Starting phenix.real_space_refine on Sun Apr 5 07:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vmo_65193/04_2026/9vmo_65193.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vmo_65193/04_2026/9vmo_65193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vmo_65193/04_2026/9vmo_65193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vmo_65193/04_2026/9vmo_65193.map" model { file = "/net/cci-nas-00/data/ceres_data/9vmo_65193/04_2026/9vmo_65193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vmo_65193/04_2026/9vmo_65193.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.630 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 60 5.16 5 C 5588 2.51 5 N 1482 2.21 5 O 1611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8741 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1798 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 96 Chain: "B" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2491 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 132 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 78 Chain: "G" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2343 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 284} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "S" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1747 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'ITN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.14, per 1000 atoms: 0.24 Number of scatterers: 8741 At special positions: 0 Unit cell: (89, 120, 126, 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 60 16.00 O 1611 8.00 N 1482 7.00 C 5588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 183 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.06 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 335.7 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2166 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 38.9% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.570A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.808A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 272 through 277 removed outlier: 4.257A pdb=" N TYR A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 Processing helix chain 'A' and resid 296 through 316 removed outlier: 3.552A pdb=" N PHE A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 356 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.547A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 28 through 62 removed outlier: 3.811A pdb=" N LEU R 36 " --> pdb=" O LYS R 32 " (cutoff:3.500A) Proline residue: R 37 - end of helix Proline residue: R 49 - end of helix removed outlier: 3.580A pdb=" N MET R 62 " --> pdb=" O TYR R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 95 removed outlier: 3.634A pdb=" N SER R 85 " --> pdb=" O LEU R 81 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU R 86 " --> pdb=" O TYR R 82 " (cutoff:3.500A) Proline residue: R 87 - end of helix Processing helix chain 'R' and resid 103 through 137 Processing helix chain 'R' and resid 141 through 145 Processing helix chain 'R' and resid 146 through 166 removed outlier: 3.848A pdb=" N ALA R 150 " --> pdb=" O LYS R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 171 Processing helix chain 'R' and resid 185 through 189 removed outlier: 3.633A pdb=" N SER R 189 " --> pdb=" O LEU R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 207 Processing helix chain 'R' and resid 207 through 227 Processing helix chain 'R' and resid 233 through 271 Proline residue: R 256 - end of helix removed outlier: 3.581A pdb=" N LEU R 269 " --> pdb=" O ILE R 265 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER R 271 " --> pdb=" O SER R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 293 Proline residue: R 289 - end of helix removed outlier: 3.533A pdb=" N ALA R 292 " --> pdb=" O ARG R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 303 Processing helix chain 'R' and resid 306 through 320 Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.670A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.638A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.961A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.844A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.639A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.371A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.607A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.775A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.848A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.285A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1317 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: 1.45 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1395 1.28 - 1.42: 2400 1.42 - 1.55: 5048 1.55 - 1.69: 6 1.69 - 1.82: 82 Bond restraints: 8931 Sorted by residual: bond pdb=" C3 ITN R 401 " pdb=" C4 ITN R 401 " ideal model delta sigma weight residual 1.332 1.522 -0.190 2.00e-02 2.50e+03 9.06e+01 bond pdb=" C LEU A 358 " pdb=" O LEU A 358 " ideal model delta sigma weight residual 1.236 1.155 0.081 1.34e-02 5.57e+03 3.62e+01 bond pdb=" N LEU A 358 " pdb=" CA LEU A 358 " ideal model delta sigma weight residual 1.456 1.374 0.081 1.35e-02 5.49e+03 3.61e+01 bond pdb=" C TYR A 356 " pdb=" O TYR A 356 " ideal model delta sigma weight residual 1.237 1.147 0.090 1.62e-02 3.81e+03 3.06e+01 bond pdb=" C ASN A 357 " pdb=" O ASN A 357 " ideal model delta sigma weight residual 1.235 1.144 0.092 1.66e-02 3.63e+03 3.05e+01 ... (remaining 8926 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.54: 12038 3.54 - 7.08: 97 7.08 - 10.63: 13 10.63 - 14.17: 4 14.17 - 17.71: 2 Bond angle restraints: 12154 Sorted by residual: angle pdb=" N ALA B 309 " pdb=" CA ALA B 309 " pdb=" C ALA B 309 " ideal model delta sigma weight residual 112.24 125.93 -13.69 1.28e+00 6.10e-01 1.14e+02 angle pdb=" N ASN A 357 " pdb=" CA ASN A 357 " pdb=" C ASN A 357 " ideal model delta sigma weight residual 113.23 125.13 -11.90 1.22e+00 6.72e-01 9.51e+01 angle pdb=" C LEU B 308 " pdb=" CA LEU B 308 " pdb=" CB LEU B 308 " ideal model delta sigma weight residual 110.11 94.11 16.00 1.89e+00 2.80e-01 7.17e+01 angle pdb=" N LEU B 308 " pdb=" CA LEU B 308 " pdb=" C LEU B 308 " ideal model delta sigma weight residual 112.45 122.33 -9.88 1.39e+00 5.18e-01 5.05e+01 angle pdb=" C LEU A 358 " pdb=" CA LEU A 358 " pdb=" CB LEU A 358 " ideal model delta sigma weight residual 109.65 119.03 -9.38 1.74e+00 3.30e-01 2.91e+01 ... (remaining 12149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4635 17.72 - 35.43: 477 35.43 - 53.15: 107 53.15 - 70.86: 25 70.86 - 88.58: 10 Dihedral angle restraints: 5254 sinusoidal: 1904 harmonic: 3350 Sorted by residual: dihedral pdb=" CA ILE A 55 " pdb=" C ILE A 55 " pdb=" N TYR A 56 " pdb=" CA TYR A 56 " ideal model delta harmonic sigma weight residual 180.00 137.27 42.73 0 5.00e+00 4.00e-02 7.30e+01 dihedral pdb=" C TYR A 356 " pdb=" N TYR A 356 " pdb=" CA TYR A 356 " pdb=" CB TYR A 356 " ideal model delta harmonic sigma weight residual -122.60 -139.53 16.93 0 2.50e+00 1.60e-01 4.58e+01 dihedral pdb=" C ASN A 357 " pdb=" N ASN A 357 " pdb=" CA ASN A 357 " pdb=" CB ASN A 357 " ideal model delta harmonic sigma weight residual -122.60 -139.43 16.83 0 2.50e+00 1.60e-01 4.53e+01 ... (remaining 5251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1403 0.149 - 0.297: 11 0.297 - 0.446: 1 0.446 - 0.594: 0 0.594 - 0.743: 3 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA TYR A 356 " pdb=" N TYR A 356 " pdb=" C TYR A 356 " pdb=" CB TYR A 356 " both_signs ideal model delta sigma weight residual False 2.51 1.77 0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CA ASN A 357 " pdb=" N ASN A 357 " pdb=" C ASN A 357 " pdb=" CB ASN A 357 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CA ALA B 309 " pdb=" N ALA B 309 " pdb=" C ALA B 309 " pdb=" CB ALA B 309 " both_signs ideal model delta sigma weight residual False 2.48 1.83 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 1415 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 ITN R 401 " 0.121 2.00e-02 2.50e+03 2.07e-01 4.27e+02 pdb=" C3 ITN R 401 " -0.358 2.00e-02 2.50e+03 pdb=" C4 ITN R 401 " 0.117 2.00e-02 2.50e+03 pdb=" C5 ITN R 401 " 0.120 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 290 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO A 291 " 0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 357 " -0.018 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ASN A 357 " 0.069 2.00e-02 2.50e+03 pdb=" O ASN A 357 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU A 358 " -0.024 2.00e-02 2.50e+03 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 330 2.72 - 3.26: 8512 3.26 - 3.81: 14837 3.81 - 4.35: 18984 4.35 - 4.90: 31868 Nonbonded interactions: 74531 Sorted by model distance: nonbonded pdb=" NH2 ARG R 110 " pdb=" O CYS R 183 " model vdw 2.170 3.120 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.192 3.040 nonbonded pdb=" OD2 ASP B 27 " pdb=" OG SER G 31 " model vdw 2.205 3.040 nonbonded pdb=" O SER R 189 " pdb=" NH2 ARG R 268 " model vdw 2.209 3.120 nonbonded pdb=" NH1 ARG R 131 " pdb=" OH TYR R 218 " model vdw 2.214 3.120 ... (remaining 74526 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: 1.340 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: 0.150 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.700 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 : 0.007 0.190 8933 Z= 0.323 Angle : 0.938 17.710 12158 Z= 0.531 Chirality : 0.063 0.743 1418 Planarity : 0.009 0.207 1534 Dihedral : 15.797 88.580 3082 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 17.03 % Favored : 82.97 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1134 helix: 0.84 (0.24), residues: 398 sheet: 0.46 (0.30), residues: 293 loop : -0.65 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 241 TYR 0.021 0.003 TYR R 118 PHE 0.028 0.003 PHE R 127 TRP 0.033 0.004 TRP R 65 HIS 0.006 0.002 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00672 ( 8931) covalent geometry : angle 0.93786 (12154) SS BOND : bond 0.01931 ( 2) SS BOND : angle 0.65308 ( 4) hydrogen bonds : bond 0.13294 ( 467) hydrogen bonds : angle 6.05043 ( 1317) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.365 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.8006 time to fit residues: 108.3407 Evaluate side-chains 120 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.0370 chunk 106 optimal weight: 2.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 216 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 340 ASN R 34 HIS R 294 ASN S 159 ASN S 174 GLN S 182 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.057254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.052158 restraints weight = 14869.251| |-----------------------------------------------------------------------------| r_work (start): 0.2546 rms_B_bonded: 0.84 r_work: 0.2484 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.2412 rms_B_bonded: 1.86 restraints_weight: 0.2500 r_work (final): 0.2412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8933 Z= 0.135 Angle : 0.591 6.993 12158 Z= 0.323 Chirality : 0.044 0.146 1418 Planarity : 0.005 0.052 1534 Dihedral : 5.699 80.183 1238 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.07 % Allowed : 15.94 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.25), residues: 1134 helix: 1.96 (0.25), residues: 396 sheet: 0.71 (0.31), residues: 275 loop : -0.39 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 318 TYR 0.018 0.002 TYR S 178 PHE 0.019 0.002 PHE A 189 TRP 0.016 0.002 TRP A 211 HIS 0.003 0.001 HIS R 34 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8931) covalent geometry : angle 0.59078 (12154) SS BOND : bond 0.01141 ( 2) SS BOND : angle 0.70737 ( 4) hydrogen bonds : bond 0.05236 ( 467) hydrogen bonds : angle 4.89724 ( 1317) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.332 Fit side-chains REVERT: A 234 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: A 333 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8310 (t0) REVERT: B 59 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8398 (m-80) outliers start: 19 outliers final: 5 residues processed: 135 average time/residue: 0.8103 time to fit residues: 114.7864 Evaluate side-chains 126 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 0.0020 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 94 optimal weight: 0.0050 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 34 HIS R 294 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.058251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.053094 restraints weight = 14780.139| |-----------------------------------------------------------------------------| r_work (start): 0.2567 rms_B_bonded: 0.84 r_work: 0.2506 rms_B_bonded: 1.05 restraints_weight: 0.5000 r_work: 0.2435 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work (final): 0.2435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8933 Z= 0.120 Angle : 0.544 6.411 12158 Z= 0.296 Chirality : 0.042 0.144 1418 Planarity : 0.004 0.046 1534 Dihedral : 5.451 84.321 1238 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.07 % Allowed : 16.27 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.25), residues: 1134 helix: 2.28 (0.25), residues: 399 sheet: 0.71 (0.31), residues: 280 loop : -0.27 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 190 TYR 0.014 0.001 TYR S 178 PHE 0.019 0.001 PHE A 189 TRP 0.016 0.002 TRP A 211 HIS 0.004 0.001 HIS R 34 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8931) covalent geometry : angle 0.54438 (12154) SS BOND : bond 0.01058 ( 2) SS BOND : angle 0.69918 ( 4) hydrogen bonds : bond 0.04729 ( 467) hydrogen bonds : angle 4.61941 ( 1317) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.350 Fit side-chains REVERT: A 234 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: A 261 GLN cc_start: 0.8112 (mm110) cc_final: 0.7905 (mm-40) REVERT: A 333 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8276 (t0) REVERT: B 59 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8408 (m-80) outliers start: 19 outliers final: 7 residues processed: 137 average time/residue: 0.8477 time to fit residues: 121.5810 Evaluate side-chains 129 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 180 ARG Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 103 optimal weight: 0.0000 chunk 34 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 0.0030 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 261 GLN B 340 ASN R 34 HIS S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.058357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.053171 restraints weight = 14970.276| |-----------------------------------------------------------------------------| r_work (start): 0.2569 rms_B_bonded: 0.85 r_work: 0.2507 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.2436 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8933 Z= 0.119 Angle : 0.541 7.240 12158 Z= 0.292 Chirality : 0.042 0.140 1418 Planarity : 0.004 0.045 1534 Dihedral : 5.384 85.530 1238 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.97 % Allowed : 16.70 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.25), residues: 1134 helix: 2.40 (0.25), residues: 399 sheet: 0.69 (0.31), residues: 280 loop : -0.21 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 288 TYR 0.014 0.002 TYR S 178 PHE 0.019 0.002 PHE A 189 TRP 0.015 0.002 TRP A 211 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8931) covalent geometry : angle 0.54056 (12154) SS BOND : bond 0.01006 ( 2) SS BOND : angle 0.71026 ( 4) hydrogen bonds : bond 0.04628 ( 467) hydrogen bonds : angle 4.55096 ( 1317) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.339 Fit side-chains REVERT: A 46 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8334 (ttpt) REVERT: A 333 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8285 (t0) REVERT: B 59 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: R 131 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7977 (mtt-85) outliers start: 18 outliers final: 7 residues processed: 138 average time/residue: 0.8480 time to fit residues: 122.5092 Evaluate side-chains 132 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 131 ARG Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 180 ARG Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain S residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 84 optimal weight: 0.5980 chunk 96 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 103 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 340 ASN R 34 HIS R 176 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.056573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.051437 restraints weight = 14837.338| |-----------------------------------------------------------------------------| r_work (start): 0.2527 rms_B_bonded: 0.82 r_work: 0.2466 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.2394 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8933 Z= 0.153 Angle : 0.598 7.515 12158 Z= 0.321 Chirality : 0.044 0.140 1418 Planarity : 0.005 0.043 1534 Dihedral : 5.589 87.551 1238 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.75 % Allowed : 18.56 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.25), residues: 1134 helix: 2.31 (0.25), residues: 399 sheet: 0.79 (0.31), residues: 278 loop : -0.25 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 87 TYR 0.016 0.002 TYR R 118 PHE 0.019 0.002 PHE A 189 TRP 0.017 0.002 TRP A 211 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8931) covalent geometry : angle 0.59778 (12154) SS BOND : bond 0.01334 ( 2) SS BOND : angle 0.60756 ( 4) hydrogen bonds : bond 0.05108 ( 467) hydrogen bonds : angle 4.68009 ( 1317) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.350 Fit side-chains REVERT: A 333 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8268 (t0) REVERT: B 59 TYR cc_start: 0.8832 (OUTLIER) cc_final: 0.8545 (m-80) REVERT: R 131 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8061 (mtt-85) outliers start: 16 outliers final: 9 residues processed: 138 average time/residue: 0.8237 time to fit residues: 118.9776 Evaluate side-chains 133 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 131 ARG Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 180 ARG Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 340 ASN R 34 HIS R 176 ASN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.055328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.050251 restraints weight = 14883.265| |-----------------------------------------------------------------------------| r_work (start): 0.2497 rms_B_bonded: 0.83 r_work: 0.2435 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.2362 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work (final): 0.2362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8933 Z= 0.173 Angle : 0.640 8.101 12158 Z= 0.344 Chirality : 0.045 0.142 1418 Planarity : 0.005 0.045 1534 Dihedral : 5.779 89.252 1238 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.07 % Allowed : 19.21 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.25), residues: 1134 helix: 2.30 (0.25), residues: 396 sheet: 0.82 (0.31), residues: 283 loop : -0.31 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.018 0.002 TYR R 118 PHE 0.021 0.002 PHE A 189 TRP 0.017 0.002 TRP A 211 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8931) covalent geometry : angle 0.64038 (12154) SS BOND : bond 0.01510 ( 2) SS BOND : angle 0.52381 ( 4) hydrogen bonds : bond 0.05402 ( 467) hydrogen bonds : angle 4.77807 ( 1317) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.357 Fit side-chains REVERT: A 333 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8259 (t0) REVERT: B 59 TYR cc_start: 0.8839 (OUTLIER) cc_final: 0.8492 (m-80) REVERT: B 256 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.7792 (mtp180) REVERT: R 131 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8032 (mtt-85) outliers start: 19 outliers final: 10 residues processed: 138 average time/residue: 0.8200 time to fit residues: 118.4301 Evaluate side-chains 138 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 131 ARG Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 180 ARG Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 25 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 36 ASN B 340 ASN R 34 HIS R 176 ASN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.056416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.051344 restraints weight = 14882.478| |-----------------------------------------------------------------------------| r_work (start): 0.2525 rms_B_bonded: 0.81 r_work: 0.2464 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8933 Z= 0.145 Angle : 0.589 7.240 12158 Z= 0.318 Chirality : 0.044 0.142 1418 Planarity : 0.005 0.044 1534 Dihedral : 5.653 89.745 1238 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.29 % Allowed : 19.32 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.25), residues: 1134 helix: 2.36 (0.25), residues: 398 sheet: 0.77 (0.31), residues: 283 loop : -0.28 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 288 TYR 0.016 0.002 TYR S 178 PHE 0.020 0.002 PHE A 189 TRP 0.017 0.002 TRP A 211 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8931) covalent geometry : angle 0.58886 (12154) SS BOND : bond 0.01231 ( 2) SS BOND : angle 0.58293 ( 4) hydrogen bonds : bond 0.05003 ( 467) hydrogen bonds : angle 4.67915 ( 1317) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.292 Fit side-chains REVERT: A 234 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.7208 (tm-30) REVERT: A 333 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8275 (t0) REVERT: B 59 TYR cc_start: 0.8834 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: B 79 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8185 (mp) REVERT: B 256 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.7772 (mtp180) REVERT: R 131 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8042 (mtt-85) REVERT: R 288 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8261 (mtp180) outliers start: 21 outliers final: 10 residues processed: 140 average time/residue: 0.8266 time to fit residues: 121.0465 Evaluate side-chains 140 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 131 ARG Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 180 ARG Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 288 ARG Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 78 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.0050 chunk 60 optimal weight: 0.4980 chunk 111 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 36 ASN B 340 ASN R 34 HIS R 176 ASN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.057238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.052148 restraints weight = 14819.414| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 0.82 r_work: 0.2484 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8933 Z= 0.129 Angle : 0.557 6.703 12158 Z= 0.302 Chirality : 0.043 0.142 1418 Planarity : 0.004 0.045 1534 Dihedral : 5.487 88.571 1238 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.40 % Allowed : 19.21 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.25), residues: 1134 helix: 2.45 (0.25), residues: 399 sheet: 0.82 (0.31), residues: 282 loop : -0.24 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.015 0.002 TYR S 178 PHE 0.018 0.002 PHE A 189 TRP 0.016 0.002 TRP A 211 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8931) covalent geometry : angle 0.55718 (12154) SS BOND : bond 0.01044 ( 2) SS BOND : angle 0.67705 ( 4) hydrogen bonds : bond 0.04702 ( 467) hydrogen bonds : angle 4.59899 ( 1317) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 0.355 Fit side-chains REVERT: A 234 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: A 333 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8228 (t0) REVERT: B 22 ARG cc_start: 0.8736 (mtt180) cc_final: 0.8492 (mtm180) REVERT: B 59 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8500 (m-80) REVERT: B 79 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8204 (mp) REVERT: B 256 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.7717 (mtp180) REVERT: R 131 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8061 (mtt-85) REVERT: R 288 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8251 (mtp180) outliers start: 22 outliers final: 9 residues processed: 136 average time/residue: 0.8272 time to fit residues: 117.8291 Evaluate side-chains 138 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 131 ARG Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 180 ARG Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 288 ARG Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 77 optimal weight: 0.0020 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 36 ASN B 340 ASN R 34 HIS R 176 ASN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.056744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2533 r_free = 0.2533 target = 0.051696 restraints weight = 14861.551| |-----------------------------------------------------------------------------| r_work (start): 0.2534 rms_B_bonded: 0.81 r_work: 0.2473 rms_B_bonded: 1.02 restraints_weight: 0.5000 r_work: 0.2402 rms_B_bonded: 1.81 restraints_weight: 0.2500 r_work (final): 0.2402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8933 Z= 0.140 Angle : 0.582 7.143 12158 Z= 0.314 Chirality : 0.043 0.140 1418 Planarity : 0.005 0.042 1534 Dihedral : 5.528 87.976 1238 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.29 % Allowed : 19.43 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.25), residues: 1134 helix: 2.43 (0.25), residues: 399 sheet: 0.80 (0.31), residues: 287 loop : -0.19 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 22 TYR 0.015 0.002 TYR S 178 PHE 0.020 0.002 PHE A 189 TRP 0.016 0.002 TRP A 211 HIS 0.004 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8931) covalent geometry : angle 0.58244 (12154) SS BOND : bond 0.01164 ( 2) SS BOND : angle 0.63925 ( 4) hydrogen bonds : bond 0.04883 ( 467) hydrogen bonds : angle 4.62479 ( 1317) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.343 Fit side-chains REVERT: A 234 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: A 333 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8237 (t0) REVERT: B 59 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: B 79 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8180 (mp) REVERT: B 256 ARG cc_start: 0.9148 (OUTLIER) cc_final: 0.7717 (mtp180) REVERT: R 131 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8021 (mtt-85) REVERT: R 180 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8285 (mtm-85) REVERT: R 268 ARG cc_start: 0.9012 (mtp180) cc_final: 0.8770 (mtp180) REVERT: R 288 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8324 (mtp180) outliers start: 21 outliers final: 10 residues processed: 135 average time/residue: 0.8143 time to fit residues: 115.1328 Evaluate side-chains 141 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 131 ARG Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 176 ASN Chi-restraints excluded: chain R residue 180 ARG Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 288 ARG Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 95 optimal weight: 0.0870 chunk 111 optimal weight: 4.9990 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 36 ASN B 340 ASN R 34 HIS R 176 ASN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.055961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.050952 restraints weight = 14711.029| |-----------------------------------------------------------------------------| r_work (start): 0.2516 rms_B_bonded: 0.79 r_work: 0.2454 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.2383 rms_B_bonded: 1.80 restraints_weight: 0.2500 r_work (final): 0.2383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8933 Z= 0.163 Angle : 0.621 7.530 12158 Z= 0.334 Chirality : 0.044 0.140 1418 Planarity : 0.005 0.045 1534 Dihedral : 5.634 87.694 1238 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.40 % Allowed : 19.32 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1134 helix: 2.37 (0.25), residues: 398 sheet: 0.81 (0.31), residues: 287 loop : -0.22 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 22 TYR 0.016 0.002 TYR R 118 PHE 0.021 0.002 PHE A 189 TRP 0.016 0.002 TRP A 211 HIS 0.005 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8931) covalent geometry : angle 0.62068 (12154) SS BOND : bond 0.01314 ( 2) SS BOND : angle 0.63421 ( 4) hydrogen bonds : bond 0.05166 ( 467) hydrogen bonds : angle 4.69958 ( 1317) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.335 Fit side-chains REVERT: A 234 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: A 333 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8281 (t0) REVERT: B 59 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8504 (m-80) REVERT: B 79 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8172 (mp) REVERT: B 163 ASP cc_start: 0.8473 (p0) cc_final: 0.8205 (p0) REVERT: B 256 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.7749 (mtp180) REVERT: R 131 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8030 (mtt-85) REVERT: R 288 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8257 (mtp180) outliers start: 22 outliers final: 12 residues processed: 136 average time/residue: 0.8429 time to fit residues: 119.9668 Evaluate side-chains 143 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain R residue 131 ARG Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 176 ASN Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 288 ARG Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 65 LYS Chi-restraints excluded: chain S residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 0.8980 chunk 97 optimal weight: 0.3980 chunk 99 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN B 36 ASN B 340 ASN R 34 HIS R 176 ASN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.056101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2518 r_free = 0.2518 target = 0.051055 restraints weight = 14732.912| |-----------------------------------------------------------------------------| r_work (start): 0.2518 rms_B_bonded: 0.80 r_work: 0.2458 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 1.79 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 8933 Z= 0.187 Angle : 0.917 59.191 12158 Z= 0.540 Chirality : 0.046 0.509 1418 Planarity : 0.005 0.109 1534 Dihedral : 5.683 87.693 1238 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.26 % Favored : 96.65 % Rotamer: Outliers : 2.29 % Allowed : 19.32 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.25), residues: 1134 helix: 2.38 (0.25), residues: 398 sheet: 0.80 (0.31), residues: 287 loop : -0.22 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.016 0.002 TYR R 118 PHE 0.020 0.002 PHE A 189 TRP 0.017 0.002 TRP A 211 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 8931) covalent geometry : angle 0.91700 (12154) SS BOND : bond 0.01248 ( 2) SS BOND : angle 0.64448 ( 4) hydrogen bonds : bond 0.05131 ( 467) hydrogen bonds : angle 4.69678 ( 1317) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.11 seconds wall clock time: 61 minutes 45.10 seconds (3705.10 seconds total)