Starting phenix.real_space_refine on Tue Sep 24 07:38:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/09_2024/7f1s_31424.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/09_2024/7f1s_31424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/09_2024/7f1s_31424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/09_2024/7f1s_31424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/09_2024/7f1s_31424.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1s_31424/09_2024/7f1s_31424.cif" } resolution = 2.8 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1442 atoms to isotropic. 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 42 5.16 5 C 4009 2.51 5 N 1055 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6209 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2051 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 8, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 5, 'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 127 Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1588 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 12, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 91 Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2338 Classifications: {'peptide': 320} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 314} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 232 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Time building chain proxies: 4.11, per 1000 atoms: 0.66 Number of scatterers: 6209 At special positions: 0 Unit cell: (113.905, 112.86, 72.105, 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 42 16.00 O 1103 8.00 N 1055 7.00 C 4009 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 101 " - pdb=" SG CYS R 178 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 880.6 milliseconds 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 45.3% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'R' and resid 33 through 58 removed outlier: 3.790A pdb=" N TYR R 37 " --> pdb=" O LEU R 33 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER R 38 " --> pdb=" O PRO R 34 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE R 41 " --> pdb=" O TYR R 37 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N PHE R 45 " --> pdb=" O PHE R 41 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASN R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.062A pdb=" N TYR R 68 " --> pdb=" O MET R 64 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU R 72 " --> pdb=" O TYR R 68 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU R 77 " --> pdb=" O ALA R 73 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 87 removed outlier: 4.105A pdb=" N PHE R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA R 87 " --> pdb=" O VAL R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 132 removed outlier: 3.597A pdb=" N GLN R 102 " --> pdb=" O ASN R 98 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY R 115 " --> pdb=" O GLY R 111 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE R 120 " --> pdb=" O ILE R 116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL R 130 " --> pdb=" O ARG R 126 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS R 132 " --> pdb=" O LEU R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 140 removed outlier: 4.061A pdb=" N LYS R 138 " --> pdb=" O VAL R 134 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 166 removed outlier: 4.079A pdb=" N VAL R 147 " --> pdb=" O THR R 143 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE R 151 " --> pdb=" O VAL R 147 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR R 152 " --> pdb=" O THR R 148 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA R 156 " --> pdb=" O THR R 152 " (cutoff:3.500A) Proline residue: R 162 - end of helix Processing helix chain 'R' and resid 186 through 201 removed outlier: 3.596A pdb=" N ILE R 200 " --> pdb=" O LEU R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 220 removed outlier: 3.517A pdb=" N TYR R 214 " --> pdb=" O MET R 210 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 248 removed outlier: 4.074A pdb=" N ARG R 232 " --> pdb=" O LYS R 228 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N TYR R 244 " --> pdb=" O ILE R 240 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE R 245 " --> pdb=" O MET R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 260 removed outlier: 3.947A pdb=" N LEU R 257 " --> pdb=" O ILE R 253 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 269 Processing helix chain 'R' and resid 270 through 277 removed outlier: 4.241A pdb=" N ARG R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN R 277 " --> pdb=" O ASN R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 288 Processing helix chain 'R' and resid 292 through 298 Processing helix chain 'R' and resid 303 through 313 removed outlier: 3.744A pdb=" N TYR R 307 " --> pdb=" O LYS R 303 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL R 310 " --> pdb=" O ASN R 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.550A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A 24 " --> pdb=" O ASP A 20 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.568A pdb=" N SER A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.968A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.781A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.658A pdb=" N ALA A 300 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.523A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.576A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'R' and resid 168 through 171 removed outlier: 3.717A pdb=" N GLN R 170 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N THR R 177 " --> pdb=" O GLN R 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.841A pdb=" N VAL A 185 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.982A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.577A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.987A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.609A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.885A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.231A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.541A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 828 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1989 1.35 - 1.46: 1606 1.46 - 1.58: 2690 1.58 - 1.70: 0 1.70 - 1.82: 57 Bond restraints: 6342 Sorted by residual: bond pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.27e+00 bond pdb=" CA LEU R 33 " pdb=" C LEU R 33 " ideal model delta sigma weight residual 1.525 1.541 -0.016 2.10e-02 2.27e+03 5.99e-01 bond pdb=" C PRO R 34 " pdb=" N PRO R 35 " ideal model delta sigma weight residual 1.336 1.345 -0.009 1.25e-02 6.40e+03 5.21e-01 bond pdb=" CB GLN R 194 " pdb=" CG GLN R 194 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 5.13e-01 bond pdb=" CA GLU C 47 " pdb=" C GLU C 47 " ideal model delta sigma weight residual 1.526 1.535 -0.010 1.36e-02 5.41e+03 4.97e-01 ... (remaining 6337 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 8501 1.62 - 3.24: 116 3.24 - 4.87: 23 4.87 - 6.49: 12 6.49 - 8.11: 2 Bond angle restraints: 8654 Sorted by residual: angle pdb=" C ASN R 268 " pdb=" N CYS R 269 " pdb=" CA CYS R 269 " ideal model delta sigma weight residual 121.54 126.09 -4.55 1.91e+00 2.74e-01 5.67e+00 angle pdb=" CA LEU R 161 " pdb=" CB LEU R 161 " pdb=" CG LEU R 161 " ideal model delta sigma weight residual 116.30 124.41 -8.11 3.50e+00 8.16e-02 5.37e+00 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 123.91 127.56 -3.65 1.66e+00 3.63e-01 4.82e+00 angle pdb=" N LEU B 300 " pdb=" CA LEU B 300 " pdb=" C LEU B 300 " ideal model delta sigma weight residual 114.31 111.60 2.71 1.29e+00 6.01e-01 4.40e+00 angle pdb=" C CYS R 224 " pdb=" N ARG R 225 " pdb=" CA ARG R 225 " ideal model delta sigma weight residual 122.08 125.08 -3.00 1.47e+00 4.63e-01 4.17e+00 ... (remaining 8649 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 3465 17.53 - 35.07: 180 35.07 - 52.60: 14 52.60 - 70.14: 6 70.14 - 87.67: 4 Dihedral angle restraints: 3669 sinusoidal: 1207 harmonic: 2462 Sorted by residual: dihedral pdb=" CA ASN R 293 " pdb=" CB ASN R 293 " pdb=" CG ASN R 293 " pdb=" OD1 ASN R 293 " ideal model delta sinusoidal sigma weight residual -90.00 -156.28 66.28 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CB LYS A 29 " pdb=" CG LYS A 29 " pdb=" CD LYS A 29 " pdb=" CE LYS A 29 " ideal model delta sinusoidal sigma weight residual 60.00 118.28 -58.28 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA GLN B 220 " pdb=" CB GLN B 220 " pdb=" CG GLN B 220 " pdb=" CD GLN B 220 " ideal model delta sinusoidal sigma weight residual -60.00 -105.58 45.58 3 1.50e+01 4.44e-03 8.19e+00 ... (remaining 3666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 624 0.030 - 0.061: 309 0.061 - 0.091: 66 0.091 - 0.121: 38 0.121 - 0.152: 5 Chirality restraints: 1042 Sorted by residual: chirality pdb=" CA THR B 196 " pdb=" N THR B 196 " pdb=" C THR B 196 " pdb=" CB THR B 196 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA THR B 164 " pdb=" N THR B 164 " pdb=" C THR B 164 " pdb=" CB THR B 164 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 1039 not shown) Planarity restraints: 1085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 38 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO B 39 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 39 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 39 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 33 " -0.037 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO R 34 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 34 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 34 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 ... (remaining 1082 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1047 2.76 - 3.30: 6289 3.30 - 3.83: 10363 3.83 - 4.37: 12405 4.37 - 4.90: 21056 Nonbonded interactions: 51160 Sorted by model distance: nonbonded pdb=" O ASN R 163 " pdb=" OG1 THR R 167 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR R 108 " pdb=" OE1 GLU R 283 " model vdw 2.252 3.040 nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.259 3.120 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.296 3.120 nonbonded pdb=" NE2 HIS B 225 " pdb=" OG1 THR B 243 " model vdw 2.332 3.120 ... (remaining 51155 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: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.590 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 0.002 0.021 6342 Z= 0.125 Angle : 0.552 8.112 8654 Z= 0.289 Chirality : 0.039 0.152 1042 Planarity : 0.004 0.073 1085 Dihedral : 10.910 87.669 2068 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: -1.65 (0.27), residues: 833 helix: -2.04 (0.24), residues: 291 sheet: 0.68 (0.41), residues: 155 loop : -0.95 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 153 HIS 0.005 0.001 HIS R 132 PHE 0.007 0.001 PHE B 151 TYR 0.015 0.001 TYR R 251 ARG 0.007 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: R 74 ILE cc_start: 0.8504 (mt) cc_final: 0.8128 (mp) REVERT: R 100 MET cc_start: 0.6810 (tmm) cc_final: 0.6562 (tmm) REVERT: R 138 LYS cc_start: 0.8182 (ptmm) cc_final: 0.7967 (pttp) REVERT: R 295 ILE cc_start: 0.8450 (tp) cc_final: 0.8133 (pp) REVERT: A 230 TYR cc_start: 0.7133 (p90) cc_final: 0.6704 (p90) REVERT: B 188 MET cc_start: 0.8085 (mmm) cc_final: 0.7831 (mmp) REVERT: B 209 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7591 (mmtm) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 1.0456 time to fit residues: 167.5971 Evaluate side-chains 101 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 261 GLN A 294 ASN B 176 GLN B 230 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6342 Z= 0.233 Angle : 0.636 8.723 8654 Z= 0.326 Chirality : 0.043 0.145 1042 Planarity : 0.005 0.052 1085 Dihedral : 3.838 17.207 894 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.35 % Allowed : 15.44 % Favored : 82.21 % 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 (0.28), residues: 833 helix: -0.53 (0.27), residues: 333 sheet: 0.60 (0.41), residues: 165 loop : -0.76 (0.34), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 211 HIS 0.006 0.001 HIS R 132 PHE 0.015 0.001 PHE R 45 TYR 0.021 0.002 TYR R 307 ARG 0.008 0.001 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 0.675 Fit side-chains REVERT: R 110 ILE cc_start: 0.8876 (mp) cc_final: 0.8517 (mp) REVERT: R 197 LYS cc_start: 0.7896 (pttp) cc_final: 0.6605 (mmpt) REVERT: R 235 ARG cc_start: 0.7325 (tpt170) cc_final: 0.6994 (tpt170) REVERT: R 280 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7946 (tp-100) REVERT: A 21 ARG cc_start: 0.8289 (ttp-110) cc_final: 0.8081 (ttp-110) REVERT: A 230 TYR cc_start: 0.7644 (p90) cc_final: 0.7209 (p90) REVERT: A 247 MET cc_start: 0.8224 (mtm) cc_final: 0.7997 (mtt) REVERT: A 304 GLN cc_start: 0.8664 (tt0) cc_final: 0.8380 (tt0) REVERT: B 188 MET cc_start: 0.8583 (mmm) cc_final: 0.8220 (mmm) REVERT: B 228 ASP cc_start: 0.7840 (p0) cc_final: 0.7611 (p0) REVERT: B 230 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7833 (m110) outliers start: 14 outliers final: 6 residues processed: 130 average time/residue: 1.0930 time to fit residues: 149.7832 Evaluate side-chains 112 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6342 Z= 0.190 Angle : 0.593 8.958 8654 Z= 0.304 Chirality : 0.042 0.179 1042 Planarity : 0.004 0.052 1085 Dihedral : 3.695 17.465 894 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.85 % Allowed : 17.62 % Favored : 79.53 % 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: -0.27 (0.29), residues: 833 helix: 0.10 (0.28), residues: 331 sheet: 0.52 (0.41), residues: 165 loop : -0.70 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS R 132 PHE 0.011 0.001 PHE B 222 TYR 0.015 0.001 TYR R 307 ARG 0.008 0.001 ARG R 140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: R 110 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8554 (mp) REVERT: R 235 ARG cc_start: 0.7310 (tpt170) cc_final: 0.6839 (tpt170) REVERT: R 241 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7991 (mmt) REVERT: R 280 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7925 (tp-100) REVERT: A 230 TYR cc_start: 0.7543 (p90) cc_final: 0.7193 (p90) REVERT: B 228 ASP cc_start: 0.7899 (p0) cc_final: 0.7645 (p0) REVERT: B 230 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.7830 (m110) REVERT: B 259 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7055 (mt0) outliers start: 17 outliers final: 10 residues processed: 130 average time/residue: 1.1023 time to fit residues: 151.1642 Evaluate side-chains 117 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 103 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 241 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6342 Z= 0.204 Angle : 0.591 9.156 8654 Z= 0.304 Chirality : 0.042 0.165 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.683 17.778 894 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.02 % Allowed : 20.64 % Favored : 76.34 % 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: -0.10 (0.29), residues: 833 helix: 0.41 (0.28), residues: 329 sheet: 0.44 (0.39), residues: 173 loop : -0.71 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS R 132 PHE 0.008 0.001 PHE B 222 TYR 0.018 0.001 TYR R 297 ARG 0.008 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: R 235 ARG cc_start: 0.7352 (tpt170) cc_final: 0.6815 (tpt170) REVERT: R 280 GLN cc_start: 0.8297 (tp-100) cc_final: 0.7993 (tp-100) REVERT: A 230 TYR cc_start: 0.7554 (p90) cc_final: 0.7217 (p90) REVERT: B 188 MET cc_start: 0.8429 (mmm) cc_final: 0.7975 (mmm) REVERT: B 228 ASP cc_start: 0.7896 (p0) cc_final: 0.7584 (p0) REVERT: B 230 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.7601 (m110) REVERT: B 259 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6981 (mt0) outliers start: 18 outliers final: 15 residues processed: 122 average time/residue: 0.9641 time to fit residues: 124.7522 Evaluate side-chains 115 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6342 Z= 0.192 Angle : 0.592 9.021 8654 Z= 0.305 Chirality : 0.041 0.148 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.696 18.001 894 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.52 % Allowed : 21.31 % Favored : 75.17 % 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: -0.10 (0.29), residues: 833 helix: 0.51 (0.28), residues: 335 sheet: 0.33 (0.39), residues: 173 loop : -0.79 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS R 132 PHE 0.008 0.001 PHE B 222 TYR 0.018 0.001 TYR R 297 ARG 0.007 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.762 Fit side-chains revert: symmetry clash REVERT: R 235 ARG cc_start: 0.7401 (tpt170) cc_final: 0.6887 (tpt170) REVERT: A 230 TYR cc_start: 0.7456 (p90) cc_final: 0.7206 (p90) REVERT: A 308 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7828 (mt-10) REVERT: B 188 MET cc_start: 0.8355 (mmm) cc_final: 0.7932 (mmm) REVERT: B 259 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6947 (mt0) outliers start: 21 outliers final: 13 residues processed: 120 average time/residue: 0.9834 time to fit residues: 124.9637 Evaluate side-chains 110 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 96 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6342 Z= 0.281 Angle : 0.642 10.043 8654 Z= 0.331 Chirality : 0.043 0.165 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.919 19.362 894 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.36 % Allowed : 22.99 % Favored : 73.66 % 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: -0.06 (0.29), residues: 833 helix: 0.60 (0.28), residues: 332 sheet: 0.06 (0.39), residues: 175 loop : -0.64 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.003 0.001 HIS B 91 PHE 0.017 0.001 PHE B 292 TYR 0.014 0.002 TYR R 297 ARG 0.009 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 0.744 Fit side-chains REVERT: R 100 MET cc_start: 0.6248 (tmm) cc_final: 0.5714 (tmm) REVERT: R 235 ARG cc_start: 0.7505 (tpt170) cc_final: 0.7050 (tpt170) REVERT: R 241 MET cc_start: 0.8346 (mmm) cc_final: 0.8060 (mmt) REVERT: A 18 MET cc_start: 0.7529 (mmt) cc_final: 0.7324 (mmt) REVERT: A 230 TYR cc_start: 0.7779 (p90) cc_final: 0.7546 (p90) REVERT: A 251 ASP cc_start: 0.8611 (t0) cc_final: 0.8390 (t0) REVERT: B 78 LYS cc_start: 0.8836 (mptp) cc_final: 0.8625 (mmtm) REVERT: B 188 MET cc_start: 0.8436 (mmm) cc_final: 0.8068 (mmm) REVERT: B 259 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.7030 (mt0) outliers start: 20 outliers final: 15 residues processed: 115 average time/residue: 1.0378 time to fit residues: 126.1085 Evaluate side-chains 110 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 31 optimal weight: 0.0000 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN A 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6342 Z= 0.202 Angle : 0.617 9.095 8654 Z= 0.317 Chirality : 0.042 0.148 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.868 18.952 894 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.18 % Allowed : 24.66 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.29), residues: 833 helix: 0.65 (0.29), residues: 331 sheet: 0.04 (0.39), residues: 175 loop : -0.59 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS R 132 PHE 0.007 0.001 PHE B 222 TYR 0.018 0.001 TYR R 297 ARG 0.009 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 0.735 Fit side-chains REVERT: R 100 MET cc_start: 0.6351 (tmm) cc_final: 0.5795 (tmm) REVERT: R 110 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8720 (mp) REVERT: R 235 ARG cc_start: 0.7335 (tpt170) cc_final: 0.7127 (tpt170) REVERT: B 78 LYS cc_start: 0.8841 (mptp) cc_final: 0.8625 (mmtm) REVERT: B 188 MET cc_start: 0.8340 (mmm) cc_final: 0.8044 (mmm) REVERT: B 259 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6998 (mt0) REVERT: B 260 GLU cc_start: 0.7267 (tp30) cc_final: 0.6982 (tp30) outliers start: 13 outliers final: 11 residues processed: 113 average time/residue: 1.0598 time to fit residues: 126.4293 Evaluate side-chains 107 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 0.0070 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 69 optimal weight: 0.0050 overall best weight: 0.6014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6342 Z= 0.202 Angle : 0.625 9.806 8654 Z= 0.320 Chirality : 0.042 0.149 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.851 18.571 894 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.35 % Allowed : 25.67 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.02 (0.29), residues: 833 helix: 0.64 (0.28), residues: 331 sheet: -0.01 (0.39), residues: 176 loop : -0.55 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS R 132 PHE 0.013 0.001 PHE B 292 TYR 0.017 0.001 TYR R 297 ARG 0.009 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.682 Fit side-chains REVERT: R 110 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8744 (mp) REVERT: R 158 PHE cc_start: 0.7931 (t80) cc_final: 0.7647 (t80) REVERT: R 235 ARG cc_start: 0.7286 (tpt170) cc_final: 0.7059 (tpt170) REVERT: B 78 LYS cc_start: 0.8836 (mptp) cc_final: 0.8609 (mmtm) REVERT: B 188 MET cc_start: 0.8355 (mmm) cc_final: 0.8030 (mmm) REVERT: B 260 GLU cc_start: 0.7383 (tp30) cc_final: 0.7024 (tp30) outliers start: 14 outliers final: 10 residues processed: 112 average time/residue: 1.0351 time to fit residues: 122.4207 Evaluate side-chains 107 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 44 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 48 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6342 Z= 0.208 Angle : 0.648 9.338 8654 Z= 0.330 Chirality : 0.042 0.150 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.847 18.496 894 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.68 % Allowed : 25.17 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.00 (0.29), residues: 833 helix: 0.67 (0.28), residues: 331 sheet: -0.04 (0.39), residues: 176 loop : -0.52 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 132 PHE 0.008 0.001 PHE R 118 TYR 0.017 0.001 TYR R 297 ARG 0.010 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.711 Fit side-chains REVERT: R 100 MET cc_start: 0.6350 (tmm) cc_final: 0.5823 (tmm) REVERT: R 158 PHE cc_start: 0.7903 (t80) cc_final: 0.7603 (t80) REVERT: R 235 ARG cc_start: 0.7367 (tpt170) cc_final: 0.7133 (tpt170) REVERT: A 208 ARG cc_start: 0.8439 (ttp80) cc_final: 0.8227 (ttp80) REVERT: B 57 LYS cc_start: 0.8999 (ptpp) cc_final: 0.8663 (ptmm) REVERT: B 188 MET cc_start: 0.8398 (mmm) cc_final: 0.8075 (mmm) outliers start: 16 outliers final: 12 residues processed: 115 average time/residue: 0.9718 time to fit residues: 118.4558 Evaluate side-chains 110 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.6980 chunk 82 optimal weight: 0.0470 chunk 76 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 50 optimal weight: 0.0050 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.7294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6342 Z= 0.225 Angle : 0.659 9.365 8654 Z= 0.340 Chirality : 0.042 0.153 1042 Planarity : 0.004 0.054 1085 Dihedral : 3.902 18.542 894 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.01 % Allowed : 25.67 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.03 (0.29), residues: 833 helix: 0.65 (0.28), residues: 331 sheet: -0.13 (0.39), residues: 176 loop : -0.51 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 132 PHE 0.018 0.001 PHE B 292 TYR 0.016 0.002 TYR R 297 ARG 0.011 0.001 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.724 Fit side-chains REVERT: R 158 PHE cc_start: 0.7943 (t80) cc_final: 0.7640 (t80) REVERT: R 235 ARG cc_start: 0.7419 (tpt170) cc_final: 0.7119 (tpt170) REVERT: A 208 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8250 (ttp80) REVERT: B 57 LYS cc_start: 0.9058 (ptpp) cc_final: 0.8674 (ptmm) REVERT: B 188 MET cc_start: 0.8404 (mmm) cc_final: 0.8083 (mmm) outliers start: 12 outliers final: 13 residues processed: 111 average time/residue: 0.9866 time to fit residues: 115.8893 Evaluate side-chains 108 residues out of total 735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 8.9990 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 47 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 293 ASN A 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.110094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.086701 restraints weight = 13376.727| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.89 r_work: 0.3293 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6342 Z= 0.224 Angle : 0.680 9.591 8654 Z= 0.349 Chirality : 0.043 0.179 1042 Planarity : 0.004 0.053 1085 Dihedral : 3.975 19.030 894 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.52 % Allowed : 25.17 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.04 (0.29), residues: 833 helix: 0.62 (0.28), residues: 331 sheet: -0.17 (0.39), residues: 176 loop : -0.45 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 132 PHE 0.008 0.001 PHE A 196 TYR 0.016 0.001 TYR R 297 ARG 0.011 0.001 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2757.67 seconds wall clock time: 48 minutes 52.75 seconds (2932.75 seconds total)