Starting phenix.real_space_refine on Sat Aug 23 07:18:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f0j_28758/08_2025/8f0j_28758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0j_28758/08_2025/8f0j_28758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f0j_28758/08_2025/8f0j_28758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0j_28758/08_2025/8f0j_28758.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f0j_28758/08_2025/8f0j_28758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0j_28758/08_2025/8f0j_28758.map" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 67 5.16 5 C 6237 2.51 5 N 1605 2.21 5 O 1765 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9678 Number of models: 1 Model: "" Number of chains: 12 Chain: "P" Number of atoms: 277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 277 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} 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: 3058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 3058 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 354} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "A" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1844 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 32 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: "P" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'D6M': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D6M:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 444 Unusual residues: {'NAG': 2, 'P42': 1, 'PLM': 8, 'PTY': 3, 'Y01': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "R" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.55, per 1000 atoms: 0.26 Number of scatterers: 9678 At special positions: 0 Unit cell: (109.85, 100.1, 143.65, 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 67 16.00 P 4 15.00 O 1765 8.00 N 1605 7.00 C 6237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS P 2 " - 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=2, symmetry=0 Links applied NAG-ASN " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 130 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 359.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2178 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 13 sheets defined 43.1% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 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 19 removed outlier: 3.727A pdb=" N HIS P 18 " --> pdb=" O ASN P 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 62 removed outlier: 3.643A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 135 removed outlier: 3.911A pdb=" N ASN R 135 " --> pdb=" O THR R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 Processing helix chain 'R' and resid 208 through 215 Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.748A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (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 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 330 Proline residue: R 304 - end of helix Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 removed outlier: 3.572A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 408 Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.571A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.504A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.792A pdb=" N ARG A 283 " --> pdb=" O LYS A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.505A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.345A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.957A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.474A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.528A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.688A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.509A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 89 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.396A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.605A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.592A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.091A 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: 6.780A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.559A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.209A 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: 4.266A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.259A 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: 3.534A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.955A 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: 3.764A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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: 5.798A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1507 1.31 - 1.43: 2698 1.43 - 1.56: 5551 1.56 - 1.69: 9 1.69 - 1.81: 96 Bond restraints: 9861 Sorted by residual: bond pdb=" C LYS P 21 " pdb=" O LYS P 21 " ideal model delta sigma weight residual 1.242 1.182 0.059 1.00e-02 1.00e+04 3.54e+01 bond pdb=" C02 D6M P 101 " pdb=" N03 D6M P 101 " ideal model delta sigma weight residual 1.339 1.452 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" N VAL R 250 " pdb=" CA VAL R 250 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.15e-02 7.56e+03 1.21e+01 bond pdb=" C07 D6M P 101 " pdb=" O08 D6M P 101 " ideal model delta sigma weight residual 1.247 1.185 0.062 2.00e-02 2.50e+03 9.68e+00 bond pdb=" N ILE R 248 " pdb=" CA ILE R 248 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.89e+00 ... (remaining 9856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 13013 2.00 - 4.01: 231 4.01 - 6.01: 26 6.01 - 8.02: 4 8.02 - 10.02: 3 Bond angle restraints: 13277 Sorted by residual: angle pdb=" N ILE R 248 " pdb=" CA ILE R 248 " pdb=" C ILE R 248 " ideal model delta sigma weight residual 110.72 115.31 -4.59 1.01e+00 9.80e-01 2.06e+01 angle pdb=" N VAL R 293 " pdb=" CA VAL R 293 " pdb=" C VAL R 293 " ideal model delta sigma weight residual 112.17 107.88 4.29 9.50e-01 1.11e+00 2.04e+01 angle pdb=" N SER P 19 " pdb=" CA SER P 19 " pdb=" C SER P 19 " ideal model delta sigma weight residual 110.53 104.74 5.79 1.32e+00 5.74e-01 1.93e+01 angle pdb=" N ILE R 319 " pdb=" CA ILE R 319 " pdb=" C ILE R 319 " ideal model delta sigma weight residual 111.58 106.98 4.60 1.06e+00 8.90e-01 1.89e+01 angle pdb=" CA GLY P 33 " pdb=" C GLY P 33 " pdb=" O GLY P 33 " ideal model delta sigma weight residual 122.28 118.30 3.98 1.00e+00 1.00e+00 1.58e+01 ... (remaining 13272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.13: 5696 24.13 - 48.26: 293 48.26 - 72.39: 58 72.39 - 96.52: 19 96.52 - 120.65: 5 Dihedral angle restraints: 6071 sinusoidal: 2696 harmonic: 3375 Sorted by residual: dihedral pdb=" C THR R 254 " pdb=" N THR R 254 " pdb=" CA THR R 254 " pdb=" CB THR R 254 " ideal model delta harmonic sigma weight residual -122.00 -136.85 14.85 0 2.50e+00 1.60e-01 3.53e+01 dihedral pdb=" N THR R 254 " pdb=" C THR R 254 " pdb=" CA THR R 254 " pdb=" CB THR R 254 " ideal model delta harmonic sigma weight residual 123.40 134.35 -10.95 0 2.50e+00 1.60e-01 1.92e+01 dihedral pdb=" CAM P42 R 509 " pdb=" CAN P42 R 509 " pdb=" CAO P42 R 509 " pdb=" CAP P42 R 509 " ideal model delta sinusoidal sigma weight residual 179.85 -59.50 -120.65 1 3.00e+01 1.11e-03 1.61e+01 ... (remaining 6068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1352 0.095 - 0.190: 81 0.190 - 0.284: 4 0.284 - 0.379: 1 0.379 - 0.474: 2 Chirality restraints: 1440 Sorted by residual: chirality pdb=" CA THR R 254 " pdb=" N THR R 254 " pdb=" C THR R 254 " pdb=" CB THR R 254 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" C6 PTY R 504 " pdb=" C1 PTY R 504 " pdb=" C5 PTY R 504 " pdb=" O7 PTY R 504 " both_signs ideal model delta sigma weight residual False 2.49 2.04 0.45 2.00e-01 2.50e+01 5.05e+00 chirality pdb=" C6 PTY R 508 " pdb=" C1 PTY R 508 " pdb=" C5 PTY R 508 " pdb=" O7 PTY R 508 " both_signs ideal model delta sigma weight residual False 2.49 2.18 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 1437 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL P 17 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C VAL P 17 " -0.026 2.00e-02 2.50e+03 pdb=" O VAL P 17 " 0.010 2.00e-02 2.50e+03 pdb=" N HIS P 18 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 303 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO R 304 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 304 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 304 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR R 254 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.52e+00 pdb=" C THR R 254 " 0.021 2.00e-02 2.50e+03 pdb=" O THR R 254 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU R 255 " -0.007 2.00e-02 2.50e+03 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1829 2.78 - 3.31: 9039 3.31 - 3.84: 16058 3.84 - 4.37: 20380 4.37 - 4.90: 33984 Nonbonded interactions: 81290 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.246 3.040 nonbonded pdb=" OE1 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.317 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.319 3.040 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.352 3.120 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.376 3.040 ... (remaining 81285 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.070 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 9872 Z= 0.305 Angle : 0.614 10.024 13297 Z= 0.373 Chirality : 0.048 0.474 1440 Planarity : 0.003 0.038 1646 Dihedral : 15.417 120.653 3872 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.40 % Allowed : 5.36 % Favored : 94.23 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.22), residues: 1141 helix: -1.49 (0.19), residues: 439 sheet: -0.12 (0.32), residues: 231 loop : -0.70 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 317 TYR 0.013 0.001 TYR P 37 PHE 0.010 0.001 PHE R 235 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS R 302 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 9861) covalent geometry : angle 0.61289 (13277) SS BOND : bond 0.00169 ( 7) SS BOND : angle 0.38695 ( 14) hydrogen bonds : bond 0.24082 ( 475) hydrogen bonds : angle 7.66531 ( 1335) Misc. bond : bond 0.07685 ( 2) link_NAG-ASN : bond 0.00320 ( 2) link_NAG-ASN : angle 1.70406 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 167 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: R 59 MET cc_start: 0.2331 (mtm) cc_final: 0.1359 (ttt) REVERT: R 295 THR cc_start: 0.6162 (t) cc_final: 0.5960 (t) REVERT: R 306 MET cc_start: 0.7539 (mmm) cc_final: 0.7337 (mmm) REVERT: A 60 MET cc_start: 0.3732 (mtm) cc_final: 0.3141 (mmt) REVERT: N 87 LYS cc_start: 0.7713 (mttt) cc_final: 0.7451 (mttm) outliers start: 4 outliers final: 3 residues processed: 171 average time/residue: 0.7591 time to fit residues: 137.2578 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 10 GLN P 18 HIS R 60 GLN ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN R 226 HIS R 257 GLN R 288 ASN A 218 ASN B 13 GLN B 16 ASN G 11 GLN G 24 ASN N 13 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.205601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.177493 restraints weight = 7514.787| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 0.58 r_work: 0.3651 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3588 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9872 Z= 0.210 Angle : 0.710 7.849 13297 Z= 0.374 Chirality : 0.047 0.163 1440 Planarity : 0.006 0.063 1646 Dihedral : 13.612 103.648 1763 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.33 % Allowed : 9.62 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.24), residues: 1141 helix: 0.98 (0.23), residues: 442 sheet: 0.23 (0.32), residues: 235 loop : -0.27 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 251 TYR 0.016 0.002 TYR R 391 PHE 0.027 0.003 PHE R 235 TRP 0.028 0.003 TRP A 234 HIS 0.007 0.002 HIS P 18 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 9861) covalent geometry : angle 0.70829 (13277) SS BOND : bond 0.00444 ( 7) SS BOND : angle 1.16521 ( 14) hydrogen bonds : bond 0.06416 ( 475) hydrogen bonds : angle 5.27221 ( 1335) Misc. bond : bond 0.00019 ( 2) link_NAG-ASN : bond 0.00146 ( 2) link_NAG-ASN : angle 1.61892 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.414 Fit side-chains REVERT: R 59 MET cc_start: 0.2429 (mtm) cc_final: 0.1401 (ptm) REVERT: R 143 LYS cc_start: 0.5348 (ttpt) cc_final: 0.4980 (tttt) REVERT: R 220 LYS cc_start: 0.5865 (OUTLIER) cc_final: 0.5483 (mttt) REVERT: R 346 MET cc_start: 0.7208 (mmp) cc_final: 0.6783 (mmm) REVERT: R 367 MET cc_start: 0.5137 (tpp) cc_final: 0.4798 (tpp) REVERT: R 386 PHE cc_start: 0.7377 (m-80) cc_final: 0.7100 (m-80) REVERT: A 19 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7127 (tt0) outliers start: 23 outliers final: 10 residues processed: 149 average time/residue: 0.7872 time to fit residues: 123.8991 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 220 LYS Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 17 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 68 optimal weight: 0.0270 chunk 72 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 34 optimal weight: 0.0980 chunk 110 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.208473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.182545 restraints weight = 7582.711| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 0.57 r_work: 0.3718 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work: 0.3561 rms_B_bonded: 3.84 restraints_weight: 0.1250 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9872 Z= 0.107 Angle : 0.496 6.266 13297 Z= 0.268 Chirality : 0.040 0.150 1440 Planarity : 0.004 0.039 1646 Dihedral : 12.096 89.746 1763 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.82 % Allowed : 11.13 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1141 helix: 1.97 (0.24), residues: 443 sheet: 0.46 (0.33), residues: 234 loop : -0.06 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 258 TYR 0.012 0.001 TYR R 149 PHE 0.015 0.001 PHE R 235 TRP 0.019 0.001 TRP A 234 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9861) covalent geometry : angle 0.49454 (13277) SS BOND : bond 0.00258 ( 7) SS BOND : angle 0.65763 ( 14) hydrogen bonds : bond 0.04677 ( 475) hydrogen bonds : angle 4.66502 ( 1335) Misc. bond : bond 0.00011 ( 2) link_NAG-ASN : bond 0.00120 ( 2) link_NAG-ASN : angle 1.38206 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.290 Fit side-chains REVERT: R 59 MET cc_start: 0.2602 (mtm) cc_final: 0.1522 (ptm) REVERT: R 143 LYS cc_start: 0.5289 (ttpt) cc_final: 0.5042 (tttt) REVERT: R 208 ASN cc_start: 0.5280 (t0) cc_final: 0.4929 (m110) REVERT: R 300 ILE cc_start: 0.7293 (mt) cc_final: 0.7045 (mp) REVERT: R 346 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6661 (mmm) REVERT: R 367 MET cc_start: 0.5161 (tpp) cc_final: 0.4823 (tpp) REVERT: R 386 PHE cc_start: 0.7397 (m-80) cc_final: 0.7163 (m-80) REVERT: B 340 ASN cc_start: 0.6661 (t0) cc_final: 0.6304 (t0) outliers start: 18 outliers final: 6 residues processed: 149 average time/residue: 0.7439 time to fit residues: 117.0166 Evaluate side-chains 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 346 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 37 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN N 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.206630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.180424 restraints weight = 7558.496| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 0.60 r_work: 0.3748 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work: 0.3601 rms_B_bonded: 3.57 restraints_weight: 0.1250 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9872 Z= 0.139 Angle : 0.560 6.394 13297 Z= 0.300 Chirality : 0.042 0.149 1440 Planarity : 0.004 0.039 1646 Dihedral : 12.266 88.746 1760 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.72 % Allowed : 12.35 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.25), residues: 1141 helix: 2.17 (0.24), residues: 443 sheet: 0.46 (0.33), residues: 235 loop : 0.01 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 347 TYR 0.012 0.002 TYR A 358 PHE 0.020 0.002 PHE R 235 TRP 0.024 0.002 TRP A 234 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9861) covalent geometry : angle 0.55946 (13277) SS BOND : bond 0.00327 ( 7) SS BOND : angle 0.80149 ( 14) hydrogen bonds : bond 0.05192 ( 475) hydrogen bonds : angle 4.76733 ( 1335) Misc. bond : bond 0.00025 ( 2) link_NAG-ASN : bond 0.00114 ( 2) link_NAG-ASN : angle 1.39202 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.372 Fit side-chains REVERT: R 59 MET cc_start: 0.2535 (mtm) cc_final: 0.1275 (ptm) REVERT: R 143 LYS cc_start: 0.5217 (ttpt) cc_final: 0.4833 (pttt) REVERT: R 208 ASN cc_start: 0.5291 (t0) cc_final: 0.4784 (m110) REVERT: R 300 ILE cc_start: 0.7285 (mt) cc_final: 0.7056 (mp) REVERT: R 346 MET cc_start: 0.7132 (mmp) cc_final: 0.6651 (mmm) REVERT: B 340 ASN cc_start: 0.6671 (t0) cc_final: 0.6354 (t0) outliers start: 17 outliers final: 11 residues processed: 142 average time/residue: 0.6804 time to fit residues: 102.4389 Evaluate side-chains 144 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 87 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN R 277 HIS A 390 GLN B 13 GLN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.205837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.180682 restraints weight = 7536.080| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 0.55 r_work: 0.3685 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work: 0.3543 rms_B_bonded: 3.29 restraints_weight: 0.1250 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9872 Z= 0.155 Angle : 0.592 6.747 13297 Z= 0.316 Chirality : 0.043 0.150 1440 Planarity : 0.005 0.043 1646 Dihedral : 12.636 89.766 1760 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.13 % Allowed : 12.55 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.25), residues: 1141 helix: 2.07 (0.24), residues: 443 sheet: 0.48 (0.33), residues: 235 loop : -0.04 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 347 TYR 0.011 0.002 TYR R 391 PHE 0.022 0.002 PHE R 235 TRP 0.026 0.002 TRP A 234 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9861) covalent geometry : angle 0.59153 (13277) SS BOND : bond 0.00431 ( 7) SS BOND : angle 0.83639 ( 14) hydrogen bonds : bond 0.05395 ( 475) hydrogen bonds : angle 4.85065 ( 1335) Misc. bond : bond 0.00056 ( 2) link_NAG-ASN : bond 0.00195 ( 2) link_NAG-ASN : angle 1.42320 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 141 time to evaluate : 0.309 Fit side-chains REVERT: R 59 MET cc_start: 0.2832 (mtm) cc_final: 0.1522 (ptm) REVERT: R 143 LYS cc_start: 0.5216 (ttpt) cc_final: 0.4805 (pttt) REVERT: R 300 ILE cc_start: 0.7334 (mt) cc_final: 0.7056 (mp) REVERT: B 340 ASN cc_start: 0.6661 (t0) cc_final: 0.6317 (t0) outliers start: 21 outliers final: 13 residues processed: 152 average time/residue: 0.6121 time to fit residues: 98.3078 Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 295 THR Chi-restraints excluded: chain R residue 330 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 20.0000 chunk 56 optimal weight: 0.0670 chunk 76 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN A 390 GLN B 13 GLN N 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.208616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.182819 restraints weight = 7629.102| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 0.56 r_work: 0.3728 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work: 0.3553 rms_B_bonded: 4.25 restraints_weight: 0.1250 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9872 Z= 0.102 Angle : 0.486 5.908 13297 Z= 0.262 Chirality : 0.040 0.144 1440 Planarity : 0.004 0.045 1646 Dihedral : 11.877 89.862 1760 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.62 % Allowed : 13.77 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.25), residues: 1141 helix: 2.50 (0.24), residues: 443 sheet: 0.49 (0.33), residues: 234 loop : 0.04 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 347 TYR 0.012 0.001 TYR R 149 PHE 0.012 0.001 PHE R 235 TRP 0.019 0.001 TRP A 234 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 9861) covalent geometry : angle 0.48562 (13277) SS BOND : bond 0.00241 ( 7) SS BOND : angle 0.62297 ( 14) hydrogen bonds : bond 0.04209 ( 475) hydrogen bonds : angle 4.48128 ( 1335) Misc. bond : bond 0.00027 ( 2) link_NAG-ASN : bond 0.00150 ( 2) link_NAG-ASN : angle 1.23362 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.310 Fit side-chains REVERT: R 59 MET cc_start: 0.2738 (mtm) cc_final: 0.1515 (ptm) REVERT: R 143 LYS cc_start: 0.5102 (ttpt) cc_final: 0.4730 (pttt) REVERT: R 208 ASN cc_start: 0.5557 (t0) cc_final: 0.5077 (m110) REVERT: R 300 ILE cc_start: 0.7232 (mt) cc_final: 0.6936 (mp) REVERT: R 346 MET cc_start: 0.7322 (mmp) cc_final: 0.6731 (mmm) REVERT: A 38 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7090 (mpt-90) REVERT: B 340 ASN cc_start: 0.6664 (t0) cc_final: 0.6322 (t0) outliers start: 16 outliers final: 9 residues processed: 148 average time/residue: 0.7069 time to fit residues: 110.6628 Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 5.9990 chunk 107 optimal weight: 0.0770 chunk 50 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN B 13 GLN N 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.207847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.181060 restraints weight = 7572.201| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 0.62 r_work: 0.3725 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9872 Z= 0.112 Angle : 0.506 5.939 13297 Z= 0.272 Chirality : 0.040 0.144 1440 Planarity : 0.004 0.040 1646 Dihedral : 11.694 89.739 1760 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.42 % Allowed : 13.87 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.25), residues: 1141 helix: 2.51 (0.24), residues: 444 sheet: 0.48 (0.33), residues: 234 loop : 0.06 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 347 TYR 0.011 0.001 TYR R 149 PHE 0.015 0.001 PHE R 235 TRP 0.021 0.001 TRP A 234 HIS 0.003 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9861) covalent geometry : angle 0.50547 (13277) SS BOND : bond 0.00273 ( 7) SS BOND : angle 0.66305 ( 14) hydrogen bonds : bond 0.04444 ( 475) hydrogen bonds : angle 4.51569 ( 1335) Misc. bond : bond 0.00031 ( 2) link_NAG-ASN : bond 0.00153 ( 2) link_NAG-ASN : angle 1.23720 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.359 Fit side-chains REVERT: R 59 MET cc_start: 0.2674 (mtm) cc_final: 0.1413 (ptm) REVERT: R 143 LYS cc_start: 0.4979 (ttpt) cc_final: 0.4650 (pttt) REVERT: R 208 ASN cc_start: 0.5434 (t0) cc_final: 0.5061 (m110) REVERT: R 300 ILE cc_start: 0.7143 (mt) cc_final: 0.6884 (mp) REVERT: B 340 ASN cc_start: 0.6450 (t0) cc_final: 0.6181 (t0) outliers start: 14 outliers final: 10 residues processed: 140 average time/residue: 0.6265 time to fit residues: 92.7735 Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN B 13 GLN N 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.206115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.177765 restraints weight = 7463.759| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 0.60 r_work: 0.3659 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work: 0.3510 rms_B_bonded: 3.87 restraints_weight: 0.1250 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9872 Z= 0.153 Angle : 0.588 6.355 13297 Z= 0.312 Chirality : 0.043 0.152 1440 Planarity : 0.004 0.042 1646 Dihedral : 12.230 88.787 1760 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.52 % Allowed : 13.97 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.25), residues: 1141 helix: 2.27 (0.24), residues: 443 sheet: 0.47 (0.33), residues: 235 loop : 0.03 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 347 TYR 0.012 0.002 TYR R 191 PHE 0.022 0.002 PHE R 235 TRP 0.025 0.002 TRP A 234 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9861) covalent geometry : angle 0.58654 (13277) SS BOND : bond 0.00395 ( 7) SS BOND : angle 0.85413 ( 14) hydrogen bonds : bond 0.05218 ( 475) hydrogen bonds : angle 4.76790 ( 1335) Misc. bond : bond 0.00050 ( 2) link_NAG-ASN : bond 0.00193 ( 2) link_NAG-ASN : angle 1.39140 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.405 Fit side-chains REVERT: R 59 MET cc_start: 0.2630 (mtm) cc_final: 0.1475 (ptm) REVERT: R 143 LYS cc_start: 0.5150 (ttpt) cc_final: 0.4917 (tttt) REVERT: R 204 GLU cc_start: 0.5329 (OUTLIER) cc_final: 0.5055 (mm-30) REVERT: R 208 ASN cc_start: 0.5556 (t0) cc_final: 0.5107 (m110) REVERT: R 300 ILE cc_start: 0.7308 (mt) cc_final: 0.7028 (mp) REVERT: R 346 MET cc_start: 0.7404 (mmp) cc_final: 0.6836 (mmm) REVERT: A 390 GLN cc_start: 0.7500 (mt0) cc_final: 0.7275 (mt0) REVERT: B 340 ASN cc_start: 0.6690 (t0) cc_final: 0.6355 (t0) outliers start: 15 outliers final: 10 residues processed: 147 average time/residue: 0.6947 time to fit residues: 107.7565 Evaluate side-chains 150 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 204 GLU Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 1.9990 chunk 83 optimal weight: 0.0020 chunk 15 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 overall best weight: 1.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN B 13 GLN N 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.207215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.180734 restraints weight = 7487.297| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 0.61 r_work: 0.3743 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9872 Z= 0.121 Angle : 0.528 6.013 13297 Z= 0.283 Chirality : 0.041 0.144 1440 Planarity : 0.004 0.041 1646 Dihedral : 11.971 88.905 1760 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.21 % Allowed : 14.47 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.25), residues: 1141 helix: 2.41 (0.24), residues: 443 sheet: 0.49 (0.34), residues: 235 loop : 0.05 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 347 TYR 0.018 0.001 TYR R 191 PHE 0.016 0.002 PHE R 235 TRP 0.022 0.002 TRP A 234 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 9861) covalent geometry : angle 0.52770 (13277) SS BOND : bond 0.00324 ( 7) SS BOND : angle 0.70641 ( 14) hydrogen bonds : bond 0.04645 ( 475) hydrogen bonds : angle 4.60936 ( 1335) Misc. bond : bond 0.00038 ( 2) link_NAG-ASN : bond 0.00175 ( 2) link_NAG-ASN : angle 1.24979 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.392 Fit side-chains REVERT: R 59 MET cc_start: 0.2600 (mtm) cc_final: 0.1345 (ptm) REVERT: R 143 LYS cc_start: 0.4972 (ttpt) cc_final: 0.4657 (pttt) REVERT: R 300 ILE cc_start: 0.7145 (mt) cc_final: 0.6885 (mp) REVERT: R 346 MET cc_start: 0.7147 (mmp) cc_final: 0.6599 (mmm) outliers start: 12 outliers final: 11 residues processed: 147 average time/residue: 0.6546 time to fit residues: 101.9145 Evaluate side-chains 150 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN R 208 ASN B 13 GLN N 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.206700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.180526 restraints weight = 7466.752| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 0.53 r_work: 0.3668 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work: 0.3499 rms_B_bonded: 3.99 restraints_weight: 0.1250 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9872 Z= 0.138 Angle : 0.568 6.870 13297 Z= 0.303 Chirality : 0.042 0.147 1440 Planarity : 0.004 0.041 1646 Dihedral : 12.206 88.773 1760 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.42 % Allowed : 14.47 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.25), residues: 1141 helix: 2.31 (0.24), residues: 443 sheet: 0.49 (0.33), residues: 235 loop : 0.04 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 347 TYR 0.015 0.002 TYR R 191 PHE 0.020 0.002 PHE R 235 TRP 0.024 0.002 TRP A 234 HIS 0.004 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9861) covalent geometry : angle 0.56731 (13277) SS BOND : bond 0.00354 ( 7) SS BOND : angle 0.93360 ( 14) hydrogen bonds : bond 0.04983 ( 475) hydrogen bonds : angle 4.72243 ( 1335) Misc. bond : bond 0.00048 ( 2) link_NAG-ASN : bond 0.00183 ( 2) link_NAG-ASN : angle 1.27907 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.383 Fit side-chains REVERT: R 59 MET cc_start: 0.2677 (mtm) cc_final: 0.1481 (ptm) REVERT: R 300 ILE cc_start: 0.7277 (mt) cc_final: 0.6992 (mp) REVERT: R 346 MET cc_start: 0.7384 (mmp) cc_final: 0.6773 (mmm) outliers start: 14 outliers final: 12 residues processed: 146 average time/residue: 0.6301 time to fit residues: 97.3539 Evaluate side-chains 151 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 49 MET Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 chunk 89 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 44 optimal weight: 0.0970 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 144 ASN R 208 ASN B 13 GLN N 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.208261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.183049 restraints weight = 7575.141| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 0.53 r_work: 0.3702 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3633 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work: 0.3561 rms_B_bonded: 3.34 restraints_weight: 0.1250 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9872 Z= 0.108 Angle : 0.508 7.055 13297 Z= 0.272 Chirality : 0.040 0.142 1440 Planarity : 0.004 0.047 1646 Dihedral : 11.856 84.965 1760 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.11 % Allowed : 15.08 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.25), residues: 1141 helix: 2.53 (0.24), residues: 444 sheet: 0.52 (0.34), residues: 234 loop : 0.07 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 347 TYR 0.024 0.001 TYR R 191 PHE 0.014 0.001 PHE R 235 TRP 0.019 0.002 TRP A 234 HIS 0.003 0.001 HIS R 377 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 9861) covalent geometry : angle 0.50712 (13277) SS BOND : bond 0.00280 ( 7) SS BOND : angle 0.80210 ( 14) hydrogen bonds : bond 0.04308 ( 475) hydrogen bonds : angle 4.50186 ( 1335) Misc. bond : bond 0.00034 ( 2) link_NAG-ASN : bond 0.00163 ( 2) link_NAG-ASN : angle 1.16759 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6003.54 seconds wall clock time: 102 minutes 37.24 seconds (6157.24 seconds total)