Starting phenix.real_space_refine on Wed Sep 17 08:13:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1h_63571/09_2025/9m1h_63571.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1h_63571/09_2025/9m1h_63571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m1h_63571/09_2025/9m1h_63571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1h_63571/09_2025/9m1h_63571.map" model { file = "/net/cci-nas-00/data/ceres_data/9m1h_63571/09_2025/9m1h_63571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1h_63571/09_2025/9m1h_63571.cif" } resolution = 2.55 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= 0.071 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 4459 2.51 5 N 1266 2.21 5 O 1283 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7055 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2123 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 272} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "C" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2591 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 1.76, per 1000 atoms: 0.25 Number of scatterers: 7055 At special positions: 0 Unit cell: (75.808, 102.176, 121.952, 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 1283 8.00 N 1266 7.00 C 4459 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.61 Conformation dependent library (CDL) restraints added in 387.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 48.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 36 through 65 removed outlier: 3.526A pdb=" N ILE A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 43 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 68 No H-bonds generated for 'chain 'A' and resid 66 through 68' Processing helix chain 'A' and resid 69 through 102 removed outlier: 4.452A pdb=" N PHE A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) Proline residue: A 91 - end of helix removed outlier: 3.663A pdb=" N LEU A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 141 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 141 through 149 Processing helix chain 'A' and resid 150 through 171 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 196 through 224 removed outlier: 3.673A pdb=" N GLN A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 239 removed outlier: 3.827A pdb=" N LEU A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 321 removed outlier: 4.720A pdb=" N GLU A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Proline residue: A 312 - end of helix Processing helix chain 'A' and resid 325 through 342 removed outlier: 3.522A pdb=" N LEU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Proline residue: A 332 - end of helix removed outlier: 4.026A pdb=" N TRP A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 Proline residue: A 348 - end of helix Processing helix chain 'A' and resid 356 through 366 removed outlier: 3.732A pdb=" N ARG A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 32 removed outlier: 3.532A pdb=" N GLN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 32 " --> pdb=" O GLN B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.578A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 229 through 245 removed outlier: 3.971A pdb=" N GLN B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU B 235 " --> pdb=" O ASN B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 274 through 279 removed outlier: 4.142A pdb=" N TYR B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 283 removed outlier: 3.522A pdb=" N ALA B 283 " --> pdb=" O PRO B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 283' Processing helix chain 'B' and resid 298 through 318 removed outlier: 3.507A pdb=" N ILE B 315 " --> pdb=" O GLU B 311 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 359 removed outlier: 3.690A pdb=" N LEU B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 30 removed outlier: 3.574A pdb=" N CYS C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 38 Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.716A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 181 Processing sheet with id=AA2, first strand: chain 'B' and resid 184 through 191 removed outlier: 3.739A pdb=" N LEU B 34 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL B 201 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N GLY B 40 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 220 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE B 221 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N PHE B 257 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE B 223 " --> pdb=" O PHE B 257 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN B 259 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 225 " --> pdb=" O ASN B 259 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'C' and resid 63 through 68 removed outlier: 6.874A pdb=" N ALA C 78 " --> pdb=" O TYR C 64 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET C 66 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL C 76 " --> pdb=" O MET C 66 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TRP C 68 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU C 74 " --> pdb=" O TRP C 68 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 84 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA C 97 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 86 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 110 removed outlier: 7.077A pdb=" N GLY C 120 " --> pdb=" O MET C 106 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N CYS C 108 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA C 118 " --> pdb=" O CYS C 108 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TYR C 110 " --> pdb=" O TYR C 116 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N TYR C 116 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASN C 130 " --> pdb=" O VAL C 140 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL C 140 " --> pdb=" O ASN C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.555A pdb=" N CYS C 153 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ASP C 175 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLN C 181 " --> pdb=" O ASP C 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 192 through 197 removed outlier: 7.168A pdb=" N GLY C 207 " --> pdb=" O MET C 193 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU C 195 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL C 205 " --> pdb=" O LEU C 195 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU C 197 " --> pdb=" O LEU C 203 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU C 203 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 225 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ASP C 217 " --> pdb=" O CYS C 223 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N CYS C 223 " --> pdb=" O ASP C 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 234 through 239 removed outlier: 3.595A pdb=" N ALA C 236 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR C 254 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N CYS C 255 " --> pdb=" O THR C 268 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR C 268 " --> pdb=" O CYS C 255 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU C 257 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 264 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 278 through 283 removed outlier: 6.593A pdb=" N GLY C 293 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL C 281 " --> pdb=" O LEU C 291 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 291 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N PHE C 283 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU C 289 " --> pdb=" O PHE C 283 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ASP C 303 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG C 309 " --> pdb=" O ASP C 303 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1110 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: 1.15 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1152 1.27 - 1.41: 1757 1.41 - 1.54: 4140 1.54 - 1.67: 65 1.67 - 1.81: 66 Bond restraints: 7180 Sorted by residual: bond pdb=" C PHE A 334 " pdb=" O PHE A 334 " ideal model delta sigma weight residual 1.236 1.137 0.099 1.22e-02 6.72e+03 6.64e+01 bond pdb=" C12 P2E A 501 " pdb=" C8 P2E A 501 " ideal model delta sigma weight residual 1.538 1.378 0.160 2.00e-02 2.50e+03 6.36e+01 bond pdb=" CA ALA G 44 " pdb=" C ALA G 44 " ideal model delta sigma weight residual 1.524 1.423 0.101 1.29e-02 6.01e+03 6.07e+01 bond pdb=" C10 P2E A 501 " pdb=" C9 P2E A 501 " ideal model delta sigma weight residual 1.512 1.358 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C ARG A 135 " pdb=" O ARG A 135 " ideal model delta sigma weight residual 1.236 1.136 0.099 1.31e-02 5.83e+03 5.76e+01 ... (remaining 7175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 9584 3.43 - 6.86: 117 6.86 - 10.29: 19 10.29 - 13.72: 3 13.72 - 17.15: 3 Bond angle restraints: 9726 Sorted by residual: angle pdb=" N PHE A 334 " pdb=" CA PHE A 334 " pdb=" C PHE A 334 " ideal model delta sigma weight residual 111.69 99.76 11.93 1.23e+00 6.61e-01 9.40e+01 angle pdb=" N THR B 251 " pdb=" CA THR B 251 " pdb=" C THR B 251 " ideal model delta sigma weight residual 113.89 100.00 13.89 1.58e+00 4.01e-01 7.73e+01 angle pdb=" N VAL A 137 " pdb=" CA VAL A 137 " pdb=" C VAL A 137 " ideal model delta sigma weight residual 111.00 103.27 7.73 1.09e+00 8.42e-01 5.03e+01 angle pdb=" C THR B 251 " pdb=" N ILE B 252 " pdb=" CA ILE B 252 " ideal model delta sigma weight residual 122.93 114.07 8.86 1.26e+00 6.30e-01 4.94e+01 angle pdb=" O ALA A 340 " pdb=" C ALA A 340 " pdb=" N SER A 341 " ideal model delta sigma weight residual 122.22 114.78 7.44 1.17e+00 7.31e-01 4.04e+01 ... (remaining 9721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.64: 4064 13.64 - 27.28: 174 27.28 - 40.92: 49 40.92 - 54.56: 25 54.56 - 68.20: 11 Dihedral angle restraints: 4323 sinusoidal: 1701 harmonic: 2622 Sorted by residual: dihedral pdb=" C LEU A 38 " pdb=" N LEU A 38 " pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " ideal model delta harmonic sigma weight residual -122.60 -135.90 13.30 0 2.50e+00 1.60e-01 2.83e+01 dihedral pdb=" N SER A 341 " pdb=" C SER A 341 " pdb=" CA SER A 341 " pdb=" CB SER A 341 " ideal model delta harmonic sigma weight residual 122.80 111.71 11.09 0 2.50e+00 1.60e-01 1.97e+01 dihedral pdb=" N THR B 251 " pdb=" C THR B 251 " pdb=" CA THR B 251 " pdb=" CB THR B 251 " ideal model delta harmonic sigma weight residual 123.40 112.85 10.55 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 4320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1075 0.120 - 0.240: 33 0.240 - 0.360: 8 0.360 - 0.480: 3 0.480 - 0.600: 4 Chirality restraints: 1123 Sorted by residual: chirality pdb=" CA ARG A 135 " pdb=" N ARG A 135 " pdb=" C ARG A 135 " pdb=" CB ARG A 135 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.99e+00 chirality pdb=" CA PRO G 48 " pdb=" N PRO G 48 " pdb=" C PRO G 48 " pdb=" CB PRO G 48 " both_signs ideal model delta sigma weight residual False 2.72 2.15 0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" CA LEU A 38 " pdb=" N LEU A 38 " pdb=" C LEU A 38 " pdb=" CB LEU A 38 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.57e+00 ... (remaining 1120 not shown) Planarity restraints: 1243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 332 " -0.026 2.00e-02 2.50e+03 4.94e-02 2.44e+01 pdb=" C PRO A 332 " 0.085 2.00e-02 2.50e+03 pdb=" O PRO A 332 " -0.030 2.00e-02 2.50e+03 pdb=" N LEU A 333 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 162 " 0.024 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C ALA A 162 " -0.084 2.00e-02 2.50e+03 pdb=" O ALA A 162 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA A 163 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 36 " 0.022 2.00e-02 2.50e+03 4.37e-02 1.91e+01 pdb=" C PRO A 36 " -0.076 2.00e-02 2.50e+03 pdb=" O PRO A 36 " 0.028 2.00e-02 2.50e+03 pdb=" N ALA A 37 " 0.026 2.00e-02 2.50e+03 ... (remaining 1240 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 268 2.71 - 3.26: 7487 3.26 - 3.80: 11209 3.80 - 4.35: 14853 4.35 - 4.90: 24775 Nonbonded interactions: 58592 Sorted by model distance: nonbonded pdb=" O ALA B 318 " pdb=" OG SER B 319 " model vdw 2.162 3.040 nonbonded pdb=" O ARG C 319 " pdb=" OG SER C 336 " model vdw 2.209 3.040 nonbonded pdb=" O ASP C 168 " pdb=" OG1 THR C 169 " model vdw 2.225 3.040 nonbonded pdb=" O LYS B 51 " pdb=" NH1 ARG B 54 " model vdw 2.267 3.120 nonbonded pdb=" OD1 ASP C 272 " pdb=" ND2 ASN C 273 " model vdw 2.279 3.120 ... (remaining 58587 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: 2.270 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.340 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 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 : 0.010 0.160 7180 Z= 0.706 Angle : 0.892 17.153 9726 Z= 0.545 Chirality : 0.065 0.600 1123 Planarity : 0.005 0.088 1243 Dihedral : 10.109 68.197 2625 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.62 % Allowed : 3.36 % Favored : 95.02 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.27), residues: 898 helix: -0.75 (0.25), residues: 398 sheet: -0.50 (0.39), residues: 163 loop : -1.63 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.011 0.001 TYR A 179 PHE 0.015 0.001 PHE A 41 TRP 0.009 0.001 TRP C 87 HIS 0.018 0.001 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00997 ( 7180) covalent geometry : angle 0.89184 ( 9726) hydrogen bonds : bond 0.15393 ( 384) hydrogen bonds : angle 6.89904 ( 1110) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 205 time to evaluate : 0.289 Fit side-chains REVERT: B 47 SER cc_start: 0.6835 (m) cc_final: 0.6358 (p) REVERT: B 250 ARG cc_start: 0.7821 (ptp-170) cc_final: 0.7500 (ptp-170) REVERT: B 323 ARG cc_start: 0.7174 (ptt90) cc_final: 0.6392 (ptt-90) REVERT: B 336 THR cc_start: 0.8261 (p) cc_final: 0.8032 (t) REVERT: C 43 ASP cc_start: 0.8025 (t0) cc_final: 0.7810 (p0) REVERT: C 125 ILE cc_start: 0.7404 (tt) cc_final: 0.7072 (mp) REVERT: C 191 ASP cc_start: 0.7071 (m-30) cc_final: 0.6739 (m-30) REVERT: C 264 GLN cc_start: 0.7611 (pt0) cc_final: 0.7296 (pt0) REVERT: G 37 MET cc_start: 0.6559 (mtp) cc_final: 0.6286 (mtp) outliers start: 12 outliers final: 4 residues processed: 214 average time/residue: 0.5944 time to fit residues: 133.5356 Evaluate side-chains 112 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 361 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 344 GLN B 43 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN C 181 GLN C 273 ASN C 345 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.179604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135638 restraints weight = 8369.518| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.35 r_work: 0.3607 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7180 Z= 0.181 Angle : 0.629 6.413 9726 Z= 0.327 Chirality : 0.045 0.169 1123 Planarity : 0.005 0.060 1243 Dihedral : 5.975 54.673 1030 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.17 % Allowed : 13.46 % Favored : 82.37 % 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 aren not related in a simple way. whole: 0.32 (0.28), residues: 898 helix: 1.15 (0.26), residues: 395 sheet: 0.14 (0.37), residues: 184 loop : -0.84 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 224 TYR 0.018 0.002 TYR B 30 PHE 0.017 0.002 PHE C 156 TRP 0.020 0.002 TRP A 310 HIS 0.009 0.003 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 7180) covalent geometry : angle 0.62894 ( 9726) hydrogen bonds : bond 0.04169 ( 384) hydrogen bonds : angle 4.37405 ( 1110) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.7544 (ttt) cc_final: 0.7211 (ttm) REVERT: A 153 ARG cc_start: 0.6266 (mtm180) cc_final: 0.5947 (mpp80) REVERT: A 313 MET cc_start: 0.8244 (tpt) cc_final: 0.7864 (tpt) REVERT: A 330 GLN cc_start: 0.7010 (mt0) cc_final: 0.6756 (mt0) REVERT: B 14 GLU cc_start: 0.6767 (tt0) cc_final: 0.6356 (pp20) REVERT: B 17 LYS cc_start: 0.6546 (mttm) cc_final: 0.5970 (ptpt) REVERT: B 24 GLN cc_start: 0.7116 (tp40) cc_final: 0.6733 (mp10) REVERT: B 250 ARG cc_start: 0.7854 (ptp-170) cc_final: 0.7286 (ptp-170) REVERT: B 323 ARG cc_start: 0.7516 (ptt90) cc_final: 0.6969 (ptt90) REVERT: C 43 ASP cc_start: 0.8359 (t0) cc_final: 0.7626 (p0) REVERT: C 53 ARG cc_start: 0.7884 (mmt180) cc_final: 0.5557 (ptt180) REVERT: C 73 ARG cc_start: 0.8108 (ttt90) cc_final: 0.7813 (ttt-90) REVERT: C 184 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8847 (m) REVERT: C 191 ASP cc_start: 0.8330 (m-30) cc_final: 0.7962 (m-30) REVERT: C 202 ARG cc_start: 0.7582 (mmt-90) cc_final: 0.6790 (mmm-85) REVERT: C 205 VAL cc_start: 0.9047 (p) cc_final: 0.8787 (m) REVERT: C 261 ARG cc_start: 0.6873 (OUTLIER) cc_final: 0.5970 (mtp180) REVERT: C 264 GLN cc_start: 0.8290 (pt0) cc_final: 0.7667 (pt0) REVERT: G 20 MET cc_start: 0.7543 (tpp) cc_final: 0.7339 (tpp) REVERT: G 37 MET cc_start: 0.7129 (mtp) cc_final: 0.6923 (mtp) outliers start: 31 outliers final: 11 residues processed: 153 average time/residue: 0.5343 time to fit residues: 86.4083 Evaluate side-chains 117 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 251 THR Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 261 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 0.0570 chunk 85 optimal weight: 8.9990 chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.178749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134887 restraints weight = 8259.453| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.32 r_work: 0.3604 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7180 Z= 0.121 Angle : 0.534 6.177 9726 Z= 0.277 Chirality : 0.041 0.151 1123 Planarity : 0.004 0.043 1243 Dihedral : 5.091 44.650 1028 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.63 % Allowed : 16.42 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.28), residues: 898 helix: 1.91 (0.26), residues: 392 sheet: 0.21 (0.37), residues: 185 loop : -0.63 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 139 TYR 0.012 0.001 TYR B 30 PHE 0.015 0.002 PHE B 189 TRP 0.010 0.001 TRP C 174 HIS 0.005 0.001 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7180) covalent geometry : angle 0.53368 ( 9726) hydrogen bonds : bond 0.03627 ( 384) hydrogen bonds : angle 4.04547 ( 1110) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.266 Fit side-chains REVERT: A 313 MET cc_start: 0.8172 (tpt) cc_final: 0.7789 (tpt) REVERT: A 330 GLN cc_start: 0.6932 (mt0) cc_final: 0.6678 (mt0) REVERT: B 14 GLU cc_start: 0.6882 (tt0) cc_final: 0.6494 (pp20) REVERT: B 17 LYS cc_start: 0.6570 (mttm) cc_final: 0.6052 (ptpt) REVERT: B 24 GLN cc_start: 0.7174 (tp40) cc_final: 0.6715 (mp-120) REVERT: B 188 LYS cc_start: 0.8379 (mttt) cc_final: 0.7986 (mmmt) REVERT: B 247 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7453 (ptm160) REVERT: B 250 ARG cc_start: 0.7818 (ptp-170) cc_final: 0.7109 (ptp-170) REVERT: B 281 GLU cc_start: 0.7350 (mp0) cc_final: 0.6189 (tp30) REVERT: B 309 ARG cc_start: 0.7312 (ttp80) cc_final: 0.6984 (ttm-80) REVERT: B 323 ARG cc_start: 0.7498 (ptt90) cc_final: 0.6894 (ptt90) REVERT: B 337 GLU cc_start: 0.7788 (pm20) cc_final: 0.7540 (pm20) REVERT: C 53 ARG cc_start: 0.8005 (mmt180) cc_final: 0.5744 (ptt180) REVERT: C 202 ARG cc_start: 0.7757 (mmt-90) cc_final: 0.7027 (mmm160) REVERT: C 205 VAL cc_start: 0.8993 (p) cc_final: 0.8755 (m) REVERT: C 259 ASP cc_start: 0.7673 (t70) cc_final: 0.7321 (t0) REVERT: C 261 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.5840 (mtp180) REVERT: C 263 ASP cc_start: 0.7372 (t70) cc_final: 0.6854 (t0) REVERT: C 264 GLN cc_start: 0.8268 (pt0) cc_final: 0.7658 (pt0) REVERT: G 20 MET cc_start: 0.7590 (tpp) cc_final: 0.7356 (tpt) REVERT: G 35 ASP cc_start: 0.6527 (OUTLIER) cc_final: 0.6322 (m-30) outliers start: 27 outliers final: 8 residues processed: 139 average time/residue: 0.5937 time to fit residues: 86.8452 Evaluate side-chains 122 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 111 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 261 ARG Chi-restraints excluded: chain G residue 35 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.0070 chunk 2 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS A 182 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.174216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.130813 restraints weight = 8264.140| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.33 r_work: 0.3582 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7180 Z= 0.130 Angle : 0.543 6.119 9726 Z= 0.283 Chirality : 0.041 0.163 1123 Planarity : 0.004 0.045 1243 Dihedral : 5.021 44.948 1025 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.17 % Allowed : 16.02 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.28), residues: 898 helix: 2.03 (0.26), residues: 396 sheet: 0.38 (0.37), residues: 183 loop : -0.71 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 139 TYR 0.014 0.001 TYR B 30 PHE 0.016 0.002 PHE B 189 TRP 0.013 0.001 TRP B 211 HIS 0.006 0.002 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7180) covalent geometry : angle 0.54332 ( 9726) hydrogen bonds : bond 0.03676 ( 384) hydrogen bonds : angle 4.07165 ( 1110) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.299 Fit side-chains REVERT: A 212 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8277 (mm) REVERT: A 313 MET cc_start: 0.8216 (tpt) cc_final: 0.7914 (tpt) REVERT: A 330 GLN cc_start: 0.6951 (mt0) cc_final: 0.6628 (mt0) REVERT: B 14 GLU cc_start: 0.7020 (tt0) cc_final: 0.6587 (pp20) REVERT: B 17 LYS cc_start: 0.6691 (mttm) cc_final: 0.6196 (ptpt) REVERT: B 22 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7838 (tp-100) REVERT: B 24 GLN cc_start: 0.7250 (tp40) cc_final: 0.6833 (mp-120) REVERT: B 247 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7556 (ptm160) REVERT: B 250 ARG cc_start: 0.7860 (ptp-170) cc_final: 0.7579 (ptp-170) REVERT: B 281 GLU cc_start: 0.7497 (mp0) cc_final: 0.6384 (tp30) REVERT: B 309 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7070 (ttm-80) REVERT: B 337 GLU cc_start: 0.7823 (pm20) cc_final: 0.7549 (pm20) REVERT: C 53 ARG cc_start: 0.8061 (mmt180) cc_final: 0.5767 (ptt180) REVERT: C 180 GLN cc_start: 0.8117 (mm110) cc_final: 0.7703 (mp10) REVERT: C 202 ARG cc_start: 0.7816 (mmt-90) cc_final: 0.7152 (mmm160) REVERT: C 205 VAL cc_start: 0.8982 (p) cc_final: 0.8780 (m) REVERT: C 252 ASP cc_start: 0.6173 (t0) cc_final: 0.5903 (t0) REVERT: C 259 ASP cc_start: 0.7814 (t70) cc_final: 0.7376 (t0) REVERT: C 264 GLN cc_start: 0.8192 (pt0) cc_final: 0.7563 (pt0) REVERT: G 20 MET cc_start: 0.7610 (tpp) cc_final: 0.7353 (tpt) REVERT: G 35 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6595 (m-30) outliers start: 31 outliers final: 12 residues processed: 124 average time/residue: 0.6033 time to fit residues: 78.5113 Evaluate side-chains 115 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 35 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS B 28 GLN ** B 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.171610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.127394 restraints weight = 8340.407| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.33 r_work: 0.3523 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7180 Z= 0.182 Angle : 0.593 7.625 9726 Z= 0.311 Chirality : 0.043 0.168 1123 Planarity : 0.004 0.046 1243 Dihedral : 5.370 46.564 1024 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.44 % Allowed : 16.02 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.28), residues: 898 helix: 1.77 (0.25), residues: 406 sheet: 0.31 (0.36), residues: 185 loop : -0.63 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 139 TYR 0.013 0.002 TYR B 30 PHE 0.017 0.002 PHE B 189 TRP 0.010 0.001 TRP B 211 HIS 0.007 0.002 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7180) covalent geometry : angle 0.59333 ( 9726) hydrogen bonds : bond 0.04277 ( 384) hydrogen bonds : angle 4.27955 ( 1110) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 108 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 153 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.6053 (mpp80) REVERT: A 212 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8299 (mm) REVERT: A 313 MET cc_start: 0.8270 (tpt) cc_final: 0.7744 (tpt) REVERT: A 330 GLN cc_start: 0.6941 (mt0) cc_final: 0.6642 (mt0) REVERT: B 14 GLU cc_start: 0.7222 (tt0) cc_final: 0.6849 (tm-30) REVERT: B 17 LYS cc_start: 0.6892 (mttm) cc_final: 0.6377 (ptpt) REVERT: B 24 GLN cc_start: 0.7196 (tp40) cc_final: 0.6765 (mp-120) REVERT: B 188 LYS cc_start: 0.8523 (mttt) cc_final: 0.8051 (mmmt) REVERT: B 193 LYS cc_start: 0.8101 (mtpm) cc_final: 0.7767 (mtmm) REVERT: B 200 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7533 (p0) REVERT: B 247 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7594 (ptm160) REVERT: B 250 ARG cc_start: 0.7946 (ptp-170) cc_final: 0.7646 (ptp-170) REVERT: B 281 GLU cc_start: 0.7623 (mp0) cc_final: 0.6564 (tp30) REVERT: B 309 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7274 (ttt180) REVERT: B 323 ARG cc_start: 0.7711 (ptt90) cc_final: 0.7482 (ptt90) REVERT: B 337 GLU cc_start: 0.7921 (pm20) cc_final: 0.7639 (pm20) REVERT: C 43 ASP cc_start: 0.8311 (t0) cc_final: 0.7570 (p0) REVERT: C 201 THR cc_start: 0.7276 (m) cc_final: 0.6762 (p) REVERT: C 202 ARG cc_start: 0.8189 (mmt-90) cc_final: 0.7417 (mmm160) REVERT: C 252 ASP cc_start: 0.6307 (t0) cc_final: 0.6063 (t0) REVERT: C 264 GLN cc_start: 0.8312 (pt0) cc_final: 0.7748 (pt0) REVERT: G 20 MET cc_start: 0.7658 (tpp) cc_final: 0.7422 (tpt) REVERT: G 35 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6933 (m-30) outliers start: 33 outliers final: 18 residues processed: 127 average time/residue: 0.5750 time to fit residues: 76.9651 Evaluate side-chains 121 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 35 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 79 optimal weight: 0.0870 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.175796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.132336 restraints weight = 8410.997| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.30 r_work: 0.3585 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7180 Z= 0.117 Angle : 0.527 6.095 9726 Z= 0.275 Chirality : 0.041 0.153 1123 Planarity : 0.004 0.047 1243 Dihedral : 5.050 45.444 1024 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.63 % Allowed : 18.30 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.28), residues: 898 helix: 2.04 (0.26), residues: 402 sheet: 0.39 (0.36), residues: 185 loop : -0.61 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 139 TYR 0.012 0.001 TYR B 30 PHE 0.015 0.001 PHE B 189 TRP 0.013 0.001 TRP C 174 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7180) covalent geometry : angle 0.52668 ( 9726) hydrogen bonds : bond 0.03645 ( 384) hydrogen bonds : angle 4.06940 ( 1110) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.328 Fit side-chains REVERT: A 212 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8317 (mm) REVERT: A 313 MET cc_start: 0.8271 (tpt) cc_final: 0.7915 (tpt) REVERT: A 330 GLN cc_start: 0.6838 (mt0) cc_final: 0.6573 (mt0) REVERT: B 14 GLU cc_start: 0.7070 (tt0) cc_final: 0.6724 (tm-30) REVERT: B 17 LYS cc_start: 0.6824 (mttm) cc_final: 0.6308 (ptpt) REVERT: B 22 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7744 (tp-100) REVERT: B 24 GLN cc_start: 0.7092 (tp40) cc_final: 0.6640 (mp-120) REVERT: B 188 LYS cc_start: 0.8543 (mttt) cc_final: 0.8094 (mmmt) REVERT: B 193 LYS cc_start: 0.8070 (mtpm) cc_final: 0.7767 (mtmm) REVERT: B 247 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7555 (ptm160) REVERT: B 250 ARG cc_start: 0.7862 (ptp-170) cc_final: 0.7570 (ptp-170) REVERT: B 281 GLU cc_start: 0.7563 (mp0) cc_final: 0.6631 (tp30) REVERT: B 309 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7129 (ttt180) REVERT: B 323 ARG cc_start: 0.7668 (ptt90) cc_final: 0.7458 (ptt90) REVERT: B 337 GLU cc_start: 0.7867 (pm20) cc_final: 0.7662 (pm20) REVERT: C 43 ASP cc_start: 0.8266 (t0) cc_final: 0.7537 (p0) REVERT: C 201 THR cc_start: 0.7214 (m) cc_final: 0.6838 (p) REVERT: C 202 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7343 (mmm160) REVERT: C 252 ASP cc_start: 0.6139 (t0) cc_final: 0.5931 (t0) REVERT: C 264 GLN cc_start: 0.8277 (pt0) cc_final: 0.7694 (pt0) REVERT: G 20 MET cc_start: 0.7570 (tpp) cc_final: 0.7323 (tpt) REVERT: G 35 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6899 (m-30) REVERT: G 58 ASN cc_start: 0.4003 (t0) cc_final: 0.3789 (t0) outliers start: 27 outliers final: 12 residues processed: 116 average time/residue: 0.5733 time to fit residues: 70.3102 Evaluate side-chains 110 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain G residue 35 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 0.0670 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.172419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.127895 restraints weight = 8203.923| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.33 r_work: 0.3536 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7180 Z= 0.152 Angle : 0.557 7.317 9726 Z= 0.290 Chirality : 0.042 0.172 1123 Planarity : 0.004 0.047 1243 Dihedral : 5.238 47.107 1024 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.23 % Allowed : 18.57 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.28), residues: 898 helix: 2.08 (0.25), residues: 402 sheet: 0.34 (0.36), residues: 185 loop : -0.58 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 139 TYR 0.013 0.001 TYR B 30 PHE 0.021 0.002 PHE A 41 TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7180) covalent geometry : angle 0.55677 ( 9726) hydrogen bonds : bond 0.04001 ( 384) hydrogen bonds : angle 4.18076 ( 1110) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8260 (mm) REVERT: A 313 MET cc_start: 0.8287 (tpt) cc_final: 0.7826 (tpt) REVERT: A 330 GLN cc_start: 0.6847 (mt0) cc_final: 0.6566 (mt0) REVERT: B 13 VAL cc_start: 0.7256 (p) cc_final: 0.7014 (t) REVERT: B 15 ARG cc_start: 0.7050 (OUTLIER) cc_final: 0.6696 (ttt180) REVERT: B 22 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7702 (tp-100) REVERT: B 24 GLN cc_start: 0.7006 (tp40) cc_final: 0.6550 (mp-120) REVERT: B 228 SER cc_start: 0.8093 (t) cc_final: 0.7677 (p) REVERT: B 247 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7492 (ptm160) REVERT: B 281 GLU cc_start: 0.7532 (mp0) cc_final: 0.6682 (tp30) REVERT: B 309 ARG cc_start: 0.7533 (ttp80) cc_final: 0.7176 (ttt180) REVERT: C 43 ASP cc_start: 0.8268 (t0) cc_final: 0.7538 (p0) REVERT: C 201 THR cc_start: 0.7531 (m) cc_final: 0.7222 (p) REVERT: C 202 ARG cc_start: 0.8193 (mmt-90) cc_final: 0.7360 (mmm160) REVERT: C 224 ARG cc_start: 0.8192 (mmm160) cc_final: 0.7949 (mmm160) REVERT: C 252 ASP cc_start: 0.6221 (t0) cc_final: 0.6015 (t0) REVERT: C 264 GLN cc_start: 0.8271 (pt0) cc_final: 0.7706 (pt0) REVERT: G 20 MET cc_start: 0.7618 (tpp) cc_final: 0.7381 (tpt) REVERT: G 35 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7132 (m-30) outliers start: 24 outliers final: 13 residues processed: 115 average time/residue: 0.5707 time to fit residues: 69.3266 Evaluate side-chains 111 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 46 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.172536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128469 restraints weight = 8305.654| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.32 r_work: 0.3541 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7180 Z= 0.148 Angle : 0.550 6.422 9726 Z= 0.287 Chirality : 0.041 0.172 1123 Planarity : 0.004 0.046 1243 Dihedral : 5.229 48.182 1024 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.96 % Allowed : 19.52 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.28), residues: 898 helix: 2.19 (0.26), residues: 402 sheet: 0.33 (0.37), residues: 180 loop : -0.65 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 139 TYR 0.013 0.001 TYR B 30 PHE 0.015 0.002 PHE B 189 TRP 0.010 0.001 TRP B 211 HIS 0.005 0.002 HIS B 324 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7180) covalent geometry : angle 0.55032 ( 9726) hydrogen bonds : bond 0.03921 ( 384) hydrogen bonds : angle 4.12556 ( 1110) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5992 (mmt90) cc_final: 0.4641 (ptt90) REVERT: A 212 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8283 (mm) REVERT: A 313 MET cc_start: 0.8288 (tpt) cc_final: 0.7836 (tpt) REVERT: A 330 GLN cc_start: 0.6932 (mt0) cc_final: 0.6652 (mt0) REVERT: B 15 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6695 (ttt180) REVERT: B 22 GLN cc_start: 0.7944 (mm-40) cc_final: 0.7697 (tp-100) REVERT: B 24 GLN cc_start: 0.7013 (tp40) cc_final: 0.6562 (mp-120) REVERT: B 47 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7979 (p) REVERT: B 228 SER cc_start: 0.8192 (t) cc_final: 0.7869 (p) REVERT: B 247 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7546 (ptm160) REVERT: B 281 GLU cc_start: 0.7553 (mp0) cc_final: 0.6795 (tp30) REVERT: B 309 ARG cc_start: 0.7591 (ttp80) cc_final: 0.7211 (ttt180) REVERT: C 43 ASP cc_start: 0.8258 (t0) cc_final: 0.7501 (p0) REVERT: C 201 THR cc_start: 0.7656 (m) cc_final: 0.7365 (p) REVERT: C 202 ARG cc_start: 0.8116 (mmt-90) cc_final: 0.7416 (mmm160) REVERT: C 264 GLN cc_start: 0.8284 (pt0) cc_final: 0.7763 (pt0) REVERT: G 20 MET cc_start: 0.7654 (tpp) cc_final: 0.7422 (tpt) REVERT: G 35 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7198 (m-30) outliers start: 22 outliers final: 13 residues processed: 111 average time/residue: 0.6401 time to fit residues: 74.6568 Evaluate side-chains 111 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 46 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.172977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130145 restraints weight = 8284.988| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.29 r_work: 0.3587 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7180 Z= 0.120 Angle : 0.542 7.031 9726 Z= 0.282 Chirality : 0.041 0.168 1123 Planarity : 0.004 0.046 1243 Dihedral : 5.054 48.108 1024 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.96 % Allowed : 20.32 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.29), residues: 898 helix: 2.35 (0.26), residues: 402 sheet: 0.37 (0.37), residues: 185 loop : -0.59 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 139 TYR 0.012 0.001 TYR B 30 PHE 0.014 0.001 PHE B 189 TRP 0.013 0.001 TRP C 174 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 7180) covalent geometry : angle 0.54218 ( 9726) hydrogen bonds : bond 0.03601 ( 384) hydrogen bonds : angle 4.00989 ( 1110) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.274 Fit side-chains REVERT: A 148 ARG cc_start: 0.5957 (mmt90) cc_final: 0.4614 (ptt90) REVERT: A 212 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 313 MET cc_start: 0.8265 (tpt) cc_final: 0.7857 (tpt) REVERT: A 330 GLN cc_start: 0.6889 (mt0) cc_final: 0.6619 (mt0) REVERT: B 15 ARG cc_start: 0.7192 (OUTLIER) cc_final: 0.6701 (ttt180) REVERT: B 17 LYS cc_start: 0.6908 (mttm) cc_final: 0.6354 (ptpt) REVERT: B 22 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7791 (tp-100) REVERT: B 24 GLN cc_start: 0.7126 (tp40) cc_final: 0.6656 (mp-120) REVERT: B 47 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.8010 (p) REVERT: B 188 LYS cc_start: 0.8632 (mttt) cc_final: 0.8110 (mtpt) REVERT: B 228 SER cc_start: 0.8195 (t) cc_final: 0.7988 (p) REVERT: B 247 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7480 (ptm160) REVERT: B 281 GLU cc_start: 0.7570 (mp0) cc_final: 0.6779 (tp30) REVERT: B 309 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7217 (ttt180) REVERT: C 43 ASP cc_start: 0.8232 (t0) cc_final: 0.7470 (p0) REVERT: C 201 THR cc_start: 0.7605 (m) cc_final: 0.7274 (p) REVERT: C 202 ARG cc_start: 0.8079 (mmt-90) cc_final: 0.7463 (mmm160) REVERT: C 264 GLN cc_start: 0.8253 (pt0) cc_final: 0.7611 (pt0) REVERT: G 20 MET cc_start: 0.7614 (tpp) cc_final: 0.7365 (tpt) REVERT: G 35 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7155 (m-30) outliers start: 22 outliers final: 11 residues processed: 111 average time/residue: 0.6327 time to fit residues: 73.8080 Evaluate side-chains 113 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain G residue 35 ASP Chi-restraints excluded: chain G residue 46 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 13 optimal weight: 0.0040 chunk 88 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.0770 chunk 66 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.5952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.173335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130375 restraints weight = 8254.231| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.29 r_work: 0.3589 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7180 Z= 0.122 Angle : 0.536 6.541 9726 Z= 0.281 Chirality : 0.040 0.169 1123 Planarity : 0.004 0.046 1243 Dihedral : 4.998 47.271 1024 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.29 % Allowed : 21.40 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.29), residues: 898 helix: 2.31 (0.26), residues: 407 sheet: 0.37 (0.37), residues: 180 loop : -0.65 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 139 TYR 0.012 0.001 TYR B 30 PHE 0.014 0.002 PHE B 189 TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 7180) covalent geometry : angle 0.53630 ( 9726) hydrogen bonds : bond 0.03602 ( 384) hydrogen bonds : angle 3.99384 ( 1110) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1796 Ramachandran restraints generated. 898 Oldfield, 0 Emsley, 898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.238 Fit side-chains REVERT: A 148 ARG cc_start: 0.6025 (mmt90) cc_final: 0.4681 (ptt90) REVERT: A 212 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8366 (mm) REVERT: A 313 MET cc_start: 0.8303 (tpt) cc_final: 0.7894 (tpt) REVERT: A 330 GLN cc_start: 0.7024 (mt0) cc_final: 0.6727 (mt0) REVERT: B 15 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6799 (ttt180) REVERT: B 17 LYS cc_start: 0.7040 (mttm) cc_final: 0.6484 (ptpt) REVERT: B 22 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7900 (tp-100) REVERT: B 24 GLN cc_start: 0.7232 (tp40) cc_final: 0.6795 (mp-120) REVERT: B 47 SER cc_start: 0.8329 (OUTLIER) cc_final: 0.8049 (p) REVERT: B 188 LYS cc_start: 0.8640 (mttt) cc_final: 0.8160 (mtpt) REVERT: B 247 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7532 (ptm160) REVERT: B 281 GLU cc_start: 0.7518 (mp0) cc_final: 0.6879 (tp30) REVERT: B 309 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7312 (ttt180) REVERT: B 323 ARG cc_start: 0.7724 (ptt90) cc_final: 0.7386 (ptt90) REVERT: C 201 THR cc_start: 0.7665 (m) cc_final: 0.7353 (p) REVERT: C 202 ARG cc_start: 0.8150 (mmt-90) cc_final: 0.7527 (mmm160) REVERT: C 264 GLN cc_start: 0.8301 (pt0) cc_final: 0.7689 (pt0) REVERT: G 20 MET cc_start: 0.7609 (tpp) cc_final: 0.7349 (tpt) REVERT: G 35 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7166 (m-30) outliers start: 17 outliers final: 10 residues processed: 105 average time/residue: 0.6652 time to fit residues: 73.2440 Evaluate side-chains 107 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 203 LEU Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain G residue 35 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 48 optimal weight: 0.0980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.174540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130792 restraints weight = 8310.173| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.29 r_work: 0.3591 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7180 Z= 0.132 Angle : 0.548 6.411 9726 Z= 0.285 Chirality : 0.041 0.171 1123 Planarity : 0.004 0.046 1243 Dihedral : 5.053 47.102 1024 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.29 % Allowed : 21.40 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.29), residues: 898 helix: 2.26 (0.26), residues: 408 sheet: 0.36 (0.37), residues: 180 loop : -0.67 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 139 TYR 0.013 0.001 TYR B 30 PHE 0.033 0.002 PHE A 41 TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS B 197 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7180) covalent geometry : angle 0.54779 ( 9726) hydrogen bonds : bond 0.03712 ( 384) hydrogen bonds : angle 4.02981 ( 1110) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3529.20 seconds wall clock time: 60 minutes 45.79 seconds (3645.79 seconds total)