Starting phenix.real_space_refine on Mon Jun 9 10:36:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f0j_28758/06_2025/8f0j_28758.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f0j_28758/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8f0j_28758/06_2025/8f0j_28758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f0j_28758/06_2025/8f0j_28758.map" model { file = "/net/cci-nas-00/data/ceres_data/8f0j_28758/06_2025/8f0j_28758.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f0j_28758/06_2025/8f0j_28758.cif" } resolution = 2.0 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= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP: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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} 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: 6.42, per 1000 atoms: 0.66 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: 2.49 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.01 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: 2.64 Time building geometry restraints manager: 2.89 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: 1.360 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.490 Find NCS groups from input model: 0.090 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:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.450 ------------------------------------------------------------------------------- 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 (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: -1.49 (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 TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS R 302 PHE 0.010 0.001 PHE R 235 TYR 0.013 0.001 TYR P 37 ARG 0.004 0.000 ARG A 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 2) link_NAG-ASN : angle 1.70406 ( 6) hydrogen bonds : bond 0.24082 ( 475) hydrogen bonds : angle 7.66531 ( 1335) SS BOND : bond 0.00169 ( 7) SS BOND : angle 0.38695 ( 14) covalent geometry : bond 0.00473 ( 9861) covalent geometry : angle 0.61289 (13277) Misc. bond : bond 0.07685 ( 2) *********************** 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 : 1.113 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: 1.4577 time to fit residues: 264.6725 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 : 1.145 ------------------------------------------------------------------------------- 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 94 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4248 r_free = 0.4248 target = 0.205919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.177622 restraints weight = 7396.637| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 0.55 r_work: 0.3655 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work: 0.3512 rms_B_bonded: 3.58 restraints_weight: 0.1250 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9872 Z= 0.197 Angle : 0.663 7.814 13297 Z= 0.353 Chirality : 0.046 0.157 1440 Planarity : 0.006 0.054 1646 Dihedral : 13.146 101.878 1763 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.23 % Allowed : 10.02 % Favored : 87.75 % 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: 0.44 (0.24), residues: 1141 helix: 1.01 (0.23), residues: 442 sheet: 0.22 (0.32), residues: 235 loop : -0.23 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 234 HIS 0.006 0.002 HIS B 54 PHE 0.024 0.003 PHE R 235 TYR 0.014 0.002 TYR A 358 ARG 0.006 0.001 ARG B 256 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 2) link_NAG-ASN : angle 1.52532 ( 6) hydrogen bonds : bond 0.06619 ( 475) hydrogen bonds : angle 5.25556 ( 1335) SS BOND : bond 0.00615 ( 7) SS BOND : angle 1.06708 ( 14) covalent geometry : bond 0.00409 ( 9861) covalent geometry : angle 0.66182 (13277) Misc. bond : bond 0.00018 ( 2) *********************** 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 168 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.027 Fit side-chains REVERT: R 59 MET cc_start: 0.2495 (mtm) cc_final: 0.1417 (ptm) REVERT: R 143 LYS cc_start: 0.5347 (ttpt) cc_final: 0.4990 (tttt) REVERT: R 220 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5529 (mttt) REVERT: R 346 MET cc_start: 0.7241 (mmp) cc_final: 0.6719 (mmm) REVERT: R 367 MET cc_start: 0.5167 (tpp) cc_final: 0.4802 (tpp) REVERT: R 370 LYS cc_start: 0.5636 (mtpm) cc_final: 0.5394 (mptt) REVERT: R 386 PHE cc_start: 0.7429 (m-80) cc_final: 0.7149 (m-80) REVERT: A 19 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7383 (mt0) outliers start: 22 outliers final: 9 residues processed: 157 average time/residue: 1.5166 time to fit residues: 252.3078 Evaluate side-chains 147 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 108 optimal weight: 6.9990 chunk 70 optimal weight: 0.0060 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 0.0670 chunk 66 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.209761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.183588 restraints weight = 7683.497| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 0.55 r_work: 0.3730 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work: 0.3568 rms_B_bonded: 4.11 restraints_weight: 0.1250 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9872 Z= 0.101 Angle : 0.477 6.024 13297 Z= 0.258 Chirality : 0.040 0.150 1440 Planarity : 0.004 0.038 1646 Dihedral : 11.575 89.853 1763 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.32 % Allowed : 11.13 % Favored : 87.55 % 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: 1.25 (0.25), residues: 1141 helix: 2.02 (0.24), residues: 443 sheet: 0.47 (0.33), residues: 234 loop : -0.07 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 234 HIS 0.005 0.001 HIS B 266 PHE 0.014 0.001 PHE R 235 TYR 0.012 0.001 TYR R 149 ARG 0.005 0.000 ARG R 258 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 2) link_NAG-ASN : angle 1.30453 ( 6) hydrogen bonds : bond 0.04446 ( 475) hydrogen bonds : angle 4.57457 ( 1335) SS BOND : bond 0.00276 ( 7) SS BOND : angle 0.65499 ( 14) covalent geometry : bond 0.00194 ( 9861) covalent geometry : angle 0.47621 (13277) Misc. bond : bond 0.00011 ( 2) *********************** 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 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.000 Fit side-chains REVERT: R 59 MET cc_start: 0.2631 (mtm) cc_final: 0.1509 (ptm) REVERT: R 143 LYS cc_start: 0.5277 (ttpt) cc_final: 0.5024 (tttt) REVERT: R 300 ILE cc_start: 0.7248 (mt) cc_final: 0.7006 (mp) REVERT: R 346 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6712 (mmm) REVERT: R 367 MET cc_start: 0.5176 (tpp) cc_final: 0.4812 (tpp) REVERT: R 370 LYS cc_start: 0.5593 (mtpm) cc_final: 0.5383 (mptt) REVERT: R 386 PHE cc_start: 0.7416 (m-80) cc_final: 0.7195 (m-80) REVERT: A 60 MET cc_start: 0.4145 (mtm) cc_final: 0.3421 (mmt) REVERT: B 340 ASN cc_start: 0.6645 (t0) cc_final: 0.6299 (t0) outliers start: 13 outliers final: 6 residues processed: 146 average time/residue: 1.6006 time to fit residues: 247.0622 Evaluate side-chains 137 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 1.793 ------------------------------------------------------------------------------- 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 25 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.208259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.182420 restraints weight = 7502.687| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 0.57 r_work: 0.3718 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work: 0.3572 rms_B_bonded: 3.34 restraints_weight: 0.1250 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9872 Z= 0.114 Angle : 0.506 6.311 13297 Z= 0.272 Chirality : 0.041 0.146 1440 Planarity : 0.004 0.039 1646 Dihedral : 11.453 89.814 1760 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.52 % Allowed : 12.35 % Favored : 86.13 % 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: 1.50 (0.25), residues: 1141 helix: 2.30 (0.24), residues: 444 sheet: 0.51 (0.33), residues: 234 loop : 0.03 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 234 HIS 0.003 0.001 HIS A 41 PHE 0.016 0.001 PHE R 235 TYR 0.012 0.001 TYR R 149 ARG 0.009 0.001 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00121 ( 2) link_NAG-ASN : angle 1.30405 ( 6) hydrogen bonds : bond 0.04627 ( 475) hydrogen bonds : angle 4.56297 ( 1335) SS BOND : bond 0.00273 ( 7) SS BOND : angle 0.76985 ( 14) covalent geometry : bond 0.00225 ( 9861) covalent geometry : angle 0.50486 (13277) Misc. bond : bond 0.00014 ( 2) *********************** 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 148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.021 Fit side-chains REVERT: R 59 MET cc_start: 0.2615 (mtm) cc_final: 0.1543 (ptm) REVERT: R 143 LYS cc_start: 0.5216 (ttpt) cc_final: 0.4914 (tttt) REVERT: R 208 ASN cc_start: 0.5461 (t0) cc_final: 0.4850 (m110) REVERT: R 300 ILE cc_start: 0.7207 (mt) cc_final: 0.6963 (mp) REVERT: R 346 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6668 (mmm) REVERT: R 367 MET cc_start: 0.5099 (tpp) cc_final: 0.4770 (tpp) REVERT: B 340 ASN cc_start: 0.6636 (t0) cc_final: 0.6368 (t0) outliers start: 15 outliers final: 7 residues processed: 140 average time/residue: 1.7897 time to fit residues: 265.9099 Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 346 MET Chi-restraints excluded: chain A residue 224 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.0980 chunk 87 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 0.0970 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.3578 ------------------------------------------------------------------------------- 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 277 HIS 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 = 0.4294 r_free = 0.4294 target = 0.210442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.184434 restraints weight = 7640.471| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 0.56 r_work: 0.3744 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3674 rms_B_bonded: 2.26 restraints_weight: 0.2500 r_work: 0.3589 rms_B_bonded: 3.88 restraints_weight: 0.1250 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9872 Z= 0.092 Angle : 0.455 5.830 13297 Z= 0.245 Chirality : 0.039 0.140 1440 Planarity : 0.003 0.039 1646 Dihedral : 10.885 89.107 1760 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.01 % Allowed : 13.36 % Favored : 85.63 % 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: 1.71 (0.25), residues: 1141 helix: 2.62 (0.24), residues: 440 sheet: 0.53 (0.33), residues: 233 loop : 0.07 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.002 0.001 HIS R 381 PHE 0.011 0.001 PHE A 212 TYR 0.012 0.001 TYR R 149 ARG 0.008 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 2) link_NAG-ASN : angle 1.21079 ( 6) hydrogen bonds : bond 0.03841 ( 475) hydrogen bonds : angle 4.28792 ( 1335) SS BOND : bond 0.00222 ( 7) SS BOND : angle 0.61060 ( 14) covalent geometry : bond 0.00178 ( 9861) covalent geometry : angle 0.45456 (13277) Misc. bond : bond 0.00012 ( 2) *********************** 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 150 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 1.081 Fit side-chains REVERT: R 59 MET cc_start: 0.2677 (mtm) cc_final: 0.1576 (ptm) REVERT: R 143 LYS cc_start: 0.5117 (ttpt) cc_final: 0.4766 (pttt) REVERT: R 300 ILE cc_start: 0.7111 (mt) cc_final: 0.6884 (mp) REVERT: R 346 MET cc_start: 0.7113 (mmp) cc_final: 0.6692 (mmm) REVERT: B 340 ASN cc_start: 0.6610 (t0) cc_final: 0.6350 (t0) outliers start: 10 outliers final: 7 residues processed: 145 average time/residue: 1.5370 time to fit residues: 236.0398 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 : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 102 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 0.0470 overall best weight: 2.0086 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.206856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.180942 restraints weight = 7520.987| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 0.55 r_work: 0.3681 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3615 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work: 0.3536 rms_B_bonded: 3.50 restraints_weight: 0.1250 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2511 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= 0.142 Angle : 0.558 6.098 13297 Z= 0.299 Chirality : 0.042 0.150 1440 Planarity : 0.004 0.041 1646 Dihedral : 11.863 89.128 1760 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.62 % Allowed : 13.06 % 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 (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: 1.60 (0.25), residues: 1141 helix: 2.40 (0.24), residues: 444 sheet: 0.50 (0.33), residues: 235 loop : 0.11 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 234 HIS 0.005 0.001 HIS B 54 PHE 0.020 0.002 PHE R 235 TYR 0.011 0.002 TYR A 358 ARG 0.010 0.001 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 2) link_NAG-ASN : angle 1.30793 ( 6) hydrogen bonds : bond 0.05051 ( 475) hydrogen bonds : angle 4.66745 ( 1335) SS BOND : bond 0.00374 ( 7) SS BOND : angle 0.84840 ( 14) covalent geometry : bond 0.00294 ( 9861) covalent geometry : angle 0.55711 (13277) Misc. bond : bond 0.00031 ( 2) *********************** 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 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.045 Fit side-chains REVERT: R 59 MET cc_start: 0.2662 (mtm) cc_final: 0.1494 (ptm) REVERT: R 143 LYS cc_start: 0.5236 (ttpt) cc_final: 0.4816 (pttt) REVERT: R 208 ASN cc_start: 0.5505 (t0) cc_final: 0.4761 (m110) REVERT: R 300 ILE cc_start: 0.7228 (mt) cc_final: 0.6959 (mp) REVERT: B 340 ASN cc_start: 0.6670 (t0) cc_final: 0.6398 (t0) outliers start: 16 outliers final: 9 residues processed: 144 average time/residue: 1.4638 time to fit residues: 224.8297 Evaluate side-chains 146 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 137 time to evaluate : 1.032 ------------------------------------------------------------------------------- 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 224 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 349 SER 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 30 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.208943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.182732 restraints weight = 7648.672| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 0.55 r_work: 0.3703 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work: 0.3553 rms_B_bonded: 3.69 restraints_weight: 0.1250 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9872 Z= 0.101 Angle : 0.484 5.907 13297 Z= 0.260 Chirality : 0.040 0.145 1440 Planarity : 0.004 0.039 1646 Dihedral : 11.452 89.908 1760 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.21 % Allowed : 14.17 % 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 (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: 1.77 (0.25), residues: 1141 helix: 2.64 (0.24), residues: 438 sheet: 0.54 (0.33), residues: 234 loop : 0.15 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.003 0.001 HIS R 336 PHE 0.012 0.001 PHE R 235 TYR 0.012 0.001 TYR R 191 ARG 0.009 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 2) link_NAG-ASN : angle 1.23656 ( 6) hydrogen bonds : bond 0.04172 ( 475) hydrogen bonds : angle 4.41910 ( 1335) SS BOND : bond 0.00241 ( 7) SS BOND : angle 0.61264 ( 14) covalent geometry : bond 0.00198 ( 9861) covalent geometry : angle 0.48298 (13277) Misc. bond : bond 0.00019 ( 2) *********************** 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: 12 poor density : 136 time to evaluate : 1.031 Fit side-chains REVERT: R 59 MET cc_start: 0.2728 (mtm) cc_final: 0.1558 (ptm) REVERT: R 143 LYS cc_start: 0.5137 (ttpt) cc_final: 0.4778 (pttt) REVERT: R 208 ASN cc_start: 0.5489 (t0) cc_final: 0.4742 (m110) REVERT: R 300 ILE cc_start: 0.7156 (mt) cc_final: 0.6832 (mp) REVERT: R 346 MET cc_start: 0.7277 (mmp) cc_final: 0.6658 (mmm) REVERT: A 38 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7032 (mpt-90) REVERT: B 340 ASN cc_start: 0.6653 (t0) cc_final: 0.6388 (t0) outliers start: 12 outliers final: 7 residues processed: 143 average time/residue: 1.4762 time to fit residues: 223.6584 Evaluate side-chains 141 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 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 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 85 optimal weight: 8.9990 chunk 34 optimal weight: 0.3980 chunk 36 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.205393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.177996 restraints weight = 7512.631| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 0.59 r_work: 0.3682 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work: 0.3523 rms_B_bonded: 4.04 restraints_weight: 0.1250 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9872 Z= 0.191 Angle : 0.660 7.389 13297 Z= 0.347 Chirality : 0.045 0.176 1440 Planarity : 0.005 0.053 1646 Dihedral : 12.479 89.907 1760 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.72 % Allowed : 13.36 % Favored : 84.92 % 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: 1.32 (0.25), residues: 1141 helix: 2.06 (0.24), residues: 443 sheet: 0.49 (0.33), residues: 235 loop : -0.00 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 234 HIS 0.008 0.002 HIS B 54 PHE 0.028 0.002 PHE R 235 TYR 0.014 0.002 TYR A 358 ARG 0.009 0.001 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00219 ( 2) link_NAG-ASN : angle 1.52091 ( 6) hydrogen bonds : bond 0.05744 ( 475) hydrogen bonds : angle 4.92748 ( 1335) SS BOND : bond 0.00533 ( 7) SS BOND : angle 1.00707 ( 14) covalent geometry : bond 0.00406 ( 9861) covalent geometry : angle 0.65854 (13277) Misc. bond : bond 0.00057 ( 2) *********************** 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 157 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.047 Fit side-chains REVERT: R 59 MET cc_start: 0.2728 (mtm) cc_final: 0.1500 (ptm) REVERT: R 143 LYS cc_start: 0.5206 (ttpt) cc_final: 0.4804 (pttt) REVERT: R 208 ASN cc_start: 0.5468 (t0) cc_final: 0.4862 (m110) REVERT: R 300 ILE cc_start: 0.7292 (mt) cc_final: 0.7035 (mp) REVERT: B 340 ASN cc_start: 0.6721 (t0) cc_final: 0.6380 (t0) outliers start: 17 outliers final: 10 residues processed: 149 average time/residue: 1.5291 time to fit residues: 241.7228 Evaluate side-chains 151 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 68 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 213 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 = 0.4250 r_free = 0.4250 target = 0.206382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.180159 restraints weight = 7501.235| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 0.54 r_work: 0.3674 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work: 0.3503 rms_B_bonded: 3.64 restraints_weight: 0.1250 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9872 Z= 0.142 Angle : 0.574 6.290 13297 Z= 0.306 Chirality : 0.042 0.148 1440 Planarity : 0.004 0.049 1646 Dihedral : 12.161 88.798 1760 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.42 % Allowed : 13.77 % Favored : 84.82 % 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: 1.46 (0.25), residues: 1141 helix: 2.24 (0.24), residues: 443 sheet: 0.52 (0.33), residues: 235 loop : 0.02 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 234 HIS 0.004 0.001 HIS B 54 PHE 0.020 0.002 PHE R 235 TYR 0.016 0.002 TYR B 59 ARG 0.010 0.001 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00148 ( 2) link_NAG-ASN : angle 1.39161 ( 6) hydrogen bonds : bond 0.05035 ( 475) hydrogen bonds : angle 4.74713 ( 1335) SS BOND : bond 0.00387 ( 7) SS BOND : angle 0.74732 ( 14) covalent geometry : bond 0.00295 ( 9861) covalent geometry : angle 0.57348 (13277) Misc. bond : bond 0.00051 ( 2) *********************** 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 152 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 1.128 Fit side-chains REVERT: R 59 MET cc_start: 0.2692 (mtm) cc_final: 0.1489 (ptm) REVERT: R 143 LYS cc_start: 0.5141 (ttpt) cc_final: 0.4901 (tttt) REVERT: R 300 ILE cc_start: 0.7294 (mt) cc_final: 0.7013 (mp) REVERT: R 346 MET cc_start: 0.7337 (mmp) cc_final: 0.6773 (mmm) REVERT: B 340 ASN cc_start: 0.6721 (t0) cc_final: 0.6399 (t0) outliers start: 14 outliers final: 10 residues processed: 144 average time/residue: 1.5458 time to fit residues: 235.5508 Evaluate side-chains 146 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 48 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 0.2980 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 213 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 = 0.4262 r_free = 0.4262 target = 0.207548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.181575 restraints weight = 7555.333| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 0.56 r_work: 0.3702 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work: 0.3550 rms_B_bonded: 3.74 restraints_weight: 0.1250 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9872 Z= 0.115 Angle : 0.524 6.540 13297 Z= 0.281 Chirality : 0.041 0.144 1440 Planarity : 0.004 0.046 1646 Dihedral : 11.843 89.292 1760 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.32 % Allowed : 13.97 % 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 (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: 1.63 (0.25), residues: 1141 helix: 2.47 (0.24), residues: 444 sheet: 0.52 (0.34), residues: 234 loop : 0.07 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 234 HIS 0.003 0.001 HIS R 377 PHE 0.015 0.001 PHE R 235 TYR 0.021 0.001 TYR R 191 ARG 0.010 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00159 ( 2) link_NAG-ASN : angle 1.24293 ( 6) hydrogen bonds : bond 0.04553 ( 475) hydrogen bonds : angle 4.56876 ( 1335) SS BOND : bond 0.00270 ( 7) SS BOND : angle 0.63707 ( 14) covalent geometry : bond 0.00231 ( 9861) covalent geometry : angle 0.52347 (13277) Misc. bond : bond 0.00035 ( 2) ********************** 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 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.073 Fit side-chains REVERT: R 59 MET cc_start: 0.2640 (mtm) cc_final: 0.1461 (ptm) REVERT: R 143 LYS cc_start: 0.5031 (ttpt) cc_final: 0.4603 (pttt) REVERT: R 300 ILE cc_start: 0.7229 (mt) cc_final: 0.6924 (mp) REVERT: R 346 MET cc_start: 0.7336 (mmp) cc_final: 0.6780 (mmm) REVERT: A 38 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7140 (mpt-90) REVERT: B 340 ASN cc_start: 0.6662 (t0) cc_final: 0.6335 (t0) outliers start: 13 outliers final: 9 residues processed: 138 average time/residue: 1.5062 time to fit residues: 220.5041 Evaluate side-chains 142 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 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 59 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.0970 chunk 84 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 213 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 = 0.4276 r_free = 0.4276 target = 0.208938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.181582 restraints weight = 7610.032| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 0.55 r_work: 0.3701 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work: 0.3521 rms_B_bonded: 4.63 restraints_weight: 0.1250 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9872 Z= 0.100 Angle : 0.492 6.667 13297 Z= 0.263 Chirality : 0.040 0.142 1440 Planarity : 0.004 0.044 1646 Dihedral : 11.515 87.897 1760 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.21 % Allowed : 13.97 % Favored : 84.82 % 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: 1.80 (0.25), residues: 1141 helix: 2.70 (0.24), residues: 438 sheet: 0.53 (0.33), residues: 234 loop : 0.15 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 234 HIS 0.003 0.001 HIS R 336 PHE 0.012 0.001 PHE R 235 TYR 0.022 0.001 TYR R 191 ARG 0.010 0.000 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 2) link_NAG-ASN : angle 1.14722 ( 6) hydrogen bonds : bond 0.04103 ( 475) hydrogen bonds : angle 4.39351 ( 1335) SS BOND : bond 0.00220 ( 7) SS BOND : angle 0.58642 ( 14) covalent geometry : bond 0.00197 ( 9861) covalent geometry : angle 0.49159 (13277) Misc. bond : bond 0.00030 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16355.38 seconds wall clock time: 286 minutes 26.76 seconds (17186.76 seconds total)