Starting phenix.real_space_refine on Mon Jun 9 04:44:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tyn_26188/06_2025/7tyn_26188.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tyn_26188/06_2025/7tyn_26188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tyn_26188/06_2025/7tyn_26188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tyn_26188/06_2025/7tyn_26188.map" model { file = "/net/cci-nas-00/data/ceres_data/7tyn_26188/06_2025/7tyn_26188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tyn_26188/06_2025/7tyn_26188.cif" } resolution = 2.6 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= 0.011 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 543 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 63 5.16 5 C 6025 2.51 5 N 1581 2.21 5 O 1694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9364 Number of models: 1 Model: "" Number of chains: 8 Chain: "P" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2892 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 17, 'TRANS': 355} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 275 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "A" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1881 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 349 Unusual residues: {'NAG': 2, 'P42': 1, 'PLM': 13, 'Y01': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.98, per 1000 atoms: 0.64 Number of scatterers: 9364 At special positions: 0 Unit cell: (94.1673, 158.153, 90.5455, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 1 15.00 O 1694 8.00 N 1581 7.00 C 6025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS P 1 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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=1, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 13 sheets defined 41.8% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 21 Processing helix chain 'R' and resid 38 through 62 removed outlier: 3.703A pdb=" N TYR R 56 " --> pdb=" O GLN R 52 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 137 removed outlier: 3.867A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE R 137 " --> pdb=" O MET R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 Processing helix chain 'R' and resid 178 through 205 removed outlier: 3.504A pdb=" N VAL R 205 " --> pdb=" O HIS R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.555A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 4.247A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 Processing helix chain 'R' and resid 287 through 291 removed outlier: 3.652A pdb=" N TRP R 290 " --> pdb=" O ASP R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 329 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 348 Processing helix chain 'R' and resid 348 through 353 Processing helix chain 'R' and resid 354 through 359 removed outlier: 3.539A pdb=" N PHE R 359 " --> pdb=" O GLN R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 409 removed outlier: 3.854A pdb=" N THR R 401 " --> pdb=" O GLU R 397 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE R 409 " --> pdb=" O GLN R 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.500A pdb=" N ARG A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.635A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.677A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 301 removed outlier: 3.575A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.650A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.757A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.668A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.530A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.686A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA2, first strand: chain 'R' and resid 89 through 94 removed outlier: 3.922A pdb=" N VAL R 89 " --> pdb=" O CYS R 112 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS R 112 " --> pdb=" O VAL R 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 120 through 121 removed outlier: 3.967A pdb=" N ARG R 126 " --> pdb=" O HIS R 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.274A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.867A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.682A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.573A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.784A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.498A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.696A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.844A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1311 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: 4.20 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1550 1.32 - 1.45: 2578 1.45 - 1.57: 5340 1.57 - 1.70: 2 1.70 - 1.82: 88 Bond restraints: 9558 Sorted by residual: bond pdb=" C1 NAG R 502 " pdb=" O5 NAG R 502 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.23e+01 bond pdb=" N GLY P 28 " pdb=" CA GLY P 28 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.40e-03 1.13e+04 9.31e+00 bond pdb=" N LEU R 80 " pdb=" CA LEU R 80 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.51e+00 bond pdb=" OBN P42 R 503 " pdb=" PBM P42 R 503 " ideal model delta sigma weight residual 1.657 1.606 0.051 2.00e-02 2.50e+03 6.51e+00 ... (remaining 9553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.52: 12871 4.52 - 9.03: 12 9.03 - 13.55: 0 13.55 - 18.06: 0 18.06 - 22.58: 2 Bond angle restraints: 12885 Sorted by residual: angle pdb=" CA PRO P 32 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 112.00 90.04 21.96 1.40e+00 5.10e-01 2.46e+02 angle pdb=" C THR P 31 " pdb=" N PRO P 32 " pdb=" CD PRO P 32 " ideal model delta sigma weight residual 125.00 147.58 -22.58 4.10e+00 5.95e-02 3.03e+01 angle pdb=" C THR P 27 " pdb=" CA THR P 27 " pdb=" CB THR P 27 " ideal model delta sigma weight residual 111.80 119.64 -7.84 1.46e+00 4.69e-01 2.88e+01 angle pdb=" N GLY R 78 " pdb=" CA GLY R 78 " pdb=" C GLY R 78 " ideal model delta sigma weight residual 114.37 108.36 6.01 1.26e+00 6.30e-01 2.27e+01 angle pdb=" N TYR R 131 " pdb=" CA TYR R 131 " pdb=" C TYR R 131 " ideal model delta sigma weight residual 112.92 107.38 5.54 1.23e+00 6.61e-01 2.03e+01 ... (remaining 12880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.64: 5526 24.64 - 49.29: 233 49.29 - 73.93: 36 73.93 - 98.58: 16 98.58 - 123.22: 1 Dihedral angle restraints: 5812 sinusoidal: 2453 harmonic: 3359 Sorted by residual: dihedral pdb=" CB CYS R 72 " pdb=" SG CYS R 72 " pdb=" SG CYS R 112 " pdb=" CB CYS R 112 " ideal model delta sinusoidal sigma weight residual -86.00 -27.30 -58.70 1 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" CB CYS P 1 " pdb=" SG CYS P 1 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 40.92 52.08 1 1.00e+01 1.00e-02 3.70e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -149.92 -30.08 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 5809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1400 0.120 - 0.239: 9 0.239 - 0.359: 3 0.359 - 0.479: 0 0.479 - 0.599: 1 Chirality restraints: 1413 Sorted by residual: chirality pdb=" C1 NAG R 501 " pdb=" ND2 ASN R 130 " pdb=" C2 NAG R 501 " pdb=" O5 NAG R 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.96e+00 chirality pdb=" CA THR P 27 " pdb=" N THR P 27 " pdb=" C THR P 27 " pdb=" CB THR P 27 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA TRP R 76 " pdb=" N TRP R 76 " pdb=" C TRP R 76 " pdb=" CB TRP R 76 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 1410 not shown) Planarity restraints: 1622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR P 31 " -0.049 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO P 32 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO P 32 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO P 32 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.48e+00 pdb=" N PRO R 304 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO B 236 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.018 5.00e-02 4.00e+02 ... (remaining 1619 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1097 2.75 - 3.29: 8785 3.29 - 3.83: 15304 3.83 - 4.36: 19777 4.36 - 4.90: 32888 Nonbonded interactions: 77851 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.216 3.040 nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.256 3.040 nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.262 3.040 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.264 3.120 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.279 3.040 ... (remaining 77846 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.110 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:28.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 9568 Z= 0.242 Angle : 0.629 22.577 12905 Z= 0.364 Chirality : 0.045 0.599 1413 Planarity : 0.003 0.064 1620 Dihedral : 13.818 123.221 3621 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.01 % Allowed : 12.88 % Favored : 85.11 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -2.90 (0.21), residues: 1138 helix: -3.02 (0.16), residues: 414 sheet: -0.75 (0.30), residues: 253 loop : -1.29 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 76 HIS 0.005 0.001 HIS R 302 PHE 0.012 0.001 PHE N 108 TYR 0.010 0.001 TYR R 98 ARG 0.002 0.000 ARG N 118 Details of bonding type rmsd link_NAG-ASN : bond 0.00740 ( 2) link_NAG-ASN : angle 3.35769 ( 6) hydrogen bonds : bond 0.25416 ( 459) hydrogen bonds : angle 8.82907 ( 1311) SS BOND : bond 0.00177 ( 7) SS BOND : angle 1.57224 ( 14) covalent geometry : bond 0.00390 ( 9558) covalent geometry : angle 0.62292 (12885) Misc. bond : bond 0.10849 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 192 time to evaluate : 0.937 Fit side-chains REVERT: P 32 PRO cc_start: 0.4510 (OUTLIER) cc_final: 0.4118 (Cg_exo) REVERT: R 143 LYS cc_start: 0.7422 (ttmt) cc_final: 0.7103 (ttmt) REVERT: R 174 ARG cc_start: 0.7704 (mmm-85) cc_final: 0.7389 (mtm-85) REVERT: R 229 MET cc_start: 0.8624 (tpp) cc_final: 0.8364 (tpp) REVERT: R 230 MET cc_start: 0.8015 (ttm) cc_final: 0.7812 (ttm) REVERT: R 337 MET cc_start: 0.7876 (ttp) cc_final: 0.7427 (ttm) REVERT: A 53 LYS cc_start: 0.7514 (ttpt) cc_final: 0.6784 (tttt) REVERT: A 221 MET cc_start: 0.8337 (ttp) cc_final: 0.7996 (ttp) REVERT: A 356 ARG cc_start: 0.7042 (mtm180) cc_final: 0.6839 (ptt180) REVERT: A 358 TYR cc_start: 0.8075 (m-80) cc_final: 0.7782 (m-80) REVERT: B 9 GLN cc_start: 0.7469 (tt0) cc_final: 0.7230 (tm-30) REVERT: B 19 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7710 (ttp80) REVERT: B 266 HIS cc_start: 0.7880 (t-170) cc_final: 0.7576 (t70) REVERT: G 14 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7518 (ptpt) REVERT: G 38 MET cc_start: 0.8421 (ttp) cc_final: 0.8092 (ttm) REVERT: N 19 ARG cc_start: 0.8694 (ttt90) cc_final: 0.8397 (ttt180) REVERT: N 46 GLU cc_start: 0.7742 (tt0) cc_final: 0.7448 (tt0) REVERT: N 50 ASP cc_start: 0.8635 (p0) cc_final: 0.8406 (p0) REVERT: N 123 GLN cc_start: 0.8763 (tp-100) cc_final: 0.8554 (mm-40) outliers start: 19 outliers final: 5 residues processed: 204 average time/residue: 1.5642 time to fit residues: 336.5508 Evaluate side-chains 154 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 32 PRO Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain N residue 12 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 135 ASN R 179 GLN R 302 HIS R 377 HIS R 383 GLN B 132 ASN B 220 GLN G 24 ASN ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.167966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118724 restraints weight = 9517.438| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.03 r_work: 0.3045 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9568 Z= 0.196 Angle : 0.625 8.689 12905 Z= 0.326 Chirality : 0.045 0.228 1413 Planarity : 0.005 0.045 1620 Dihedral : 9.231 107.768 1606 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.38 % Allowed : 16.37 % Favored : 80.25 % 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: -0.89 (0.22), residues: 1138 helix: -0.26 (0.22), residues: 438 sheet: -0.33 (0.32), residues: 234 loop : -0.87 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.013 0.002 TYR R 391 ARG 0.007 0.001 ARG N 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 2) link_NAG-ASN : angle 1.33549 ( 6) hydrogen bonds : bond 0.05529 ( 459) hydrogen bonds : angle 5.14411 ( 1311) SS BOND : bond 0.00355 ( 7) SS BOND : angle 2.41493 ( 14) covalent geometry : bond 0.00451 ( 9558) covalent geometry : angle 0.62015 (12885) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.924 Fit side-chains REVERT: R 112 CYS cc_start: -0.0874 (OUTLIER) cc_final: -0.1183 (m) REVERT: R 140 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6848 (tp30) REVERT: R 174 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.7273 (mtm-85) REVERT: R 196 MET cc_start: 0.8434 (mtt) cc_final: 0.8155 (mtm) REVERT: R 204 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6256 (mm-30) REVERT: R 229 MET cc_start: 0.8757 (tpp) cc_final: 0.8367 (mmm) REVERT: R 405 GLN cc_start: 0.7665 (tm-30) cc_final: 0.7172 (tm-30) REVERT: A 221 MET cc_start: 0.9103 (ttp) cc_final: 0.8827 (ttp) REVERT: A 358 TYR cc_start: 0.8600 (m-80) cc_final: 0.8252 (m-80) REVERT: B 61 MET cc_start: 0.9046 (ppp) cc_final: 0.8796 (ppp) REVERT: G 14 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7090 (ttmt) REVERT: G 38 MET cc_start: 0.8518 (ttp) cc_final: 0.8178 (ttm) REVERT: N 46 GLU cc_start: 0.8511 (tt0) cc_final: 0.8209 (tt0) REVERT: N 89 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: N 106 ASP cc_start: 0.8762 (p0) cc_final: 0.8533 (p0) REVERT: N 123 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8663 (tp40) outliers start: 32 outliers final: 13 residues processed: 180 average time/residue: 1.4045 time to fit residues: 267.5359 Evaluate side-chains 159 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 50.0000 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 11 optimal weight: 30.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 179 GLN R 227 GLN R 408 GLN A 19 GLN A 31 GLN A 213 GLN A 294 GLN B 17 GLN N 77 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.166753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.117195 restraints weight = 9626.538| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.19 r_work: 0.3017 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9568 Z= 0.192 Angle : 0.611 9.373 12905 Z= 0.316 Chirality : 0.045 0.200 1413 Planarity : 0.004 0.039 1620 Dihedral : 9.436 101.615 1598 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.91 % Allowed : 17.21 % Favored : 78.88 % 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 (0.23), residues: 1138 helix: 0.75 (0.24), residues: 447 sheet: -0.16 (0.32), residues: 234 loop : -0.73 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.015 0.002 PHE A 212 TYR 0.013 0.002 TYR R 149 ARG 0.006 0.001 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 2) link_NAG-ASN : angle 1.61967 ( 6) hydrogen bonds : bond 0.05131 ( 459) hydrogen bonds : angle 4.88377 ( 1311) SS BOND : bond 0.00399 ( 7) SS BOND : angle 2.60131 ( 14) covalent geometry : bond 0.00445 ( 9558) covalent geometry : angle 0.60446 (12885) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.922 Fit side-chains REVERT: R 174 ARG cc_start: 0.7478 (mmm-85) cc_final: 0.7276 (mtt180) REVERT: R 196 MET cc_start: 0.8469 (mtt) cc_final: 0.8131 (mtp) REVERT: R 204 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6412 (mm-30) REVERT: R 256 LYS cc_start: 0.6652 (tptt) cc_final: 0.6431 (tptm) REVERT: R 405 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7105 (tm-30) REVERT: A 221 MET cc_start: 0.9090 (ttp) cc_final: 0.8837 (ttp) REVERT: A 356 ARG cc_start: 0.7784 (mtm110) cc_final: 0.7162 (ptt180) REVERT: A 358 TYR cc_start: 0.8616 (m-80) cc_final: 0.8261 (m-80) REVERT: B 19 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7351 (ttp80) REVERT: B 61 MET cc_start: 0.9074 (ppp) cc_final: 0.8808 (ppp) REVERT: B 124 TYR cc_start: 0.9209 (m-80) cc_final: 0.8929 (m-80) REVERT: G 38 MET cc_start: 0.8562 (ttp) cc_final: 0.8156 (ttm) REVERT: N 89 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: N 123 GLN cc_start: 0.9039 (tp-100) cc_final: 0.8750 (tp40) outliers start: 37 outliers final: 19 residues processed: 170 average time/residue: 1.3858 time to fit residues: 249.8988 Evaluate side-chains 161 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 179 GLN R 227 GLN A 19 GLN A 31 GLN A 357 HIS B 17 GLN N 1 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.170296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.121365 restraints weight = 9635.616| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.94 r_work: 0.3137 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9568 Z= 0.115 Angle : 0.533 10.919 12905 Z= 0.272 Chirality : 0.042 0.160 1413 Planarity : 0.003 0.041 1620 Dihedral : 8.700 95.751 1598 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.54 % Allowed : 16.90 % Favored : 78.56 % 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: 0.49 (0.24), residues: 1138 helix: 1.46 (0.25), residues: 447 sheet: -0.12 (0.33), residues: 234 loop : -0.48 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS R 381 PHE 0.012 0.001 PHE B 253 TYR 0.012 0.001 TYR R 149 ARG 0.007 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00345 ( 2) link_NAG-ASN : angle 2.28099 ( 6) hydrogen bonds : bond 0.04049 ( 459) hydrogen bonds : angle 4.49175 ( 1311) SS BOND : bond 0.00272 ( 7) SS BOND : angle 1.95179 ( 14) covalent geometry : bond 0.00252 ( 9558) covalent geometry : angle 0.52759 (12885) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 2.274 Fit side-chains REVERT: R 140 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7045 (tp30) REVERT: R 174 ARG cc_start: 0.7527 (mmm-85) cc_final: 0.7314 (mtt180) REVERT: R 196 MET cc_start: 0.8429 (mtt) cc_final: 0.8092 (mtp) REVERT: R 204 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6396 (mm-30) REVERT: R 405 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7073 (tm-30) REVERT: A 17 LYS cc_start: 0.7535 (ttmm) cc_final: 0.6850 (pttt) REVERT: A 221 MET cc_start: 0.9074 (ttp) cc_final: 0.8819 (ttp) REVERT: A 356 ARG cc_start: 0.7578 (mtm110) cc_final: 0.7032 (ptt180) REVERT: B 19 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7406 (ttp80) REVERT: B 57 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8763 (pttp) REVERT: B 61 MET cc_start: 0.8884 (ppp) cc_final: 0.8673 (ppp) REVERT: B 124 TYR cc_start: 0.9077 (m-80) cc_final: 0.8843 (m-80) REVERT: B 219 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8139 (mtm180) REVERT: G 38 MET cc_start: 0.8576 (ttp) cc_final: 0.8222 (ttm) REVERT: N 38 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8886 (ptp-170) REVERT: N 89 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: N 123 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8676 (tp40) outliers start: 43 outliers final: 20 residues processed: 187 average time/residue: 1.5662 time to fit residues: 309.9253 Evaluate side-chains 173 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 135 ASN R 227 GLN A 19 GLN A 31 GLN A 357 HIS B 17 GLN N 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.167703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118501 restraints weight = 9590.787| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.12 r_work: 0.3038 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9568 Z= 0.171 Angle : 0.593 9.674 12905 Z= 0.305 Chirality : 0.044 0.175 1413 Planarity : 0.004 0.046 1620 Dihedral : 9.073 90.462 1598 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.65 % Allowed : 17.21 % Favored : 78.14 % 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: 0.55 (0.24), residues: 1138 helix: 1.52 (0.25), residues: 447 sheet: -0.08 (0.33), residues: 230 loop : -0.46 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 236 HIS 0.004 0.001 HIS R 381 PHE 0.014 0.002 PHE A 212 TYR 0.013 0.002 TYR R 149 ARG 0.008 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 2) link_NAG-ASN : angle 2.28869 ( 6) hydrogen bonds : bond 0.04623 ( 459) hydrogen bonds : angle 4.65438 ( 1311) SS BOND : bond 0.00347 ( 7) SS BOND : angle 2.62352 ( 14) covalent geometry : bond 0.00391 ( 9558) covalent geometry : angle 0.58486 (12885) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.310 Fit side-chains REVERT: R 140 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7020 (tp30) REVERT: R 174 ARG cc_start: 0.7539 (mmm-85) cc_final: 0.7325 (mtt180) REVERT: R 196 MET cc_start: 0.8488 (mtt) cc_final: 0.8155 (mtp) REVERT: R 204 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6423 (mm-30) REVERT: R 405 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7071 (tm-30) REVERT: A 17 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7115 (ttmm) REVERT: A 299 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6337 (tt0) REVERT: B 19 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7452 (ttp80) REVERT: B 61 MET cc_start: 0.9104 (ppp) cc_final: 0.8795 (ppp) REVERT: B 124 TYR cc_start: 0.9157 (m-80) cc_final: 0.8922 (m-80) REVERT: B 219 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8136 (mtm180) REVERT: G 38 MET cc_start: 0.8560 (ttp) cc_final: 0.8230 (ttm) REVERT: N 89 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: N 123 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8698 (tp40) outliers start: 44 outliers final: 25 residues processed: 176 average time/residue: 1.5319 time to fit residues: 285.0080 Evaluate side-chains 174 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 19 GLN A 31 GLN A 357 HIS B 17 GLN N 1 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.169024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119974 restraints weight = 9632.839| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.02 r_work: 0.3062 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9568 Z= 0.136 Angle : 0.559 9.566 12905 Z= 0.286 Chirality : 0.043 0.172 1413 Planarity : 0.004 0.049 1620 Dihedral : 8.731 82.936 1598 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.65 % Allowed : 17.85 % Favored : 77.51 % 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: 0.72 (0.24), residues: 1138 helix: 1.70 (0.25), residues: 447 sheet: -0.02 (0.33), residues: 228 loop : -0.41 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS R 381 PHE 0.012 0.001 PHE B 253 TYR 0.013 0.001 TYR R 149 ARG 0.010 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 2) link_NAG-ASN : angle 2.52938 ( 6) hydrogen bonds : bond 0.04185 ( 459) hydrogen bonds : angle 4.49032 ( 1311) SS BOND : bond 0.00330 ( 7) SS BOND : angle 2.41722 ( 14) covalent geometry : bond 0.00306 ( 9558) covalent geometry : angle 0.55138 (12885) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.947 Fit side-chains REVERT: R 140 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6986 (tp30) REVERT: R 196 MET cc_start: 0.8441 (mtt) cc_final: 0.8122 (mtp) REVERT: R 204 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6328 (mm-30) REVERT: R 405 GLN cc_start: 0.7500 (tm-30) cc_final: 0.6991 (tm-30) REVERT: A 17 LYS cc_start: 0.7514 (ttmm) cc_final: 0.6828 (pttt) REVERT: A 299 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6470 (tt0) REVERT: B 19 ARG cc_start: 0.7931 (ttp80) cc_final: 0.7356 (ttp80) REVERT: B 57 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8714 (pttp) REVERT: B 59 TYR cc_start: 0.9376 (OUTLIER) cc_final: 0.9163 (m-80) REVERT: B 61 MET cc_start: 0.9044 (ppp) cc_final: 0.8801 (ppp) REVERT: B 124 TYR cc_start: 0.9110 (m-80) cc_final: 0.8893 (m-80) REVERT: B 219 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8128 (mtm180) REVERT: G 38 MET cc_start: 0.8578 (ttp) cc_final: 0.8233 (ttm) REVERT: N 89 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.7904 (pt0) REVERT: N 123 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8659 (tp40) outliers start: 44 outliers final: 25 residues processed: 177 average time/residue: 1.4227 time to fit residues: 266.6438 Evaluate side-chains 177 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 140 GLU Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 19 GLN A 31 GLN A 357 HIS B 17 GLN N 1 GLN N 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.167953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118638 restraints weight = 9652.658| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.04 r_work: 0.3042 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9568 Z= 0.160 Angle : 0.587 9.790 12905 Z= 0.300 Chirality : 0.044 0.180 1413 Planarity : 0.004 0.052 1620 Dihedral : 8.859 79.474 1598 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.33 % Allowed : 18.27 % Favored : 77.40 % 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: 0.72 (0.24), residues: 1138 helix: 1.72 (0.25), residues: 447 sheet: -0.11 (0.32), residues: 234 loop : -0.36 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 236 HIS 0.003 0.001 HIS R 381 PHE 0.014 0.001 PHE A 212 TYR 0.013 0.001 TYR N 95 ARG 0.010 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 2) link_NAG-ASN : angle 2.92415 ( 6) hydrogen bonds : bond 0.04449 ( 459) hydrogen bonds : angle 4.55869 ( 1311) SS BOND : bond 0.00366 ( 7) SS BOND : angle 2.42548 ( 14) covalent geometry : bond 0.00366 ( 9558) covalent geometry : angle 0.57869 (12885) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 1.022 Fit side-chains REVERT: R 196 MET cc_start: 0.8469 (mtt) cc_final: 0.8147 (mtp) REVERT: R 204 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6346 (mm-30) REVERT: R 337 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7153 (ttm) REVERT: R 405 GLN cc_start: 0.7493 (tm-30) cc_final: 0.6983 (tm-30) REVERT: A 17 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7196 (ttmm) REVERT: A 299 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6461 (tt0) REVERT: B 19 ARG cc_start: 0.7913 (ttp80) cc_final: 0.7334 (ttp80) REVERT: B 57 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8720 (pttp) REVERT: B 61 MET cc_start: 0.9095 (ppp) cc_final: 0.8768 (ppp) REVERT: B 124 TYR cc_start: 0.9149 (m-80) cc_final: 0.8887 (m-80) REVERT: B 219 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8140 (mtm180) REVERT: G 38 MET cc_start: 0.8604 (ttp) cc_final: 0.8223 (ttm) REVERT: N 89 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7942 (pt0) REVERT: N 123 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8778 (tp40) outliers start: 41 outliers final: 23 residues processed: 170 average time/residue: 1.5728 time to fit residues: 282.8374 Evaluate side-chains 173 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 337 MET Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 0.0020 chunk 97 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.0170 chunk 66 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 overall best weight: 0.7830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN R 227 GLN A 19 GLN A 31 GLN A 357 HIS B 17 GLN G 59 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123396 restraints weight = 9806.057| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.77 r_work: 0.3102 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9568 Z= 0.111 Angle : 0.539 10.803 12905 Z= 0.273 Chirality : 0.041 0.175 1413 Planarity : 0.004 0.058 1620 Dihedral : 8.071 76.128 1598 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.17 % Allowed : 19.75 % Favored : 77.09 % 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: 0.96 (0.25), residues: 1138 helix: 1.98 (0.25), residues: 447 sheet: -0.06 (0.32), residues: 237 loop : -0.26 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS R 381 PHE 0.020 0.001 PHE R 172 TYR 0.013 0.001 TYR N 95 ARG 0.013 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00156 ( 2) link_NAG-ASN : angle 3.52930 ( 6) hydrogen bonds : bond 0.03827 ( 459) hydrogen bonds : angle 4.29304 ( 1311) SS BOND : bond 0.00274 ( 7) SS BOND : angle 1.89438 ( 14) covalent geometry : bond 0.00244 ( 9558) covalent geometry : angle 0.53071 (12885) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.945 Fit side-chains REVERT: R 196 MET cc_start: 0.8350 (mtt) cc_final: 0.8035 (mtp) REVERT: R 204 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6249 (mm-30) REVERT: R 229 MET cc_start: 0.8722 (mmp) cc_final: 0.8441 (mmp) REVERT: R 364 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7945 (p) REVERT: A 17 LYS cc_start: 0.7396 (ttmm) cc_final: 0.6725 (pttt) REVERT: A 299 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6405 (tt0) REVERT: B 19 ARG cc_start: 0.7795 (ttp80) cc_final: 0.7211 (ttp80) REVERT: B 61 MET cc_start: 0.8899 (ppp) cc_final: 0.8638 (ppp) REVERT: B 124 TYR cc_start: 0.9084 (m-80) cc_final: 0.8879 (m-80) REVERT: B 219 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8087 (mtm180) REVERT: B 340 ASN cc_start: 0.8322 (t160) cc_final: 0.7918 (t0) REVERT: G 20 LYS cc_start: 0.8083 (mttp) cc_final: 0.7749 (mtpt) REVERT: G 38 MET cc_start: 0.8513 (ttp) cc_final: 0.8179 (ttm) REVERT: N 87 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8024 (mtmt) REVERT: N 89 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7911 (pt0) outliers start: 30 outliers final: 15 residues processed: 169 average time/residue: 1.7936 time to fit residues: 320.9868 Evaluate side-chains 164 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 7 optimal weight: 30.0000 chunk 106 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN A 19 GLN A 31 GLN A 357 HIS A 390 GLN B 17 GLN G 59 ASN N 123 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.169106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120083 restraints weight = 9601.374| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.09 r_work: 0.3067 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9568 Z= 0.137 Angle : 0.566 8.837 12905 Z= 0.288 Chirality : 0.042 0.181 1413 Planarity : 0.004 0.064 1620 Dihedral : 8.129 77.358 1598 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.75 % Allowed : 21.01 % Favored : 76.24 % 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: 0.94 (0.25), residues: 1138 helix: 1.96 (0.25), residues: 447 sheet: -0.16 (0.32), residues: 241 loop : -0.19 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.004 0.001 HIS R 381 PHE 0.012 0.001 PHE A 212 TYR 0.012 0.001 TYR B 59 ARG 0.012 0.001 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 2) link_NAG-ASN : angle 3.79279 ( 6) hydrogen bonds : bond 0.04137 ( 459) hydrogen bonds : angle 4.39678 ( 1311) SS BOND : bond 0.00312 ( 7) SS BOND : angle 2.00758 ( 14) covalent geometry : bond 0.00311 ( 9558) covalent geometry : angle 0.55662 (12885) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.927 Fit side-chains REVERT: R 196 MET cc_start: 0.8462 (mtt) cc_final: 0.8163 (mtp) REVERT: R 204 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6374 (mm-30) REVERT: R 229 MET cc_start: 0.8715 (mmp) cc_final: 0.8358 (mmp) REVERT: R 364 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7991 (p) REVERT: A 17 LYS cc_start: 0.7538 (ttmm) cc_final: 0.6882 (pttt) REVERT: A 299 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6486 (tt0) REVERT: B 19 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7363 (ttp80) REVERT: B 61 MET cc_start: 0.9054 (ppp) cc_final: 0.8774 (ppp) REVERT: B 219 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8142 (mtm180) REVERT: G 38 MET cc_start: 0.8596 (ttp) cc_final: 0.8281 (ttm) REVERT: N 89 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7912 (pt0) outliers start: 26 outliers final: 16 residues processed: 162 average time/residue: 1.4432 time to fit residues: 247.4855 Evaluate side-chains 162 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 46 optimal weight: 0.0770 chunk 61 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 99 optimal weight: 0.0020 chunk 49 optimal weight: 0.6980 overall best weight: 0.4746 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN A 19 GLN A 31 GLN A 357 HIS A 390 GLN B 17 GLN G 59 ASN N 123 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.172577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.124299 restraints weight = 9766.136| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.19 r_work: 0.3125 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9568 Z= 0.099 Angle : 0.520 11.835 12905 Z= 0.262 Chirality : 0.040 0.168 1413 Planarity : 0.004 0.064 1620 Dihedral : 7.464 74.217 1598 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.32 % Allowed : 21.75 % Favored : 75.92 % 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: 1.23 (0.25), residues: 1138 helix: 2.33 (0.25), residues: 441 sheet: -0.07 (0.32), residues: 239 loop : -0.12 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.004 0.001 HIS R 381 PHE 0.021 0.001 PHE R 172 TYR 0.011 0.001 TYR N 95 ARG 0.014 0.000 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00115 ( 2) link_NAG-ASN : angle 3.57451 ( 6) hydrogen bonds : bond 0.03547 ( 459) hydrogen bonds : angle 4.13280 ( 1311) SS BOND : bond 0.00255 ( 7) SS BOND : angle 1.65681 ( 14) covalent geometry : bond 0.00213 ( 9558) covalent geometry : angle 0.51138 (12885) Misc. bond : bond 0.00002 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2276 Ramachandran restraints generated. 1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.961 Fit side-chains REVERT: R 196 MET cc_start: 0.8413 (mtt) cc_final: 0.8150 (mtp) REVERT: R 204 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6376 (mm-30) REVERT: R 229 MET cc_start: 0.8691 (mmp) cc_final: 0.8365 (mmp) REVERT: R 364 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.7987 (p) REVERT: A 17 LYS cc_start: 0.7343 (ttmm) cc_final: 0.6718 (pttt) REVERT: A 299 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6518 (tt0) REVERT: A 356 ARG cc_start: 0.7605 (mtm-85) cc_final: 0.7031 (ptt-90) REVERT: B 15 LYS cc_start: 0.7613 (mtpt) cc_final: 0.7334 (mtpt) REVERT: B 61 MET cc_start: 0.8887 (ppp) cc_final: 0.8548 (ppp) REVERT: B 219 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8159 (mtm180) REVERT: B 340 ASN cc_start: 0.8273 (t160) cc_final: 0.7876 (t0) REVERT: G 38 MET cc_start: 0.8492 (ttp) cc_final: 0.8260 (ttm) REVERT: N 87 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8063 (mtmt) REVERT: N 89 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8017 (pt0) REVERT: N 105 ARG cc_start: 0.7148 (ttp-110) cc_final: 0.6827 (mpp80) outliers start: 22 outliers final: 11 residues processed: 166 average time/residue: 1.4990 time to fit residues: 263.5785 Evaluate side-chains 161 residues out of total 1003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 7 CYS Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 219 CYS Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 364 SER Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 GLN A 19 GLN A 31 GLN A 357 HIS A 390 GLN B 17 GLN N 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121049 restraints weight = 9658.333| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.87 r_work: 0.3081 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9568 Z= 0.142 Angle : 0.566 9.097 12905 Z= 0.288 Chirality : 0.042 0.172 1413 Planarity : 0.004 0.067 1620 Dihedral : 7.799 76.561 1597 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.43 % Allowed : 21.44 % Favored : 76.14 % 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: 1.09 (0.25), residues: 1138 helix: 2.13 (0.25), residues: 447 sheet: -0.12 (0.32), residues: 239 loop : -0.16 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 236 HIS 0.004 0.001 HIS R 381 PHE 0.012 0.001 PHE A 212 TYR 0.014 0.001 TYR B 59 ARG 0.013 0.001 ARG N 105 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 2) link_NAG-ASN : angle 3.25865 ( 6) hydrogen bonds : bond 0.04136 ( 459) hydrogen bonds : angle 4.36343 ( 1311) SS BOND : bond 0.00421 ( 7) SS BOND : angle 2.52236 ( 14) covalent geometry : bond 0.00321 ( 9558) covalent geometry : angle 0.55566 (12885) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10118.50 seconds wall clock time: 176 minutes 27.90 seconds (10587.90 seconds total)