m-80) REVERT: B 124 TYR cc_start: 0.8252 (m-80) cc_final: 0.8005 (m-80) REVERT: B 226 GLU cc_start: 0.8369 (pm20) cc_final: 0.8119 (pm20) REVERT: B 269 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8429 (mm) REVERT: B 338 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 291 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8076 (mm) REVERT: S 4 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7156 (pp) REVERT: S 180 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8186 (tm-30) outliers start: 41 outliers final: 21 residues processed: 154 average time/residue: 0.9065 time to fit residues: 151.4885 Evaluate side-chains 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 0.0270 chunk 5 optimal weight: 3.9990 chunk 89 optimal weight: 0.0570 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN S 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.141256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.107767 restraints weight = 12043.879| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.78 r_work: 0.3443 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8485 Z= 0.157 Angle : 0.548 8.659 11568 Z= 0.281 Chirality : 0.041 0.287 1354 Planarity : 0.003 0.046 1471 Dihedral : 4.436 48.406 1212 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.60 % Allowed : 27.69 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.26), residues: 1109 helix: 0.94 (0.29), residues: 363 sheet: -0.20 (0.34), residues: 248 loop : -1.62 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.023 0.001 PHE A 376 TYR 0.010 0.001 TYR S 191 ARG 0.009 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.877 Fit side-chains REVERT: R 106 LYS cc_start: 0.8057 (tppp) cc_final: 0.7777 (tppp) REVERT: B 10 GLU cc_start: 0.7236 (pp20) cc_final: 0.6994 (pp20) REVERT: B 124 TYR cc_start: 0.8174 (m-80) cc_final: 0.7957 (m-80) REVERT: B 226 GLU cc_start: 0.8317 (pm20) cc_final: 0.8041 (pm20) REVERT: S 4 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7069 (pp) outliers start: 21 outliers final: 10 residues processed: 140 average time/residue: 0.9202 time to fit residues: 139.5334 Evaluate side-chains 129 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 88 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN S 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.138860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.105207 restraints weight = 12255.619| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.79 r_work: 0.3405 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8485 Z= 0.236 Angle : 0.586 9.406 11568 Z= 0.299 Chirality : 0.042 0.323 1354 Planarity : 0.004 0.046 1471 Dihedral : 4.564 48.298 1212 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.08 % Allowed : 26.82 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.26), residues: 1109 helix: 0.87 (0.29), residues: 362 sheet: -0.27 (0.33), residues: 256 loop : -1.62 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.021 0.002 PHE A 376 TYR 0.012 0.001 TYR B 59 ARG 0.010 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.981 Fit side-chains REVERT: R 106 LYS cc_start: 0.8059 (tppp) cc_final: 0.7775 (tppp) REVERT: B 59 TYR cc_start: 0.8438 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: B 75 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7644 (mp-120) REVERT: B 124 TYR cc_start: 0.8239 (m-80) cc_final: 0.7966 (m-80) REVERT: B 226 GLU cc_start: 0.8360 (pm20) cc_final: 0.8105 (pm20) REVERT: S 4 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7070 (pp) REVERT: S 180 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8095 (tm-30) outliers start: 33 outliers final: 16 residues processed: 145 average time/residue: 0.9500 time to fit residues: 149.7680 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 180 GLN Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 95 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.140189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.106570 restraints weight = 12257.623| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.80 r_work: 0.3424 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8485 Z= 0.188 Angle : 0.579 10.606 11568 Z= 0.292 Chirality : 0.042 0.344 1354 Planarity : 0.004 0.047 1471 Dihedral : 4.469 48.175 1212 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.71 % Allowed : 27.69 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.26), residues: 1109 helix: 0.84 (0.29), residues: 368 sheet: -0.14 (0.35), residues: 237 loop : -1.61 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE A 376 TYR 0.015 0.001 TYR B 59 ARG 0.011 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.914 Fit side-chains REVERT: R 106 LYS cc_start: 0.8111 (tppp) cc_final: 0.7877 (tppp) REVERT: R 186 CYS cc_start: 0.9025 (m) cc_final: 0.8648 (p) REVERT: B 75 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7783 (mp-120) REVERT: B 96 ARG cc_start: 0.8005 (ttm110) cc_final: 0.7738 (ttp-170) REVERT: B 124 TYR cc_start: 0.8220 (m-80) cc_final: 0.7938 (m-80) REVERT: B 226 GLU cc_start: 0.8343 (pm20) cc_final: 0.8104 (pm20) REVERT: S 4 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.7005 (pp) REVERT: S 146 SER cc_start: 0.7672 (m) cc_final: 0.7149 (t) outliers start: 30 outliers final: 19 residues processed: 139 average time/residue: 0.9057 time to fit residues: 136.6456 Evaluate side-chains 135 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 140 VAL Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 43 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 180 GLN S 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.141320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.107867 restraints weight = 12072.333| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.77 r_work: 0.3447 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8485 Z= 0.170 Angle : 0.575 10.161 11568 Z= 0.288 Chirality : 0.042 0.327 1354 Planarity : 0.004 0.052 1471 Dihedral : 4.373 47.846 1212 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.84 % Allowed : 28.18 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.26), residues: 1109 helix: 0.88 (0.28), residues: 369 sheet: -0.13 (0.35), residues: 241 loop : -1.52 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP S 47 HIS 0.004 0.001 HIS A 357 PHE 0.021 0.001 PHE A 376 TYR 0.014 0.001 TYR B 59 ARG 0.012 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.966 Fit side-chains REVERT: R 106 LYS cc_start: 0.8036 (tppp) cc_final: 0.7808 (tppp) REVERT: R 186 CYS cc_start: 0.9012 (m) cc_final: 0.8624 (p) REVERT: R 325 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5837 (OUTLIER) REVERT: B 96 ARG cc_start: 0.7975 (ttm110) cc_final: 0.7752 (ttp-170) REVERT: B 124 TYR cc_start: 0.8220 (m-80) cc_final: 0.7936 (m-80) REVERT: B 226 GLU cc_start: 0.8364 (pm20) cc_final: 0.8105 (pm20) REVERT: S 4 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6983 (pp) outliers start: 23 outliers final: 16 residues processed: 135 average time/residue: 0.8971 time to fit residues: 131.6619 Evaluate side-chains 130 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 227 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 76 optimal weight: 0.0270 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.136097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.102377 restraints weight = 12362.881| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.78 r_work: 0.3363 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8485 Z= 0.354 Angle : 0.660 10.100 11568 Z= 0.338 Chirality : 0.046 0.347 1354 Planarity : 0.004 0.059 1471 Dihedral : 4.984 49.516 1212 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.34 % Allowed : 27.81 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.25), residues: 1109 helix: 0.56 (0.28), residues: 368 sheet: -0.32 (0.33), residues: 253 loop : -1.67 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP S 47 HIS 0.007 0.001 HIS A 357 PHE 0.021 0.002 PHE R 144 TYR 0.010 0.002 TYR R 274 ARG 0.014 0.001 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.924 Fit side-chains REVERT: R 106 LYS cc_start: 0.8051 (tppp) cc_final: 0.7819 (tppp) REVERT: R 186 CYS cc_start: 0.8988 (m) cc_final: 0.8601 (p) REVERT: R 325 ILE cc_start: 0.5992 (OUTLIER) cc_final: 0.5696 (OUTLIER) REVERT: B 124 TYR cc_start: 0.8259 (m-80) cc_final: 0.7982 (m-80) REVERT: B 226 GLU cc_start: 0.8338 (pm20) cc_final: 0.8094 (pm20) REVERT: S 4 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7151 (pp) REVERT: S 187 GLN cc_start: 0.8568 (mt0) cc_final: 0.8360 (mt0) outliers start: 27 outliers final: 20 residues processed: 139 average time/residue: 0.9059 time to fit residues: 136.4844 Evaluate side-chains 134 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 109 THR Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 255 LYS Chi-restraints excluded: chain R residue 325 ILE Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 84 THR Chi-restraints excluded: chain S residue 140 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 0.0050 chunk 5 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 97 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 10 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 overall best weight: 1.2996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.139848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.106219 restraints weight = 12224.273| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.79 r_work: 0.3418 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8485 Z= 0.191 Angle : 0.609 10.015 11568 Z= 0.304 Chirality : 0.043 0.319 1354 Planarity : 0.004 0.056 1471 Dihedral : 4.628 48.840 1212 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.84 % Allowed : 28.55 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1109 helix: 0.74 (0.28), residues: 368 sheet: -0.20 (0.34), residues: 243 loop : -1.57 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP S 47 HIS 0.004 0.001 HIS A 357 PHE 0.020 0.001 PHE A 376 TYR 0.015 0.001 TYR B 59 ARG 0.013 0.001 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6049.84 seconds wall clock time: 107 minutes 26.70 seconds (6446.70 seconds total)