Starting phenix.real_space_refine on Tue Feb 3 22:48:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l84_62884/02_2026/9l84_62884_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l84_62884/02_2026/9l84_62884.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l84_62884/02_2026/9l84_62884.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l84_62884/02_2026/9l84_62884.map" model { file = "/net/cci-nas-00/data/ceres_data/9l84_62884/02_2026/9l84_62884_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l84_62884/02_2026/9l84_62884_neut.cif" } resolution = 3.22 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= 0.001 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 47 5.16 5 C 4791 2.51 5 N 1283 2.21 5 O 1351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7472 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1580 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 11, 'GLN:plan1': 3, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 122 Chain: "B" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2462 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 155 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 7, 'ASP:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 124 Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 395 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "N" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 911 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "R" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2060 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 10, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 5, 'GLU:plan': 4, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 94 Chain: "R" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'ALE': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 1.66, per 1000 atoms: 0.22 Number of scatterers: 7472 At special positions: 0 Unit cell: (75.6, 100.44, 130.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 47 16.00 O 1351 8.00 N 1283 7.00 C 4791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 216 " distance=2.03 Simple disulfide: pdb=" SG CYS R 209 " - pdb=" SG CYS R 215 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 300.9 milliseconds 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 41.2% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 15 through 40 removed outlier: 3.634A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.568A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 331 through 351 removed outlier: 4.153A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.668A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (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 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.750A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 86 removed outlier: 4.174A pdb=" N ALA R 66 " --> pdb=" O GLY R 62 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ILE R 68 " --> pdb=" O LEU R 64 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL R 69 " --> pdb=" O MET R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 111 removed outlier: 3.622A pdb=" N ILE R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 111 through 121 Processing helix chain 'R' and resid 127 through 162 Processing helix chain 'R' and resid 162 through 170 Processing helix chain 'R' and resid 171 through 191 Processing helix chain 'R' and resid 191 through 196 removed outlier: 3.689A pdb=" N LEU R 195 " --> pdb=" O PHE R 191 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 191 through 196' Processing helix chain 'R' and resid 203 through 212 removed outlier: 3.647A pdb=" N CYS R 209 " --> pdb=" O GLU R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 233 removed outlier: 3.941A pdb=" N SER R 229 " --> pdb=" O ALA R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 254 Processing helix chain 'R' and resid 321 through 350 removed outlier: 3.625A pdb=" N LEU R 326 " --> pdb=" O ALA R 322 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY R 327 " --> pdb=" O LEU R 323 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS R 336 " --> pdb=" O VAL R 332 " (cutoff:3.500A) Proline residue: R 339 - end of helix removed outlier: 3.763A pdb=" N ALA R 348 " --> pdb=" O ASN R 344 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE R 349 " --> pdb=" O VAL R 345 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 378 removed outlier: 3.541A pdb=" N LEU R 365 " --> pdb=" O PHE R 361 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN R 369 " --> pdb=" O LEU R 365 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER R 370 " --> pdb=" O GLY R 366 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA R 371 " --> pdb=" O TYR R 367 " (cutoff:3.500A) Proline residue: R 374 - end of helix Processing helix chain 'R' and resid 380 through 391 removed outlier: 3.506A pdb=" N GLY R 389 " --> pdb=" O LYS R 385 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.518A pdb=" N PHE A 219 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.608A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.979A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.510A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.595A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.546A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 4.044A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.689A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.627A pdb=" N THR N 69 " --> pdb=" O GLN N 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.035A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1095 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: 1.06 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1465 1.33 - 1.45: 1939 1.45 - 1.57: 4171 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 7635 Sorted by residual: bond pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.63e+00 bond pdb=" C4 ALE R 502 " pdb=" O2 ALE R 502 " ideal model delta sigma weight residual 1.351 1.399 -0.048 2.00e-02 2.50e+03 5.77e+00 bond pdb=" C3 ALE R 502 " pdb=" O1 ALE R 502 " ideal model delta sigma weight residual 1.353 1.396 -0.043 2.00e-02 2.50e+03 4.56e+00 bond pdb=" CBN DR7 R 501 " pdb=" NBH DR7 R 501 " ideal model delta sigma weight residual 1.356 1.323 0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C MET B 325 " pdb=" N ALA B 326 " ideal model delta sigma weight residual 1.331 1.313 0.019 1.33e-02 5.65e+03 1.98e+00 ... (remaining 7630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 10189 1.79 - 3.58: 194 3.58 - 5.37: 40 5.37 - 7.16: 11 7.16 - 8.95: 6 Bond angle restraints: 10440 Sorted by residual: angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 111.14 117.36 -6.22 1.08e+00 8.57e-01 3.32e+01 angle pdb=" CA ASP N 109 " pdb=" CB ASP N 109 " pdb=" CG ASP N 109 " ideal model delta sigma weight residual 112.60 116.46 -3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" C MET B 325 " pdb=" N ALA B 326 " pdb=" CA ALA B 326 " ideal model delta sigma weight residual 122.36 116.36 6.00 1.60e+00 3.91e-01 1.40e+01 angle pdb=" CA ASP N 109 " pdb=" C ASP N 109 " pdb=" O ASP N 109 " ideal model delta sigma weight residual 120.70 117.14 3.56 1.03e+00 9.43e-01 1.19e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 112.72 108.31 4.41 1.36e+00 5.41e-01 1.05e+01 ... (remaining 10435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3905 17.75 - 35.50: 419 35.50 - 53.26: 103 53.26 - 71.01: 24 71.01 - 88.76: 6 Dihedral angle restraints: 4457 sinusoidal: 1501 harmonic: 2956 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 57.87 35.13 1 1.00e+01 1.00e-02 1.75e+01 dihedral pdb=" CA ASP B 195 " pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta harmonic sigma weight residual -180.00 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -116.66 30.66 1 1.00e+01 1.00e-02 1.34e+01 ... (remaining 4454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 983 0.050 - 0.100: 210 0.100 - 0.150: 39 0.150 - 0.200: 1 0.200 - 0.250: 2 Chirality restraints: 1235 Sorted by residual: chirality pdb=" CA ASP N 109 " pdb=" N ASP N 109 " pdb=" C ASP N 109 " pdb=" CB ASP N 109 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C7 ALE R 502 " pdb=" C1 ALE R 502 " pdb=" C8 ALE R 502 " pdb=" O3 ALE R 502 " both_signs ideal model delta sigma weight residual False 2.28 2.49 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA DR7 R 501 " pdb=" N DR7 R 501 " pdb=" C DR7 R 501 " pdb=" CB DR7 R 501 " both_signs ideal model delta sigma weight residual False 2.46 2.64 -0.18 2.00e-01 2.50e+01 8.02e-01 ... (remaining 1232 not shown) Planarity restraints: 1323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBN DR7 R 501 " 0.100 2.00e-02 2.50e+03 3.13e-01 1.22e+03 pdb=" CBV DR7 R 501 " -0.143 2.00e-02 2.50e+03 pdb=" NBH DR7 R 501 " 0.549 2.00e-02 2.50e+03 pdb=" NBW DR7 R 501 " -0.373 2.00e-02 2.50e+03 pdb=" OAL DR7 R 501 " -0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA DR7 R 501 " 0.087 2.00e-02 2.50e+03 9.36e-02 1.10e+02 pdb=" C DR7 R 501 " -0.037 2.00e-02 2.50e+03 pdb=" O DR7 R 501 " -0.018 2.00e-02 2.50e+03 pdb=" CBT DR7 R 501 " 0.114 2.00e-02 2.50e+03 pdb=" NBG DR7 R 501 " -0.147 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE N 108 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.74e+00 pdb=" C PHE N 108 " -0.041 2.00e-02 2.50e+03 pdb=" O PHE N 108 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP N 109 " 0.014 2.00e-02 2.50e+03 ... (remaining 1320 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 186 2.70 - 3.25: 7445 3.25 - 3.80: 12230 3.80 - 4.35: 15390 4.35 - 4.90: 25595 Nonbonded interactions: 60846 Sorted by model distance: nonbonded pdb=" OD1 ASN A 292 " pdb=" N LYS A 293 " model vdw 2.145 3.120 nonbonded pdb=" O SER R 162 " pdb=" OG SER R 162 " model vdw 2.210 3.040 nonbonded pdb=" OD2 ASP R 138 " pdb=" OH TYR R 367 " model vdw 2.228 3.040 nonbonded pdb=" O TRP N 47 " pdb=" OG1 THR N 61 " model vdw 2.236 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.265 3.040 ... (remaining 60841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.600 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 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 : 0.003 0.048 7639 Z= 0.157 Angle : 0.675 8.953 10448 Z= 0.369 Chirality : 0.043 0.250 1235 Planarity : 0.010 0.313 1323 Dihedral : 16.465 88.762 2529 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.56 % Allowed : 29.38 % Favored : 70.06 % 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 are not related in a simple way. whole: -0.37 (0.27), residues: 1000 helix: 0.78 (0.27), residues: 387 sheet: -0.52 (0.34), residues: 222 loop : -1.01 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 219 TYR 0.016 0.001 TYR R 224 PHE 0.025 0.001 PHE A 222 TRP 0.025 0.002 TRP A 281 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7635) covalent geometry : angle 0.67563 (10440) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.33311 ( 8) hydrogen bonds : bond 0.20548 ( 382) hydrogen bonds : angle 7.40415 ( 1095) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 202 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 358 TYR cc_start: 0.8015 (m-80) cc_final: 0.7589 (m-80) REVERT: A 390 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8288 (tt0) REVERT: B 7 LEU cc_start: 0.8397 (tp) cc_final: 0.8168 (tp) REVERT: B 34 THR cc_start: 0.8771 (m) cc_final: 0.8364 (p) REVERT: B 98 SER cc_start: 0.8897 (t) cc_final: 0.8693 (t) REVERT: B 292 PHE cc_start: 0.7768 (m-80) cc_final: 0.7535 (m-80) REVERT: G 9 ILE cc_start: 0.8612 (pt) cc_final: 0.8375 (mt) REVERT: N 28 THR cc_start: 0.8928 (p) cc_final: 0.8704 (p) REVERT: N 32 TYR cc_start: 0.9040 (m-80) cc_final: 0.8769 (m-80) REVERT: N 69 THR cc_start: 0.8861 (t) cc_final: 0.8442 (p) REVERT: R 76 ASN cc_start: 0.7467 (m-40) cc_final: 0.7182 (m-40) REVERT: R 176 ARG cc_start: 0.8058 (mtm180) cc_final: 0.7643 (ttm-80) REVERT: R 215 CYS cc_start: 0.7166 (t) cc_final: 0.6877 (t) REVERT: R 240 MET cc_start: 0.7755 (mtm) cc_final: 0.7403 (ttm) REVERT: R 379 ARG cc_start: 0.7077 (mtm-85) cc_final: 0.6727 (mtm-85) outliers start: 4 outliers final: 1 residues processed: 203 average time/residue: 0.0751 time to fit residues: 20.7405 Evaluate side-chains 164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN N 82 GLN N 84 ASN R 90 GLN R 211 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.131350 restraints weight = 9451.505| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.16 r_work: 0.3500 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7639 Z= 0.123 Angle : 0.603 9.403 10448 Z= 0.308 Chirality : 0.042 0.176 1235 Planarity : 0.004 0.039 1323 Dihedral : 7.544 82.867 1141 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.79 % Allowed : 24.86 % Favored : 69.35 % 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 are not related in a simple way. whole: 0.09 (0.27), residues: 1000 helix: 1.33 (0.27), residues: 390 sheet: -0.23 (0.34), residues: 225 loop : -1.02 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 8 TYR 0.032 0.001 TYR R 210 PHE 0.019 0.001 PHE R 361 TRP 0.021 0.001 TRP B 82 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7635) covalent geometry : angle 0.60298 (10440) SS BOND : bond 0.00108 ( 4) SS BOND : angle 0.44264 ( 8) hydrogen bonds : bond 0.04024 ( 382) hydrogen bonds : angle 4.96772 ( 1095) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.247 Fit side-chains REVERT: A 34 LYS cc_start: 0.8422 (tttm) cc_final: 0.7792 (ttpt) REVERT: A 270 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8306 (mp) REVERT: A 278 ASN cc_start: 0.8567 (m-40) cc_final: 0.8096 (m110) REVERT: A 381 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.7957 (t0) REVERT: A 390 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8296 (tt0) REVERT: B 7 LEU cc_start: 0.8157 (tp) cc_final: 0.7921 (tp) REVERT: B 8 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7120 (mtm-85) REVERT: G 9 ILE cc_start: 0.8458 (pt) cc_final: 0.8221 (mt) REVERT: N 52 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.7941 (p) REVERT: N 69 THR cc_start: 0.8747 (t) cc_final: 0.8441 (m) REVERT: R 94 ASN cc_start: 0.8404 (m-40) cc_final: 0.8158 (m-40) REVERT: R 156 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7670 (mtt90) REVERT: R 176 ARG cc_start: 0.7863 (mtm180) cc_final: 0.7202 (mtp85) REVERT: R 224 TYR cc_start: 0.7886 (t80) cc_final: 0.7603 (t80) REVERT: R 240 MET cc_start: 0.7740 (mtm) cc_final: 0.7436 (ttm) REVERT: R 318 ARG cc_start: 0.7747 (mtp-110) cc_final: 0.7499 (tmt170) REVERT: R 379 ARG cc_start: 0.7177 (mtm-85) cc_final: 0.6632 (mtm-85) outliers start: 41 outliers final: 19 residues processed: 200 average time/residue: 0.0709 time to fit residues: 19.7028 Evaluate side-chains 178 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 354 VAL Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 95 optimal weight: 0.5980 chunk 12 optimal weight: 0.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 259 GLN N 77 ASN N 84 ASN R 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.155947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129374 restraints weight = 9587.032| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.15 r_work: 0.3464 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7639 Z= 0.125 Angle : 0.563 10.162 10448 Z= 0.287 Chirality : 0.042 0.164 1235 Planarity : 0.004 0.045 1323 Dihedral : 6.991 81.554 1141 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 5.23 % Allowed : 25.56 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.27), residues: 1000 helix: 1.38 (0.27), residues: 398 sheet: -0.14 (0.34), residues: 218 loop : -1.04 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 67 TYR 0.028 0.001 TYR R 210 PHE 0.014 0.001 PHE R 242 TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 7635) covalent geometry : angle 0.56319 (10440) SS BOND : bond 0.00097 ( 4) SS BOND : angle 0.33548 ( 8) hydrogen bonds : bond 0.03537 ( 382) hydrogen bonds : angle 4.55035 ( 1095) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8966 (m-30) cc_final: 0.8620 (m-30) REVERT: A 224 VAL cc_start: 0.7919 (OUTLIER) cc_final: 0.7697 (t) REVERT: A 267 GLN cc_start: 0.8261 (tp-100) cc_final: 0.7747 (mm-40) REVERT: A 360 TYR cc_start: 0.8927 (m-80) cc_final: 0.8720 (m-80) REVERT: A 381 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.7980 (t0) REVERT: A 390 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8320 (tt0) REVERT: B 7 LEU cc_start: 0.8131 (tp) cc_final: 0.7923 (tp) REVERT: G 9 ILE cc_start: 0.8490 (pt) cc_final: 0.8268 (mt) REVERT: N 52 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.7895 (p) REVERT: N 69 THR cc_start: 0.8793 (t) cc_final: 0.8502 (m) REVERT: R 156 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7741 (mtt90) REVERT: R 176 ARG cc_start: 0.7852 (mtm180) cc_final: 0.7210 (mtp85) REVERT: R 224 TYR cc_start: 0.8029 (t80) cc_final: 0.7822 (t80) REVERT: R 318 ARG cc_start: 0.7595 (mtp-110) cc_final: 0.7249 (tmt-80) REVERT: R 379 ARG cc_start: 0.7048 (mtm-85) cc_final: 0.6500 (mtm-85) outliers start: 37 outliers final: 24 residues processed: 196 average time/residue: 0.0669 time to fit residues: 18.0021 Evaluate side-chains 187 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 354 VAL Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 40 optimal weight: 0.0870 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124821 restraints weight = 9816.349| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.18 r_work: 0.3408 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7639 Z= 0.157 Angle : 0.578 8.329 10448 Z= 0.295 Chirality : 0.042 0.164 1235 Planarity : 0.004 0.041 1323 Dihedral : 7.031 82.985 1141 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 6.07 % Allowed : 25.42 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.27), residues: 1000 helix: 1.43 (0.27), residues: 399 sheet: -0.24 (0.35), residues: 221 loop : -0.99 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 8 TYR 0.027 0.002 TYR R 210 PHE 0.014 0.001 PHE R 361 TRP 0.017 0.001 TRP A 281 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7635) covalent geometry : angle 0.57852 (10440) SS BOND : bond 0.00117 ( 4) SS BOND : angle 0.34506 ( 8) hydrogen bonds : bond 0.03425 ( 382) hydrogen bonds : angle 4.45558 ( 1095) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9022 (m-30) cc_final: 0.8698 (m-30) REVERT: A 274 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8258 (ttmt) REVERT: A 381 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7963 (t0) REVERT: A 390 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8351 (tt0) REVERT: B 7 LEU cc_start: 0.8147 (tp) cc_final: 0.7932 (tp) REVERT: G 9 ILE cc_start: 0.8528 (pt) cc_final: 0.8318 (mt) REVERT: N 52 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.7917 (p) REVERT: N 69 THR cc_start: 0.8870 (t) cc_final: 0.8345 (p) REVERT: R 156 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7797 (mtt90) REVERT: R 176 ARG cc_start: 0.7756 (mtm180) cc_final: 0.7350 (ttm-80) REVERT: R 240 MET cc_start: 0.7859 (mtm) cc_final: 0.7386 (ttm) REVERT: R 330 MET cc_start: 0.7514 (mmp) cc_final: 0.6875 (mmp) REVERT: R 379 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6566 (mtm-85) outliers start: 43 outliers final: 31 residues processed: 192 average time/residue: 0.0631 time to fit residues: 16.6634 Evaluate side-chains 190 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 136 SER Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 354 VAL Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 8 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 60 optimal weight: 0.0770 chunk 80 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.154229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126739 restraints weight = 9583.245| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.21 r_work: 0.3434 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7639 Z= 0.121 Angle : 0.562 8.407 10448 Z= 0.286 Chirality : 0.041 0.147 1235 Planarity : 0.004 0.037 1323 Dihedral : 7.029 83.330 1141 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.66 % Allowed : 27.26 % Favored : 68.08 % 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 are not related in a simple way. whole: 0.27 (0.27), residues: 1000 helix: 1.55 (0.27), residues: 399 sheet: -0.18 (0.35), residues: 216 loop : -1.03 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 8 TYR 0.028 0.001 TYR R 210 PHE 0.015 0.001 PHE R 242 TRP 0.012 0.001 TRP A 281 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7635) covalent geometry : angle 0.56167 (10440) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.29075 ( 8) hydrogen bonds : bond 0.03214 ( 382) hydrogen bonds : angle 4.34312 ( 1095) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8978 (m-30) cc_final: 0.8586 (m-30) REVERT: A 358 TYR cc_start: 0.8228 (m-80) cc_final: 0.7525 (m-80) REVERT: A 360 TYR cc_start: 0.9038 (m-80) cc_final: 0.8781 (m-80) REVERT: A 381 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.7911 (t0) REVERT: A 390 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8361 (tt0) REVERT: B 7 LEU cc_start: 0.8221 (tp) cc_final: 0.8000 (tp) REVERT: G 9 ILE cc_start: 0.8538 (pt) cc_final: 0.8324 (mt) REVERT: N 69 THR cc_start: 0.8844 (t) cc_final: 0.8597 (m) REVERT: R 156 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7741 (mtt90) REVERT: R 176 ARG cc_start: 0.7737 (mtm180) cc_final: 0.7323 (ttm-80) REVERT: R 240 MET cc_start: 0.7936 (mtm) cc_final: 0.7476 (ttm) REVERT: R 379 ARG cc_start: 0.7201 (mtm-85) cc_final: 0.6551 (mtm-85) outliers start: 33 outliers final: 29 residues processed: 177 average time/residue: 0.0668 time to fit residues: 16.1041 Evaluate side-chains 184 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 130 PHE Chi-restraints excluded: chain R residue 136 SER Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 354 VAL Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123636 restraints weight = 9571.562| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.20 r_work: 0.3397 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7639 Z= 0.158 Angle : 0.574 7.287 10448 Z= 0.295 Chirality : 0.042 0.169 1235 Planarity : 0.004 0.039 1323 Dihedral : 7.017 83.872 1141 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 6.36 % Allowed : 25.71 % Favored : 67.94 % 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 are not related in a simple way. whole: 0.23 (0.27), residues: 1000 helix: 1.52 (0.26), residues: 399 sheet: -0.11 (0.36), residues: 210 loop : -1.10 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 67 TYR 0.028 0.002 TYR R 210 PHE 0.018 0.001 PHE R 361 TRP 0.015 0.002 TRP B 99 HIS 0.004 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7635) covalent geometry : angle 0.57454 (10440) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.33079 ( 8) hydrogen bonds : bond 0.03317 ( 382) hydrogen bonds : angle 4.36525 ( 1095) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 165 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9004 (m-30) cc_final: 0.8606 (m-30) REVERT: A 210 THR cc_start: 0.7820 (m) cc_final: 0.7559 (p) REVERT: A 274 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8208 (ttmt) REVERT: A 311 TYR cc_start: 0.6527 (t80) cc_final: 0.6271 (t80) REVERT: A 381 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.7938 (t0) REVERT: A 390 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8418 (tt0) REVERT: B 7 LEU cc_start: 0.8208 (tp) cc_final: 0.7983 (tp) REVERT: B 8 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7148 (mtm-85) REVERT: B 55 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8439 (mt) REVERT: B 84 SER cc_start: 0.8639 (m) cc_final: 0.8322 (m) REVERT: G 9 ILE cc_start: 0.8610 (pt) cc_final: 0.8374 (mp) REVERT: N 69 THR cc_start: 0.8882 (t) cc_final: 0.8414 (p) REVERT: R 98 MET cc_start: 0.8344 (ttp) cc_final: 0.7955 (tmm) REVERT: R 156 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7805 (mtt90) REVERT: R 176 ARG cc_start: 0.7964 (mtm180) cc_final: 0.7605 (ttm-80) REVERT: R 240 MET cc_start: 0.7989 (mtm) cc_final: 0.7648 (ttm) REVERT: R 249 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6703 (mmt90) REVERT: R 379 ARG cc_start: 0.7148 (mtm-85) cc_final: 0.6564 (mtm-85) outliers start: 45 outliers final: 32 residues processed: 195 average time/residue: 0.0671 time to fit residues: 17.6724 Evaluate side-chains 193 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 130 PHE Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 136 SER Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 249 ARG Chi-restraints excluded: chain R residue 332 VAL Chi-restraints excluded: chain R residue 354 VAL Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.150887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123858 restraints weight = 9760.836| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.17 r_work: 0.3402 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7639 Z= 0.133 Angle : 0.568 8.083 10448 Z= 0.288 Chirality : 0.042 0.168 1235 Planarity : 0.004 0.036 1323 Dihedral : 6.868 84.858 1141 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.65 % Allowed : 25.85 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.27), residues: 1000 helix: 1.60 (0.26), residues: 400 sheet: 0.04 (0.36), residues: 205 loop : -1.14 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 318 TYR 0.029 0.001 TYR R 210 PHE 0.015 0.001 PHE R 242 TRP 0.017 0.001 TRP A 234 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7635) covalent geometry : angle 0.56796 (10440) SS BOND : bond 0.00084 ( 4) SS BOND : angle 0.29704 ( 8) hydrogen bonds : bond 0.03159 ( 382) hydrogen bonds : angle 4.29789 ( 1095) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.191 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9034 (m-30) cc_final: 0.8620 (m-30) REVERT: A 210 THR cc_start: 0.7771 (m) cc_final: 0.7529 (p) REVERT: A 274 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8308 (ttmt) REVERT: A 358 TYR cc_start: 0.8340 (m-80) cc_final: 0.7677 (m-80) REVERT: A 381 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7979 (t0) REVERT: A 390 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8378 (tt0) REVERT: B 7 LEU cc_start: 0.8313 (tp) cc_final: 0.8086 (tp) REVERT: B 8 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7207 (mtm-85) REVERT: B 55 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8450 (mt) REVERT: B 84 SER cc_start: 0.8636 (m) cc_final: 0.8337 (m) REVERT: G 9 ILE cc_start: 0.8667 (pt) cc_final: 0.8429 (mp) REVERT: N 52 SER cc_start: 0.8474 (OUTLIER) cc_final: 0.7824 (p) REVERT: N 69 THR cc_start: 0.8903 (t) cc_final: 0.8409 (p) REVERT: R 98 MET cc_start: 0.8285 (ttp) cc_final: 0.7979 (tmm) REVERT: R 156 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7764 (mtt90) REVERT: R 176 ARG cc_start: 0.7808 (mtm180) cc_final: 0.7442 (ttm110) REVERT: R 240 MET cc_start: 0.7927 (mtm) cc_final: 0.7620 (ttm) REVERT: R 249 ARG cc_start: 0.7036 (OUTLIER) cc_final: 0.6760 (mmt90) REVERT: R 379 ARG cc_start: 0.7044 (mtm-85) cc_final: 0.6544 (mtm-85) outliers start: 40 outliers final: 32 residues processed: 191 average time/residue: 0.0644 time to fit residues: 16.8198 Evaluate side-chains 198 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 130 PHE Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 136 SER Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 249 ARG Chi-restraints excluded: chain R residue 354 VAL Chi-restraints excluded: chain R residue 380 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 0.0870 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 59 optimal weight: 0.0770 chunk 93 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.125997 restraints weight = 9798.723| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.19 r_work: 0.3433 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7639 Z= 0.111 Angle : 0.563 8.765 10448 Z= 0.284 Chirality : 0.041 0.172 1235 Planarity : 0.003 0.036 1323 Dihedral : 6.573 85.708 1141 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 5.08 % Allowed : 26.98 % Favored : 67.94 % 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 are not related in a simple way. whole: 0.47 (0.27), residues: 1000 helix: 1.79 (0.26), residues: 401 sheet: 0.09 (0.36), residues: 205 loop : -1.12 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 318 TYR 0.032 0.001 TYR R 210 PHE 0.020 0.001 PHE R 361 TRP 0.016 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7635) covalent geometry : angle 0.56319 (10440) SS BOND : bond 0.00060 ( 4) SS BOND : angle 0.31877 ( 8) hydrogen bonds : bond 0.02997 ( 382) hydrogen bonds : angle 4.19248 ( 1095) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 169 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9033 (m-30) cc_final: 0.8617 (m-30) REVERT: A 210 THR cc_start: 0.7810 (m) cc_final: 0.7604 (p) REVERT: A 274 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8296 (ttmt) REVERT: A 358 TYR cc_start: 0.8296 (m-80) cc_final: 0.7677 (m-80) REVERT: A 381 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8012 (t0) REVERT: A 390 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8378 (tt0) REVERT: B 7 LEU cc_start: 0.8304 (tp) cc_final: 0.8084 (tp) REVERT: B 8 ARG cc_start: 0.7859 (mtm-85) cc_final: 0.7205 (mtm-85) REVERT: B 55 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8435 (mt) REVERT: G 9 ILE cc_start: 0.8667 (pt) cc_final: 0.8425 (mp) REVERT: R 98 MET cc_start: 0.8303 (ttp) cc_final: 0.8057 (tmm) REVERT: R 156 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7741 (mtt90) REVERT: R 176 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7423 (ttm110) REVERT: R 240 MET cc_start: 0.7924 (mtm) cc_final: 0.7605 (ttm) REVERT: R 249 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6644 (mmt90) REVERT: R 379 ARG cc_start: 0.7043 (mtm-85) cc_final: 0.6571 (mtm-85) outliers start: 36 outliers final: 26 residues processed: 189 average time/residue: 0.0652 time to fit residues: 16.7514 Evaluate side-chains 195 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 130 PHE Chi-restraints excluded: chain R residue 136 SER Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 176 ARG Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 249 ARG Chi-restraints excluded: chain R residue 354 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 11 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.153471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126339 restraints weight = 9699.623| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.19 r_work: 0.3439 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7639 Z= 0.110 Angle : 0.565 9.667 10448 Z= 0.285 Chirality : 0.041 0.154 1235 Planarity : 0.003 0.036 1323 Dihedral : 6.550 85.758 1141 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 5.08 % Allowed : 27.12 % Favored : 67.80 % 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 are not related in a simple way. whole: 0.57 (0.27), residues: 1000 helix: 1.87 (0.26), residues: 401 sheet: 0.15 (0.36), residues: 205 loop : -1.07 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 318 TYR 0.032 0.001 TYR R 210 PHE 0.014 0.001 PHE R 242 TRP 0.017 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7635) covalent geometry : angle 0.56555 (10440) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.33946 ( 8) hydrogen bonds : bond 0.02966 ( 382) hydrogen bonds : angle 4.14927 ( 1095) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9032 (m-30) cc_final: 0.8620 (m-30) REVERT: A 274 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8297 (ttmt) REVERT: A 358 TYR cc_start: 0.8296 (m-80) cc_final: 0.7704 (m-80) REVERT: A 381 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8016 (t0) REVERT: A 390 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8376 (tt0) REVERT: B 7 LEU cc_start: 0.8306 (tp) cc_final: 0.8087 (tp) REVERT: B 8 ARG cc_start: 0.7907 (mtm-85) cc_final: 0.7229 (mtm-85) REVERT: B 55 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8430 (mt) REVERT: G 9 ILE cc_start: 0.8672 (pt) cc_final: 0.8427 (mp) REVERT: R 98 MET cc_start: 0.8278 (ttp) cc_final: 0.8074 (tmm) REVERT: R 156 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7734 (mtt90) REVERT: R 176 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7384 (ttm110) REVERT: R 240 MET cc_start: 0.7910 (mtm) cc_final: 0.7556 (ttm) REVERT: R 249 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6626 (mmt90) REVERT: R 379 ARG cc_start: 0.7026 (mtm-85) cc_final: 0.6567 (mtm-85) outliers start: 36 outliers final: 29 residues processed: 180 average time/residue: 0.0700 time to fit residues: 17.2543 Evaluate side-chains 193 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 130 PHE Chi-restraints excluded: chain R residue 136 SER Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 176 ARG Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 249 ARG Chi-restraints excluded: chain R residue 354 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 77 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 57 optimal weight: 0.0010 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127807 restraints weight = 9730.815| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.19 r_work: 0.3451 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7639 Z= 0.109 Angle : 0.561 10.454 10448 Z= 0.283 Chirality : 0.041 0.149 1235 Planarity : 0.004 0.037 1323 Dihedral : 6.323 85.920 1141 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.94 % Allowed : 27.54 % Favored : 67.51 % 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 are not related in a simple way. whole: 0.65 (0.27), residues: 1000 helix: 1.93 (0.26), residues: 401 sheet: 0.21 (0.37), residues: 205 loop : -1.03 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 318 TYR 0.032 0.001 TYR R 210 PHE 0.022 0.001 PHE R 361 TRP 0.019 0.001 TRP A 234 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 7635) covalent geometry : angle 0.56135 (10440) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.34905 ( 8) hydrogen bonds : bond 0.02936 ( 382) hydrogen bonds : angle 4.11861 ( 1095) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2000 Ramachandran restraints generated. 1000 Oldfield, 0 Emsley, 1000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9032 (m-30) cc_final: 0.8624 (m-30) REVERT: A 210 THR cc_start: 0.8099 (p) cc_final: 0.7858 (t) REVERT: A 274 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8313 (ttmt) REVERT: A 358 TYR cc_start: 0.8272 (m-80) cc_final: 0.7542 (m-80) REVERT: A 360 TYR cc_start: 0.8883 (m-80) cc_final: 0.8571 (m-80) REVERT: A 381 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8071 (t0) REVERT: A 390 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8382 (tt0) REVERT: B 7 LEU cc_start: 0.8306 (tp) cc_final: 0.8092 (tp) REVERT: B 55 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8410 (mt) REVERT: G 9 ILE cc_start: 0.8672 (pt) cc_final: 0.8425 (mp) REVERT: R 156 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7750 (mtt90) REVERT: R 176 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.7442 (ttm110) REVERT: R 240 MET cc_start: 0.7900 (mtm) cc_final: 0.7495 (ttm) REVERT: R 249 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6606 (mmt90) REVERT: R 379 ARG cc_start: 0.6949 (mtm-85) cc_final: 0.6539 (mtm-85) outliers start: 35 outliers final: 29 residues processed: 179 average time/residue: 0.0695 time to fit residues: 16.8687 Evaluate side-chains 189 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 78 LEU Chi-restraints excluded: chain R residue 107 MET Chi-restraints excluded: chain R residue 130 PHE Chi-restraints excluded: chain R residue 136 SER Chi-restraints excluded: chain R residue 156 ARG Chi-restraints excluded: chain R residue 176 ARG Chi-restraints excluded: chain R residue 182 VAL Chi-restraints excluded: chain R residue 249 ARG Chi-restraints excluded: chain R residue 354 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.0670 chunk 45 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 0.0010 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.6526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.152703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125583 restraints weight = 9739.850| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.18 r_work: 0.3425 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7639 Z= 0.127 Angle : 0.573 11.080 10448 Z= 0.289 Chirality : 0.042 0.156 1235 Planarity : 0.004 0.039 1323 Dihedral : 6.320 85.497 1141 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.94 % Allowed : 27.68 % Favored : 67.37 % 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 are not related in a simple way. whole: 0.65 (0.27), residues: 1000 helix: 1.92 (0.26), residues: 401 sheet: 0.23 (0.37), residues: 205 loop : -1.02 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 318 TYR 0.033 0.001 TYR R 210 PHE 0.014 0.001 PHE R 242 TRP 0.018 0.001 TRP A 234 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7635) covalent geometry : angle 0.57350 (10440) SS BOND : bond 0.00111 ( 4) SS BOND : angle 0.37672 ( 8) hydrogen bonds : bond 0.03033 ( 382) hydrogen bonds : angle 4.13255 ( 1095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1687.35 seconds wall clock time: 29 minutes 31.74 seconds (1771.74 seconds total)