Starting phenix.real_space_refine on Fri Jun 6 02:10:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m1h_63571/06_2025/9m1h_63571.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m1h_63571/06_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_63571/06_2025/9m1h_63571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m1h_63571/06_2025/9m1h_63571.map" model { file = "/net/cci-nas-00/data/ceres_data/9m1h_63571/06_2025/9m1h_63571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m1h_63571/06_2025/9m1h_63571.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.03, per 1000 atoms: 0.71 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: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.86 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: 2.07 Time building geometry restraints manager: 2.44 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: 2.030 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.410 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 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:15.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.040 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (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 TRP 0.009 0.001 TRP C 87 HIS 0.018 0.001 HIS A 145 PHE 0.015 0.001 PHE A 41 TYR 0.011 0.001 TYR A 179 ARG 0.003 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.15393 ( 384) hydrogen bonds : angle 6.89904 ( 1110) covalent geometry : bond 0.00997 ( 7180) covalent geometry : angle 0.89184 ( 9726) *********************** 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 : 0.717 Fit side-chains REVERT: B 47 SER cc_start: 0.6835 (m) cc_final: 0.6357 (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: 0.8031 (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: 0.7071 (mp) REVERT: C 191 ASP cc_start: 0.7071 (m-30) cc_final: 0.6740 (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: 1.1726 time to fit residues: 263.8846 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 : 0.780 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.8980 chunk 67 optimal weight: 0.0770 chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 69 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.184479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.142512 restraints weight = 8259.666| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.32 r_work: 0.3689 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7180 Z= 0.135 Angle : 0.573 6.337 9726 Z= 0.295 Chirality : 0.043 0.157 1123 Planarity : 0.005 0.056 1243 Dihedral : 5.541 52.852 1030 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.50 % Allowed : 14.00 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.28), residues: 898 helix: 1.39 (0.26), residues: 389 sheet: 0.02 (0.37), residues: 181 loop : -0.92 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 310 HIS 0.006 0.002 HIS A 88 PHE 0.014 0.002 PHE B 189 TYR 0.017 0.001 TYR B 30 ARG 0.005 0.001 ARG A 178 Details of bonding type rmsd hydrogen bonds : bond 0.03652 ( 384) hydrogen bonds : angle 4.15395 ( 1110) covalent geometry : bond 0.00292 ( 7180) covalent geometry : angle 0.57273 ( 9726) *********************** 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 167 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.7527 (ttt) cc_final: 0.7190 (ttm) REVERT: A 153 ARG cc_start: 0.6164 (mtm180) cc_final: 0.5867 (mpp80) REVERT: A 313 MET cc_start: 0.8155 (tpt) cc_final: 0.7670 (tpt) REVERT: A 330 GLN cc_start: 0.6907 (mt0) cc_final: 0.6674 (mt0) REVERT: B 17 LYS cc_start: 0.6116 (mttm) cc_final: 0.5589 (ptpt) REVERT: B 24 GLN cc_start: 0.7011 (tp40) cc_final: 0.6650 (mp10) REVERT: B 250 ARG cc_start: 0.7784 (ptp-170) cc_final: 0.7165 (ptp-170) REVERT: B 266 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: B 323 ARG cc_start: 0.7485 (ptt90) cc_final: 0.6985 (ptt90) REVERT: C 132 LYS cc_start: 0.7991 (mptt) cc_final: 0.7631 (mmtp) REVERT: C 139 ARG cc_start: 0.6006 (ttp-110) cc_final: 0.5568 (ppt170) REVERT: C 191 ASP cc_start: 0.8115 (m-30) cc_final: 0.7796 (m-30) REVERT: C 202 ARG cc_start: 0.7029 (mmt-90) cc_final: 0.6394 (mmm-85) REVERT: C 264 GLN cc_start: 0.8138 (pt0) cc_final: 0.7541 (pt0) REVERT: G 37 MET cc_start: 0.6818 (mtp) cc_final: 0.6578 (mtp) outliers start: 26 outliers final: 7 residues processed: 161 average time/residue: 1.1689 time to fit residues: 198.2866 Evaluate side-chains 116 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 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 266 GLU Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.176276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131925 restraints weight = 8268.694| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.33 r_work: 0.3576 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7180 Z= 0.158 Angle : 0.589 7.433 9726 Z= 0.308 Chirality : 0.043 0.150 1123 Planarity : 0.004 0.052 1243 Dihedral : 5.318 55.697 1027 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.11 % Allowed : 14.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.28), residues: 898 helix: 1.73 (0.26), residues: 395 sheet: 0.24 (0.37), residues: 182 loop : -0.67 (0.36), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 104 HIS 0.007 0.002 HIS B 324 PHE 0.017 0.002 PHE C 156 TYR 0.014 0.001 TYR B 30 ARG 0.005 0.001 ARG C 224 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 384) hydrogen bonds : angle 4.25911 ( 1110) covalent geometry : bond 0.00360 ( 7180) covalent geometry : angle 0.58898 ( 9726) *********************** 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 154 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.813 Fit side-chains REVERT: A 212 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8249 (mm) REVERT: A 313 MET cc_start: 0.8194 (tpt) cc_final: 0.7821 (tpt) REVERT: A 330 GLN cc_start: 0.6848 (mt0) cc_final: 0.6578 (mt0) REVERT: B 14 GLU cc_start: 0.6926 (tt0) cc_final: 0.6524 (pp20) REVERT: B 17 LYS cc_start: 0.6497 (mttm) cc_final: 0.6009 (ptpt) REVERT: B 24 GLN cc_start: 0.7119 (tp40) cc_final: 0.6664 (mp-120) REVERT: B 247 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7525 (ptm160) REVERT: B 250 ARG cc_start: 0.7813 (ptp-170) cc_final: 0.7210 (ptp-170) REVERT: B 323 ARG cc_start: 0.7475 (ptt90) cc_final: 0.6901 (ptt90) REVERT: C 43 ASP cc_start: 0.8343 (t0) cc_final: 0.7565 (p0) REVERT: C 53 ARG cc_start: 0.7938 (mmt180) cc_final: 0.5615 (ptt180) REVERT: C 132 LYS cc_start: 0.8078 (mptt) cc_final: 0.7804 (mmtp) REVERT: C 202 ARG cc_start: 0.7863 (mmt-90) cc_final: 0.7036 (mmm-85) REVERT: C 264 GLN cc_start: 0.8319 (pt0) cc_final: 0.7736 (pt0) REVERT: G 20 MET cc_start: 0.7588 (tpp) cc_final: 0.7351 (tpt) REVERT: G 35 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6352 (m-30) outliers start: 38 outliers final: 15 residues processed: 136 average time/residue: 1.2298 time to fit residues: 176.0598 Evaluate side-chains 124 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 106 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 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 47 SER Chi-restraints excluded: chain B residue 187 THR 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 316 SER Chi-restraints excluded: chain B residue 361 VAL 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 G residue 35 ASP Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 46 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 41 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 28 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 HIS B 213 GLN C 273 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.175311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130840 restraints weight = 8382.010| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.35 r_work: 0.3571 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4424 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= 0.145 Angle : 0.569 6.411 9726 Z= 0.299 Chirality : 0.042 0.163 1123 Planarity : 0.004 0.056 1243 Dihedral : 5.183 53.429 1025 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.44 % Allowed : 15.88 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.28), residues: 898 helix: 1.85 (0.26), residues: 398 sheet: 0.17 (0.37), residues: 184 loop : -0.74 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 174 HIS 0.006 0.002 HIS B 324 PHE 0.015 0.002 PHE B 189 TYR 0.013 0.001 TYR B 30 ARG 0.009 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 384) hydrogen bonds : angle 4.18450 ( 1110) covalent geometry : bond 0.00331 ( 7180) covalent geometry : angle 0.56899 ( 9726) *********************** 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 134 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.738 Fit side-chains REVERT: A 153 ARG cc_start: 0.6328 (OUTLIER) cc_final: 0.5998 (mpp80) REVERT: A 212 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8296 (mm) REVERT: A 313 MET cc_start: 0.8181 (tpt) cc_final: 0.7888 (tpt) REVERT: A 330 GLN cc_start: 0.6957 (mt0) cc_final: 0.6637 (mt0) REVERT: B 14 GLU cc_start: 0.7096 (tt0) cc_final: 0.6610 (pp20) REVERT: B 17 LYS cc_start: 0.6745 (mttm) cc_final: 0.6243 (ptpt) REVERT: B 22 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7785 (tp-100) REVERT: B 24 GLN cc_start: 0.7109 (tp40) cc_final: 0.6689 (mp-120) REVERT: B 188 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7682 (mmmt) REVERT: B 200 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7480 (p0) REVERT: B 247 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7582 (ptm160) REVERT: B 250 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.7558 (ptp-170) REVERT: B 281 GLU cc_start: 0.7514 (mp0) cc_final: 0.6386 (tp30) REVERT: C 43 ASP cc_start: 0.8303 (t0) cc_final: 0.7566 (p0) REVERT: C 53 ARG cc_start: 0.8070 (mmt180) cc_final: 0.5783 (ptt180) REVERT: C 132 LYS cc_start: 0.8225 (mptt) cc_final: 0.7904 (mmtp) REVERT: C 202 ARG cc_start: 0.7949 (mmt-90) cc_final: 0.7236 (mmm160) REVERT: C 264 GLN cc_start: 0.8198 (pt0) cc_final: 0.7619 (pt0) REVERT: G 20 MET cc_start: 0.7618 (tpp) cc_final: 0.7362 (tpt) REVERT: G 35 ASP cc_start: 0.6781 (OUTLIER) cc_final: 0.6514 (m-30) outliers start: 33 outliers final: 13 residues processed: 119 average time/residue: 1.2214 time to fit residues: 152.9333 Evaluate side-chains 118 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 197 HIS 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 247 ARG Chi-restraints excluded: chain B residue 310 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 203 LEU 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 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 HIS B 324 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.171571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.128068 restraints weight = 8233.622| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.32 r_work: 0.3553 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7180 Z= 0.176 Angle : 0.594 6.896 9726 Z= 0.313 Chirality : 0.043 0.171 1123 Planarity : 0.004 0.053 1243 Dihedral : 5.284 47.467 1024 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 5.25 % Allowed : 15.48 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.28), residues: 898 helix: 1.79 (0.25), residues: 400 sheet: 0.05 (0.36), residues: 186 loop : -0.69 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 211 HIS 0.006 0.002 HIS B 324 PHE 0.017 0.002 PHE B 189 TYR 0.013 0.001 TYR B 30 ARG 0.009 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 384) hydrogen bonds : angle 4.27018 ( 1110) covalent geometry : bond 0.00410 ( 7180) covalent geometry : angle 0.59406 ( 9726) *********************** 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 143 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.739 Fit side-chains REVERT: A 212 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8260 (mm) REVERT: A 313 MET cc_start: 0.8234 (tpt) cc_final: 0.7921 (tpt) REVERT: A 330 GLN cc_start: 0.6929 (mt0) cc_final: 0.6642 (mt0) REVERT: A 345 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7488 (mt) REVERT: B 14 GLU cc_start: 0.7242 (tt0) cc_final: 0.6844 (tm-30) REVERT: B 17 LYS cc_start: 0.6838 (mttm) cc_final: 0.6317 (ptpt) REVERT: B 22 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7818 (tp-100) REVERT: B 24 GLN cc_start: 0.7214 (tp40) cc_final: 0.6783 (mp-120) REVERT: B 188 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7609 (mmmt) REVERT: B 193 LYS cc_start: 0.8134 (mtpm) cc_final: 0.7805 (mtmm) REVERT: B 200 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7541 (p0) REVERT: B 247 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7641 (ptm160) REVERT: B 250 ARG cc_start: 0.7991 (ptp-170) cc_final: 0.7685 (ptp-170) REVERT: B 266 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: B 281 GLU cc_start: 0.7543 (mp0) cc_final: 0.6670 (tm-30) REVERT: C 43 ASP cc_start: 0.8338 (t0) cc_final: 0.7601 (p0) REVERT: C 132 LYS cc_start: 0.8238 (mptt) cc_final: 0.8018 (mmtp) REVERT: C 202 ARG cc_start: 0.8145 (mmt-90) cc_final: 0.7391 (mmm160) REVERT: C 252 ASP cc_start: 0.6172 (t0) cc_final: 0.5927 (t0) REVERT: C 264 GLN cc_start: 0.8311 (pt0) cc_final: 0.7686 (pt0) REVERT: G 20 MET cc_start: 0.7576 (tpp) cc_final: 0.7348 (tpt) REVERT: G 35 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6711 (m-30) outliers start: 39 outliers final: 19 residues processed: 128 average time/residue: 1.1334 time to fit residues: 153.3012 Evaluate side-chains 123 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 345 ILE 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 188 LYS Chi-restraints excluded: chain B residue 197 HIS 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 266 GLU 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 140 VAL 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 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 83 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.0270 chunk 73 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 31 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN B 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.177572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.134250 restraints weight = 8322.647| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.28 r_work: 0.3611 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7180 Z= 0.110 Angle : 0.527 6.141 9726 Z= 0.278 Chirality : 0.040 0.159 1123 Planarity : 0.004 0.051 1243 Dihedral : 4.946 44.977 1024 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.63 % Allowed : 17.77 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.28), residues: 898 helix: 2.13 (0.26), residues: 400 sheet: 0.19 (0.37), residues: 175 loop : -0.69 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 174 HIS 0.007 0.001 HIS B 197 PHE 0.016 0.001 PHE B 189 TYR 0.012 0.001 TYR B 30 ARG 0.012 0.000 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 384) hydrogen bonds : angle 4.03990 ( 1110) covalent geometry : bond 0.00231 ( 7180) covalent geometry : angle 0.52652 ( 9726) *********************** 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 134 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8341 (mm) REVERT: A 313 MET cc_start: 0.8255 (tpt) cc_final: 0.7904 (tpt) REVERT: A 330 GLN cc_start: 0.6841 (mt0) cc_final: 0.6580 (mt0) REVERT: A 345 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7445 (mt) REVERT: B 14 GLU cc_start: 0.7121 (tt0) cc_final: 0.6740 (tm-30) REVERT: B 17 LYS cc_start: 0.6838 (mttm) cc_final: 0.6334 (ptpt) REVERT: B 22 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7813 (tp-100) REVERT: B 24 GLN cc_start: 0.7053 (tp40) cc_final: 0.6598 (mp-120) REVERT: B 193 LYS cc_start: 0.8157 (mtpm) cc_final: 0.7841 (mtmm) REVERT: B 247 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7532 (ptm160) REVERT: B 250 ARG cc_start: 0.7864 (ptp-170) cc_final: 0.7498 (ptp-170) REVERT: B 281 GLU cc_start: 0.7545 (mp0) cc_final: 0.6542 (tp30) REVERT: B 323 ARG cc_start: 0.7626 (ptt90) cc_final: 0.7375 (ptt90) REVERT: C 43 ASP cc_start: 0.8287 (t0) cc_final: 0.7559 (p0) REVERT: C 132 LYS cc_start: 0.8265 (mptt) cc_final: 0.7982 (mmtp) REVERT: C 202 ARG cc_start: 0.8220 (mmt-90) cc_final: 0.7460 (mmm160) REVERT: C 252 ASP cc_start: 0.6055 (t0) cc_final: 0.5820 (t0) REVERT: C 264 GLN cc_start: 0.8284 (pt0) cc_final: 0.7653 (pt0) REVERT: G 20 MET cc_start: 0.7529 (tpp) cc_final: 0.7297 (tpt) REVERT: G 35 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6590 (m-30) outliers start: 27 outliers final: 12 residues processed: 123 average time/residue: 1.1415 time to fit residues: 148.3829 Evaluate side-chains 122 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 188 LYS 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 140 VAL 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 G residue 30 SER 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 50 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.175515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.131632 restraints weight = 8273.112| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.30 r_work: 0.3577 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4852 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= 0.137 Angle : 0.544 7.130 9726 Z= 0.286 Chirality : 0.041 0.166 1123 Planarity : 0.004 0.050 1243 Dihedral : 5.088 45.622 1024 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.04 % Allowed : 18.03 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.28), residues: 898 helix: 2.05 (0.25), residues: 406 sheet: 0.17 (0.36), residues: 180 loop : -0.76 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 174 HIS 0.006 0.001 HIS B 197 PHE 0.023 0.002 PHE A 41 TYR 0.013 0.001 TYR B 30 ARG 0.007 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 384) hydrogen bonds : angle 4.09896 ( 1110) covalent geometry : bond 0.00312 ( 7180) covalent geometry : angle 0.54447 ( 9726) *********************** 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 131 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8318 (mm) REVERT: A 313 MET cc_start: 0.8262 (tpt) cc_final: 0.7841 (tpt) REVERT: A 330 GLN cc_start: 0.6854 (mt0) cc_final: 0.6579 (mt0) REVERT: A 345 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7418 (mt) REVERT: B 14 GLU cc_start: 0.7048 (tt0) cc_final: 0.6690 (tm-30) REVERT: B 15 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6763 (ttt180) REVERT: B 17 LYS cc_start: 0.6884 (mttm) cc_final: 0.6356 (ptpt) REVERT: B 24 GLN cc_start: 0.7069 (tp40) cc_final: 0.6616 (mp-120) REVERT: B 193 LYS cc_start: 0.8114 (mtpm) cc_final: 0.7804 (mtmm) REVERT: B 250 ARG cc_start: 0.7903 (ptp-170) cc_final: 0.7616 (ptp-170) REVERT: B 281 GLU cc_start: 0.7571 (mp0) cc_final: 0.6637 (tp30) REVERT: C 43 ASP cc_start: 0.8275 (t0) cc_final: 0.7542 (p0) REVERT: C 132 LYS cc_start: 0.8284 (mptt) cc_final: 0.8080 (mmtp) REVERT: C 224 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7983 (mmm160) REVERT: C 252 ASP cc_start: 0.6205 (t0) cc_final: 0.5983 (t0) REVERT: C 264 GLN cc_start: 0.8289 (pt0) cc_final: 0.7681 (pt0) REVERT: G 20 MET cc_start: 0.7590 (tpp) cc_final: 0.7365 (tpt) REVERT: G 35 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6831 (m-30) REVERT: G 58 ASN cc_start: 0.3984 (t0) cc_final: 0.3768 (t0) outliers start: 30 outliers final: 13 residues processed: 120 average time/residue: 1.2031 time to fit residues: 152.4215 Evaluate side-chains 114 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 345 ILE 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 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 140 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain G residue 35 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 70 optimal weight: 0.1980 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 195 ASN ** 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 = 0.4128 r_free = 0.4128 target = 0.176067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.132395 restraints weight = 8297.893| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.28 r_work: 0.3608 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4909 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= 0.126 Angle : 0.533 6.085 9726 Z= 0.281 Chirality : 0.041 0.166 1123 Planarity : 0.004 0.050 1243 Dihedral : 5.015 45.549 1024 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.23 % Allowed : 18.98 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 898 helix: 2.17 (0.26), residues: 407 sheet: 0.16 (0.36), residues: 180 loop : -0.75 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 174 HIS 0.007 0.001 HIS B 197 PHE 0.016 0.001 PHE B 189 TYR 0.013 0.001 TYR B 30 ARG 0.009 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 384) hydrogen bonds : angle 4.02673 ( 1110) covalent geometry : bond 0.00284 ( 7180) covalent geometry : angle 0.53321 ( 9726) *********************** 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 127 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 153 ARG cc_start: 0.6453 (OUTLIER) cc_final: 0.6229 (ttm170) REVERT: A 212 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 313 MET cc_start: 0.8295 (tpt) cc_final: 0.7873 (tpt) REVERT: A 330 GLN cc_start: 0.6882 (mt0) cc_final: 0.6595 (mt0) REVERT: A 345 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7481 (mt) REVERT: B 14 GLU cc_start: 0.7176 (tt0) cc_final: 0.6847 (tm-30) REVERT: B 15 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6783 (ttt180) REVERT: B 17 LYS cc_start: 0.6949 (mttm) cc_final: 0.6387 (ptpt) REVERT: B 22 GLN cc_start: 0.8033 (mm-40) cc_final: 0.7805 (tp-100) REVERT: B 24 GLN cc_start: 0.7067 (tp40) cc_final: 0.6609 (mp-120) REVERT: B 188 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7566 (mmtt) REVERT: B 228 SER cc_start: 0.8033 (t) cc_final: 0.7660 (p) REVERT: B 281 GLU cc_start: 0.7630 (mp0) cc_final: 0.6693 (tp30) REVERT: B 323 ARG cc_start: 0.7782 (ptt90) cc_final: 0.7517 (ptt90) REVERT: C 43 ASP cc_start: 0.8262 (t0) cc_final: 0.7509 (p0) REVERT: C 264 GLN cc_start: 0.8311 (pt0) cc_final: 0.7724 (pt0) REVERT: G 20 MET cc_start: 0.7571 (tpp) cc_final: 0.7337 (tpt) REVERT: G 35 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6845 (m-30) outliers start: 24 outliers final: 10 residues processed: 121 average time/residue: 1.2449 time to fit residues: 158.3578 Evaluate side-chains 111 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 15 ARG 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 310 LYS Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain G residue 35 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 0.0970 chunk 88 optimal weight: 0.3980 chunk 75 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 76 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.176773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132919 restraints weight = 8413.942| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.30 r_work: 0.3614 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7180 Z= 0.119 Angle : 0.548 7.639 9726 Z= 0.291 Chirality : 0.040 0.160 1123 Planarity : 0.004 0.056 1243 Dihedral : 4.974 45.822 1024 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.69 % Allowed : 20.05 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.29), residues: 898 helix: 2.33 (0.26), residues: 407 sheet: 0.18 (0.37), residues: 180 loop : -0.72 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 174 HIS 0.007 0.001 HIS B 197 PHE 0.031 0.002 PHE A 41 TYR 0.012 0.001 TYR B 30 ARG 0.013 0.000 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 384) hydrogen bonds : angle 3.97257 ( 1110) covalent geometry : bond 0.00264 ( 7180) covalent geometry : angle 0.54801 ( 9726) *********************** 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 119 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5893 (mmt90) cc_final: 0.4600 (ptm160) REVERT: A 153 ARG cc_start: 0.6445 (OUTLIER) cc_final: 0.6147 (mpp80) REVERT: A 212 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8376 (mm) REVERT: A 313 MET cc_start: 0.8298 (tpt) cc_final: 0.7943 (tpt) REVERT: A 330 GLN cc_start: 0.6871 (mt0) cc_final: 0.6555 (mt0) REVERT: B 13 VAL cc_start: 0.7367 (p) cc_final: 0.7063 (t) REVERT: B 15 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6703 (ttt180) REVERT: B 17 LYS cc_start: 0.7003 (mttm) cc_final: 0.6423 (ptpt) REVERT: B 22 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7844 (tp-100) REVERT: B 24 GLN cc_start: 0.7101 (tp40) cc_final: 0.6678 (mp-120) REVERT: B 228 SER cc_start: 0.8093 (t) cc_final: 0.7751 (p) REVERT: B 281 GLU cc_start: 0.7618 (mp0) cc_final: 0.6753 (tp30) REVERT: C 202 ARG cc_start: 0.8295 (mmt-90) cc_final: 0.7635 (mmm160) REVERT: C 264 GLN cc_start: 0.8306 (pt0) cc_final: 0.7725 (pt0) REVERT: C 271 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7087 (t-170) REVERT: G 20 MET cc_start: 0.7569 (tpp) cc_final: 0.7329 (tpt) REVERT: G 35 ASP cc_start: 0.7163 (OUTLIER) cc_final: 0.6751 (m-30) outliers start: 20 outliers final: 12 residues processed: 113 average time/residue: 1.2456 time to fit residues: 148.0439 Evaluate side-chains 113 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 LEU 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 310 LYS Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 271 HIS Chi-restraints excluded: chain C residue 341 LEU 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 81 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 33 optimal weight: 0.0670 chunk 76 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN ** B 195 ASN ** 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 = 0.4116 r_free = 0.4116 target = 0.173510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130437 restraints weight = 8329.256| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.31 r_work: 0.3607 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7180 Z= 0.131 Angle : 0.561 7.132 9726 Z= 0.298 Chirality : 0.041 0.159 1123 Planarity : 0.004 0.054 1243 Dihedral : 5.070 47.589 1024 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.69 % Allowed : 20.05 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.29), residues: 898 helix: 2.33 (0.26), residues: 407 sheet: 0.16 (0.37), residues: 180 loop : -0.74 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 174 HIS 0.007 0.001 HIS B 197 PHE 0.016 0.001 PHE B 189 TYR 0.014 0.001 TYR B 30 ARG 0.009 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 384) hydrogen bonds : angle 4.02693 ( 1110) covalent geometry : bond 0.00295 ( 7180) covalent geometry : angle 0.56069 ( 9726) ********************** 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 114 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.803 Fit side-chains revert: symmetry clash REVERT: A 148 ARG cc_start: 0.5951 (mmt90) cc_final: 0.4664 (ptt90) REVERT: A 153 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.6231 (mpp80) REVERT: A 212 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8365 (mm) REVERT: A 313 MET cc_start: 0.8303 (tpt) cc_final: 0.7891 (tpt) REVERT: A 330 GLN cc_start: 0.6942 (mt0) cc_final: 0.6616 (mt0) REVERT: A 345 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7420 (mt) REVERT: B 13 VAL cc_start: 0.7365 (p) cc_final: 0.7081 (t) REVERT: B 14 GLU cc_start: 0.7339 (tt0) cc_final: 0.6893 (tm-30) REVERT: B 15 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6771 (ttt180) REVERT: B 17 LYS cc_start: 0.6967 (mttm) cc_final: 0.6414 (ptpt) REVERT: B 24 GLN cc_start: 0.7125 (tp40) cc_final: 0.6661 (mp-120) REVERT: B 228 SER cc_start: 0.8162 (t) cc_final: 0.7912 (p) REVERT: B 281 GLU cc_start: 0.7599 (mp0) cc_final: 0.6852 (tp30) REVERT: B 323 ARG cc_start: 0.7532 (ptt90) cc_final: 0.7310 (ptt90) REVERT: C 202 ARG cc_start: 0.8291 (mmt-90) cc_final: 0.7637 (mmm160) REVERT: C 264 GLN cc_start: 0.8340 (pt0) cc_final: 0.7734 (pt0) REVERT: G 20 MET cc_start: 0.7629 (tpp) cc_final: 0.7381 (tpt) REVERT: G 35 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6839 (m-30) outliers start: 20 outliers final: 13 residues processed: 107 average time/residue: 1.2680 time to fit residues: 143.0730 Evaluate side-chains 112 residues out of total 747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ARG Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 28 GLN 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 310 LYS Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 341 LEU 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 55 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN ** B 195 ASN ** 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 = 0.4109 r_free = 0.4109 target = 0.174433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.130584 restraints weight = 8308.152| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.28 r_work: 0.3589 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7180 Z= 0.149 Angle : 0.574 6.814 9726 Z= 0.304 Chirality : 0.041 0.162 1123 Planarity : 0.004 0.054 1243 Dihedral : 5.180 48.855 1024 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.23 % Allowed : 19.38 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.28), residues: 898 helix: 2.26 (0.26), residues: 407 sheet: 0.12 (0.37), residues: 181 loop : -0.73 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 174 HIS 0.007 0.001 HIS B 197 PHE 0.016 0.002 PHE B 189 TYR 0.017 0.001 TYR B 30 ARG 0.009 0.000 ARG C 139 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 384) hydrogen bonds : angle 4.09094 ( 1110) covalent geometry : bond 0.00344 ( 7180) covalent geometry : angle 0.57378 ( 9726) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7669.79 seconds wall clock time: 132 minutes 11.81 seconds (7931.81 seconds total)