Starting phenix.real_space_refine on Mon May 12 17:03:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g94_29861/05_2025/8g94_29861.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g94_29861/05_2025/8g94_29861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g94_29861/05_2025/8g94_29861.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g94_29861/05_2025/8g94_29861.map" model { file = "/net/cci-nas-00/data/ceres_data/8g94_29861/05_2025/8g94_29861.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g94_29861/05_2025/8g94_29861.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 65 5.16 5 C 5891 2.51 5 N 1565 2.21 5 O 1701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9222 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2316 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 6, 'TRANS': 281} Chain breaks: 2 Chain: "B" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1780 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 2 Chain: "C" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "F" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 179 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "G" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 134 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 26} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 47 Time building chain proxies: 5.88, per 1000 atoms: 0.64 Number of scatterers: 9222 At special positions: 0 Unit cell: (89.64, 118.69, 126.99, 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 65 16.00 O 1701 8.00 N 1565 7.00 C 5891 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 38.2% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 removed outlier: 4.280A pdb=" N ILE A 25 " --> pdb=" O ASN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 73 removed outlier: 3.749A pdb=" N ILE A 70 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 104 Processing helix chain 'A' and resid 106 through 112 removed outlier: 3.881A pdb=" N TYR A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 111 " --> pdb=" O THR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 148 Processing helix chain 'A' and resid 156 through 177 removed outlier: 3.561A pdb=" N LEU A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 235 removed outlier: 3.784A pdb=" N LEU A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 281 removed outlier: 3.577A pdb=" N LEU A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 292 through 314 removed outlier: 3.855A pdb=" N PHE A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Proline residue: A 308 - end of helix Processing helix chain 'A' and resid 315 through 322 removed outlier: 3.608A pdb=" N ALA A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.728A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.599A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.675A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.572A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 Processing helix chain 'B' and resid 295 through 310 Processing helix chain 'B' and resid 329 through 351 removed outlier: 4.405A pdb=" N GLN B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.606A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 24 removed outlier: 3.622A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.285A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'F' and resid 41 through 64 Processing helix chain 'G' and resid 41 through 64 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 191 removed outlier: 3.564A pdb=" N LEU B 194 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU B 37 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 224 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 61 removed outlier: 6.774A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.771A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.588A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.820A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 4.494A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.636A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.375A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.536A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1338 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: 2.58 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2929 1.34 - 1.46: 1647 1.46 - 1.57: 4729 1.57 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 9398 Sorted by residual: bond pdb=" CG LEU C 70 " pdb=" CD2 LEU C 70 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.44e+00 bond pdb=" CB ASP C 163 " pdb=" CG ASP C 163 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.02e+00 bond pdb=" CG1 ILE C 81 " pdb=" CD1 ILE C 81 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" C PHE A 76 " pdb=" O PHE A 76 " ideal model delta sigma weight residual 1.236 1.220 0.016 1.24e-02 6.50e+03 1.66e+00 bond pdb=" CG PHE C 234 " pdb=" CD1 PHE C 234 " ideal model delta sigma weight residual 1.384 1.358 0.026 2.10e-02 2.27e+03 1.56e+00 ... (remaining 9393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 12336 1.75 - 3.49: 328 3.49 - 5.24: 37 5.24 - 6.98: 13 6.98 - 8.73: 8 Bond angle restraints: 12722 Sorted by residual: angle pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta sigma weight residual 121.54 130.11 -8.57 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C LYS A 75 " pdb=" N PHE A 76 " pdb=" CA PHE A 76 " ideal model delta sigma weight residual 120.38 126.88 -6.50 1.46e+00 4.69e-01 1.98e+01 angle pdb=" N PHE A 76 " pdb=" CA PHE A 76 " pdb=" C PHE A 76 " ideal model delta sigma weight residual 111.75 117.17 -5.42 1.28e+00 6.10e-01 1.80e+01 angle pdb=" N SER C 334 " pdb=" CA SER C 334 " pdb=" C SER C 334 " ideal model delta sigma weight residual 112.24 117.43 -5.19 1.28e+00 6.10e-01 1.64e+01 angle pdb=" C TYR A 81 " pdb=" N TYR A 82 " pdb=" CA TYR A 82 " ideal model delta sigma weight residual 121.54 128.27 -6.73 1.91e+00 2.74e-01 1.24e+01 ... (remaining 12717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5120 17.91 - 35.81: 391 35.81 - 53.72: 60 53.72 - 71.62: 12 71.62 - 89.53: 3 Dihedral angle restraints: 5586 sinusoidal: 2140 harmonic: 3446 Sorted by residual: dihedral pdb=" CA ARG C 304 " pdb=" C ARG C 304 " pdb=" N ALA C 305 " pdb=" CA ALA C 305 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA TRP C 339 " pdb=" C TRP C 339 " pdb=" N ASN C 340 " pdb=" CA ASN C 340 " ideal model delta harmonic sigma weight residual 180.00 158.35 21.65 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA PHE C 234 " pdb=" C PHE C 234 " pdb=" N PHE C 235 " pdb=" CA PHE C 235 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 5583 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1251 0.063 - 0.127: 212 0.127 - 0.190: 15 0.190 - 0.254: 2 0.254 - 0.317: 1 Chirality restraints: 1481 Sorted by residual: chirality pdb=" CA SER C 334 " pdb=" N SER C 334 " pdb=" C SER C 334 " pdb=" CB SER C 334 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CG LEU B 353 " pdb=" CB LEU B 353 " pdb=" CD1 LEU B 353 " pdb=" CD2 LEU B 353 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PHE A 76 " pdb=" N PHE A 76 " pdb=" C PHE A 76 " pdb=" CB PHE A 76 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 1478 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 234 " 0.022 2.00e-02 2.50e+03 1.93e-02 6.52e+00 pdb=" CG PHE C 234 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE C 234 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 234 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE C 234 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 234 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 234 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 64 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" C VAL E 64 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL E 64 " 0.014 2.00e-02 2.50e+03 pdb=" N LYS E 65 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 113 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.55e+00 pdb=" N PRO A 114 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.030 5.00e-02 4.00e+02 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1159 2.74 - 3.28: 8986 3.28 - 3.82: 15340 3.82 - 4.36: 18501 4.36 - 4.90: 32119 Nonbonded interactions: 76105 Sorted by model distance: nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.206 3.040 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.207 3.040 nonbonded pdb=" O LEU A 174 " pdb=" OH TYR A 202 " model vdw 2.247 3.040 nonbonded pdb=" O ARG C 68 " pdb=" OG SER C 84 " model vdw 2.281 3.040 nonbonded pdb=" O VAL F 48 " pdb=" OG1 THR F 52 " model vdw 2.282 3.040 ... (remaining 76100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.600 Find NCS groups from input model: 0.110 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 : 0.006 0.061 9399 Z= 0.264 Angle : 0.718 8.730 12724 Z= 0.396 Chirality : 0.047 0.317 1481 Planarity : 0.005 0.053 1586 Dihedral : 13.016 89.531 3355 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.32 (0.22), residues: 1163 helix: -0.70 (0.22), residues: 423 sheet: -1.92 (0.28), residues: 286 loop : -1.90 (0.26), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 339 HIS 0.003 0.001 HIS B 188 PHE 0.044 0.002 PHE C 234 TYR 0.014 0.002 TYR E 178 ARG 0.007 0.001 ARG E 190 Details of bonding type rmsd hydrogen bonds : bond 0.15093 ( 469) hydrogen bonds : angle 6.08223 ( 1338) SS BOND : bond 0.00192 ( 1) SS BOND : angle 0.69842 ( 2) covalent geometry : bond 0.00607 ( 9398) covalent geometry : angle 0.71850 (12722) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8482 (mttm) cc_final: 0.7811 (ptmm) REVERT: A 182 TRP cc_start: 0.7474 (t-100) cc_final: 0.6963 (t60) REVERT: B 9 ASP cc_start: 0.8477 (m-30) cc_final: 0.8163 (m-30) REVERT: C 9 GLN cc_start: 0.8310 (pp30) cc_final: 0.7995 (pp30) REVERT: C 10 GLU cc_start: 0.8620 (tt0) cc_final: 0.8053 (tt0) REVERT: C 67 SER cc_start: 0.9180 (m) cc_final: 0.8948 (t) REVERT: C 214 ARG cc_start: 0.8202 (mpp80) cc_final: 0.7971 (mtt180) REVERT: C 262 MET cc_start: 0.8177 (ttm) cc_final: 0.7762 (ttm) REVERT: D 11 GLN cc_start: 0.8874 (mm110) cc_final: 0.8663 (tp40) REVERT: D 14 LYS cc_start: 0.9178 (tppp) cc_final: 0.8821 (ttpt) REVERT: D 20 LYS cc_start: 0.9104 (mttm) cc_final: 0.8700 (mttm) REVERT: E 87 ARG cc_start: 0.8272 (mpp80) cc_final: 0.7778 (mtt90) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2769 time to fit residues: 59.6028 Evaluate side-chains 132 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 0.0370 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 GLN A 152 HIS A 303 ASN A 315 ASN B 255 ASN B 306 GLN B 331 ASN B 333 GLN C 16 ASN C 91 HIS C 156 GLN C 259 GLN D 59 ASN E 39 GLN F 47 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.070470 restraints weight = 16230.254| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.65 r_work: 0.2750 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9399 Z= 0.127 Angle : 0.558 8.276 12724 Z= 0.292 Chirality : 0.040 0.158 1481 Planarity : 0.004 0.051 1586 Dihedral : 4.413 20.315 1278 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.40 % Allowed : 8.60 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.01 (0.24), residues: 1163 helix: 0.81 (0.24), residues: 426 sheet: -1.38 (0.30), residues: 259 loop : -1.55 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP C 339 HIS 0.003 0.001 HIS C 91 PHE 0.021 0.001 PHE A 58 TYR 0.014 0.001 TYR E 215 ARG 0.005 0.000 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 469) hydrogen bonds : angle 4.70409 ( 1338) SS BOND : bond 0.00108 ( 1) SS BOND : angle 0.74764 ( 2) covalent geometry : bond 0.00274 ( 9398) covalent geometry : angle 0.55757 (12722) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 LYS cc_start: 0.8363 (mttm) cc_final: 0.7590 (tttp) REVERT: A 182 TRP cc_start: 0.7504 (t-100) cc_final: 0.6593 (t60) REVERT: A 277 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7433 (mm) REVERT: B 353 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8731 (mm) REVERT: C 9 GLN cc_start: 0.8262 (pp30) cc_final: 0.8009 (pp30) REVERT: C 10 GLU cc_start: 0.8710 (tt0) cc_final: 0.8206 (tt0) REVERT: C 37 ILE cc_start: 0.9489 (mt) cc_final: 0.9131 (tt) REVERT: C 214 ARG cc_start: 0.8806 (mpp80) cc_final: 0.8505 (mmt-90) REVERT: C 217 MET cc_start: 0.9038 (ptp) cc_final: 0.8601 (ppp) REVERT: C 262 MET cc_start: 0.9007 (ttm) cc_final: 0.8641 (ttm) REVERT: D 14 LYS cc_start: 0.9164 (tppp) cc_final: 0.8893 (ttpt) REVERT: D 18 GLN cc_start: 0.8728 (tp40) cc_final: 0.8226 (tp-100) REVERT: D 20 LYS cc_start: 0.9067 (mttm) cc_final: 0.8781 (mttm) REVERT: D 22 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8021 (mt-10) REVERT: E 87 ARG cc_start: 0.8103 (mpp80) cc_final: 0.7400 (mtt90) REVERT: E 171 GLN cc_start: 0.9045 (mm-40) cc_final: 0.8686 (mt0) outliers start: 24 outliers final: 9 residues processed: 154 average time/residue: 0.2564 time to fit residues: 53.7299 Evaluate side-chains 142 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 72 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 331 ASN D 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.107468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.068137 restraints weight = 16465.966| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.66 r_work: 0.2702 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9399 Z= 0.215 Angle : 0.566 7.113 12724 Z= 0.297 Chirality : 0.042 0.168 1481 Planarity : 0.004 0.049 1586 Dihedral : 4.392 22.130 1278 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.40 % Allowed : 11.30 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.50 (0.24), residues: 1163 helix: 1.34 (0.25), residues: 422 sheet: -1.17 (0.31), residues: 273 loop : -1.31 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 339 HIS 0.002 0.001 HIS A 201 PHE 0.024 0.001 PHE A 58 TYR 0.014 0.001 TYR C 59 ARG 0.004 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 469) hydrogen bonds : angle 4.50768 ( 1338) SS BOND : bond 0.00064 ( 1) SS BOND : angle 0.71395 ( 2) covalent geometry : bond 0.00495 ( 9398) covalent geometry : angle 0.56608 (12722) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8347 (mt0) cc_final: 0.8069 (mt0) REVERT: A 124 MET cc_start: 0.8959 (mmm) cc_final: 0.8687 (tpt) REVERT: A 148 LYS cc_start: 0.8346 (mttm) cc_final: 0.7530 (tttp) REVERT: A 182 TRP cc_start: 0.7558 (t-100) cc_final: 0.6638 (t60) REVERT: B 353 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8765 (mm) REVERT: C 9 GLN cc_start: 0.8294 (pp30) cc_final: 0.8005 (pp30) REVERT: C 10 GLU cc_start: 0.8741 (tt0) cc_final: 0.8233 (tt0) REVERT: C 37 ILE cc_start: 0.9496 (mt) cc_final: 0.9166 (tt) REVERT: C 214 ARG cc_start: 0.8831 (mpp80) cc_final: 0.8547 (mmt-90) REVERT: C 217 MET cc_start: 0.9056 (ptp) cc_final: 0.8652 (ppp) REVERT: C 262 MET cc_start: 0.9003 (ttm) cc_final: 0.8598 (ttm) REVERT: D 14 LYS cc_start: 0.9167 (tppp) cc_final: 0.8912 (ttpt) REVERT: D 18 GLN cc_start: 0.8770 (tp40) cc_final: 0.8345 (tp40) REVERT: D 20 LYS cc_start: 0.9095 (mttm) cc_final: 0.8811 (mttm) REVERT: D 22 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8125 (mt-10) REVERT: D 58 GLU cc_start: 0.8594 (pm20) cc_final: 0.8229 (pm20) outliers start: 24 outliers final: 12 residues processed: 147 average time/residue: 0.2234 time to fit residues: 44.7325 Evaluate side-chains 142 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 39 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 59 optimal weight: 0.0050 chunk 83 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 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 = 0.3578 r_free = 0.3578 target = 0.109578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.070625 restraints weight = 16325.541| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.64 r_work: 0.2753 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9399 Z= 0.112 Angle : 0.503 6.697 12724 Z= 0.265 Chirality : 0.040 0.171 1481 Planarity : 0.003 0.048 1586 Dihedral : 4.129 18.022 1278 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.30 % Allowed : 12.20 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.16 (0.25), residues: 1163 helix: 1.62 (0.25), residues: 423 sheet: -0.98 (0.32), residues: 268 loop : -1.13 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 PHE 0.025 0.001 PHE A 58 TYR 0.013 0.001 TYR C 59 ARG 0.006 0.000 ARG C 8 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 469) hydrogen bonds : angle 4.30722 ( 1338) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.22232 ( 2) covalent geometry : bond 0.00243 ( 9398) covalent geometry : angle 0.50280 (12722) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8298 (mt0) cc_final: 0.8029 (mt0) REVERT: A 148 LYS cc_start: 0.8343 (mttm) cc_final: 0.7570 (tttp) REVERT: A 180 MET cc_start: 0.8155 (mtm) cc_final: 0.7171 (ppp) REVERT: A 182 TRP cc_start: 0.7420 (t-100) cc_final: 0.6703 (t60) REVERT: A 277 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7542 (mm) REVERT: B 353 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8772 (mm) REVERT: C 9 GLN cc_start: 0.8286 (pp30) cc_final: 0.8029 (pp30) REVERT: C 10 GLU cc_start: 0.8768 (tt0) cc_final: 0.8247 (tt0) REVERT: C 37 ILE cc_start: 0.9460 (mt) cc_final: 0.9061 (tt) REVERT: C 214 ARG cc_start: 0.8798 (mpp80) cc_final: 0.8535 (mmt-90) REVERT: C 217 MET cc_start: 0.9054 (ptp) cc_final: 0.8718 (ppp) REVERT: C 262 MET cc_start: 0.8962 (ttm) cc_final: 0.8559 (ttm) REVERT: D 18 GLN cc_start: 0.8841 (tp40) cc_final: 0.8476 (tp40) REVERT: D 20 LYS cc_start: 0.9105 (mttm) cc_final: 0.8822 (mttm) REVERT: D 58 GLU cc_start: 0.8597 (pm20) cc_final: 0.8240 (pm20) outliers start: 23 outliers final: 12 residues processed: 153 average time/residue: 0.2230 time to fit residues: 46.7001 Evaluate side-chains 146 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 56 optimal weight: 0.0670 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.107324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.068043 restraints weight = 16202.513| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.64 r_work: 0.2701 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9399 Z= 0.208 Angle : 0.553 7.916 12724 Z= 0.291 Chirality : 0.041 0.173 1481 Planarity : 0.004 0.047 1586 Dihedral : 4.224 20.918 1278 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.10 % Allowed : 12.50 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.02 (0.25), residues: 1163 helix: 1.78 (0.25), residues: 423 sheet: -0.83 (0.31), residues: 276 loop : -1.07 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 339 HIS 0.002 0.001 HIS B 213 PHE 0.024 0.001 PHE A 58 TYR 0.012 0.001 TYR E 178 ARG 0.004 0.000 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.03684 ( 469) hydrogen bonds : angle 4.33720 ( 1338) SS BOND : bond 0.00029 ( 1) SS BOND : angle 0.36306 ( 2) covalent geometry : bond 0.00480 ( 9398) covalent geometry : angle 0.55342 (12722) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8328 (mt0) cc_final: 0.8020 (mt0) REVERT: A 148 LYS cc_start: 0.8305 (mttm) cc_final: 0.7495 (tttp) REVERT: A 180 MET cc_start: 0.8341 (mtm) cc_final: 0.7363 (ppp) REVERT: A 182 TRP cc_start: 0.7357 (t-100) cc_final: 0.6978 (t60) REVERT: A 277 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7520 (mm) REVERT: B 353 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8782 (mm) REVERT: C 9 GLN cc_start: 0.8311 (pp30) cc_final: 0.8050 (pp30) REVERT: C 37 ILE cc_start: 0.9496 (mt) cc_final: 0.9181 (tt) REVERT: C 214 ARG cc_start: 0.8801 (mpp80) cc_final: 0.8510 (mmt-90) REVERT: C 217 MET cc_start: 0.9036 (ptp) cc_final: 0.8635 (ppp) REVERT: C 262 MET cc_start: 0.8994 (ttm) cc_final: 0.8596 (ttm) REVERT: D 18 GLN cc_start: 0.8753 (tp40) cc_final: 0.8342 (tp40) REVERT: D 20 LYS cc_start: 0.9079 (mttm) cc_final: 0.8791 (mttm) REVERT: D 22 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7846 (mt-10) REVERT: D 58 GLU cc_start: 0.8597 (pm20) cc_final: 0.8209 (pm20) outliers start: 31 outliers final: 19 residues processed: 152 average time/residue: 0.2311 time to fit residues: 48.0993 Evaluate side-chains 155 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 305 CYS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 HIS ** B 331 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 = 0.3557 r_free = 0.3557 target = 0.108134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.068880 restraints weight = 16255.429| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.66 r_work: 0.2721 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9399 Z= 0.161 Angle : 0.533 7.699 12724 Z= 0.279 Chirality : 0.041 0.186 1481 Planarity : 0.003 0.046 1586 Dihedral : 4.153 19.501 1278 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.50 % Allowed : 13.40 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.17 (0.25), residues: 1163 helix: 1.91 (0.25), residues: 423 sheet: -0.82 (0.32), residues: 266 loop : -0.93 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 339 HIS 0.002 0.001 HIS B 213 PHE 0.025 0.001 PHE A 58 TYR 0.011 0.001 TYR E 178 ARG 0.004 0.000 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.03544 ( 469) hydrogen bonds : angle 4.28555 ( 1338) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.23645 ( 2) covalent geometry : bond 0.00369 ( 9398) covalent geometry : angle 0.53260 (12722) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 140 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8329 (mt0) cc_final: 0.8014 (mt0) REVERT: A 148 LYS cc_start: 0.8280 (mttm) cc_final: 0.7467 (tttp) REVERT: A 180 MET cc_start: 0.8250 (mtm) cc_final: 0.7325 (ppp) REVERT: A 182 TRP cc_start: 0.7333 (t-100) cc_final: 0.6959 (t60) REVERT: A 277 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7530 (mm) REVERT: B 353 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8774 (mm) REVERT: C 9 GLN cc_start: 0.8326 (pp30) cc_final: 0.8073 (pp30) REVERT: C 37 ILE cc_start: 0.9493 (mt) cc_final: 0.9177 (tt) REVERT: C 214 ARG cc_start: 0.8800 (mpp80) cc_final: 0.8520 (mmt-90) REVERT: C 217 MET cc_start: 0.9043 (ptp) cc_final: 0.8650 (ppp) REVERT: C 262 MET cc_start: 0.8973 (ttm) cc_final: 0.8590 (ttm) REVERT: D 18 GLN cc_start: 0.8749 (tp40) cc_final: 0.8334 (tp40) REVERT: D 20 LYS cc_start: 0.9078 (mttm) cc_final: 0.8798 (mttm) REVERT: D 22 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7851 (mt-10) REVERT: D 58 GLU cc_start: 0.8611 (pm20) cc_final: 0.8225 (pm20) outliers start: 25 outliers final: 16 residues processed: 153 average time/residue: 0.2253 time to fit residues: 46.9656 Evaluate side-chains 152 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 67 optimal weight: 0.2980 chunk 16 optimal weight: 9.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 HIS B 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.109548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.070587 restraints weight = 16382.800| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.65 r_work: 0.2749 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9399 Z= 0.113 Angle : 0.512 7.633 12724 Z= 0.268 Chirality : 0.040 0.182 1481 Planarity : 0.003 0.046 1586 Dihedral : 3.971 17.153 1278 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.50 % Allowed : 14.30 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.26 (0.25), residues: 1163 helix: 1.93 (0.25), residues: 432 sheet: -0.79 (0.32), residues: 268 loop : -0.88 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 PHE 0.026 0.001 PHE A 58 TYR 0.009 0.001 TYR E 178 ARG 0.007 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 469) hydrogen bonds : angle 4.18404 ( 1338) SS BOND : bond 0.00169 ( 1) SS BOND : angle 0.13974 ( 2) covalent geometry : bond 0.00251 ( 9398) covalent geometry : angle 0.51161 (12722) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8271 (mt0) cc_final: 0.7932 (mt0) REVERT: A 180 MET cc_start: 0.8275 (mtm) cc_final: 0.7140 (ppp) REVERT: A 182 TRP cc_start: 0.7266 (t-100) cc_final: 0.6989 (t60) REVERT: A 277 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7521 (mm) REVERT: B 298 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8180 (pp20) REVERT: B 353 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8743 (mm) REVERT: C 9 GLN cc_start: 0.8310 (pp30) cc_final: 0.8038 (pp30) REVERT: C 37 ILE cc_start: 0.9458 (mt) cc_final: 0.9091 (tt) REVERT: C 214 ARG cc_start: 0.8856 (mpp80) cc_final: 0.8617 (mmt-90) REVERT: C 217 MET cc_start: 0.9023 (ptp) cc_final: 0.8668 (ppp) REVERT: C 262 MET cc_start: 0.8945 (ttm) cc_final: 0.8595 (ttm) REVERT: D 18 GLN cc_start: 0.8772 (tp40) cc_final: 0.8353 (tp40) REVERT: D 20 LYS cc_start: 0.9080 (mttm) cc_final: 0.8800 (mttm) REVERT: D 22 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7850 (mt-10) REVERT: D 58 GLU cc_start: 0.8625 (pm20) cc_final: 0.8248 (pm20) outliers start: 25 outliers final: 14 residues processed: 155 average time/residue: 0.2117 time to fit residues: 45.4804 Evaluate side-chains 150 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 44 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.108031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.068770 restraints weight = 16589.982| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.68 r_work: 0.2717 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9399 Z= 0.176 Angle : 0.560 10.152 12724 Z= 0.289 Chirality : 0.041 0.203 1481 Planarity : 0.003 0.045 1586 Dihedral : 4.085 18.844 1278 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.30 % Allowed : 14.50 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.37 (0.25), residues: 1163 helix: 2.02 (0.25), residues: 432 sheet: -0.74 (0.32), residues: 266 loop : -0.80 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 339 HIS 0.002 0.001 HIS B 213 PHE 0.023 0.001 PHE A 58 TYR 0.011 0.001 TYR E 178 ARG 0.005 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 469) hydrogen bonds : angle 4.26771 ( 1338) SS BOND : bond 0.00080 ( 1) SS BOND : angle 0.21089 ( 2) covalent geometry : bond 0.00410 ( 9398) covalent geometry : angle 0.55970 (12722) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8262 (mt0) cc_final: 0.7943 (mt0) REVERT: A 180 MET cc_start: 0.8195 (mtm) cc_final: 0.7177 (ppp) REVERT: A 182 TRP cc_start: 0.7300 (t-100) cc_final: 0.7027 (t60) REVERT: A 277 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7537 (mm) REVERT: B 353 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8804 (mm) REVERT: C 9 GLN cc_start: 0.8293 (pp30) cc_final: 0.8010 (pp30) REVERT: C 37 ILE cc_start: 0.9471 (mt) cc_final: 0.9076 (tt) REVERT: C 130 GLU cc_start: 0.9223 (mp0) cc_final: 0.8970 (mp0) REVERT: C 214 ARG cc_start: 0.8805 (mpp80) cc_final: 0.8579 (mmt-90) REVERT: C 217 MET cc_start: 0.9031 (ptp) cc_final: 0.8653 (ppp) REVERT: C 262 MET cc_start: 0.8978 (ttm) cc_final: 0.8636 (ttm) REVERT: D 18 GLN cc_start: 0.8760 (tp40) cc_final: 0.8329 (tp40) REVERT: D 20 LYS cc_start: 0.9089 (mttm) cc_final: 0.8817 (mttm) REVERT: D 22 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7832 (mt-10) REVERT: D 58 GLU cc_start: 0.8620 (pm20) cc_final: 0.8234 (pm20) outliers start: 23 outliers final: 16 residues processed: 148 average time/residue: 0.2312 time to fit residues: 47.5116 Evaluate side-chains 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 14 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 59 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.110090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.071333 restraints weight = 16190.976| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.63 r_work: 0.2772 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9399 Z= 0.110 Angle : 0.528 9.049 12724 Z= 0.273 Chirality : 0.040 0.194 1481 Planarity : 0.003 0.045 1586 Dihedral : 3.901 17.001 1278 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.90 % Allowed : 14.80 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.49 (0.25), residues: 1163 helix: 2.11 (0.25), residues: 432 sheet: -0.72 (0.32), residues: 268 loop : -0.69 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 PHE 0.020 0.001 PHE A 58 TYR 0.009 0.001 TYR E 178 ARG 0.006 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 469) hydrogen bonds : angle 4.15935 ( 1338) SS BOND : bond 0.00252 ( 1) SS BOND : angle 0.21947 ( 2) covalent geometry : bond 0.00242 ( 9398) covalent geometry : angle 0.52838 (12722) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8179 (mt0) cc_final: 0.7855 (mt0) REVERT: A 180 MET cc_start: 0.8100 (mtm) cc_final: 0.6976 (ppp) REVERT: A 182 TRP cc_start: 0.7255 (t-100) cc_final: 0.6999 (t60) REVERT: A 277 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7514 (mm) REVERT: C 9 GLN cc_start: 0.8317 (pp30) cc_final: 0.8032 (pp30) REVERT: C 37 ILE cc_start: 0.9447 (mt) cc_final: 0.9113 (tt) REVERT: C 130 GLU cc_start: 0.9201 (mp0) cc_final: 0.8969 (mp0) REVERT: C 214 ARG cc_start: 0.8824 (mpp80) cc_final: 0.8598 (mmt-90) REVERT: C 217 MET cc_start: 0.9025 (ptp) cc_final: 0.8718 (ppp) REVERT: D 13 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.8335 (ttm110) REVERT: D 18 GLN cc_start: 0.8789 (tp40) cc_final: 0.8366 (tp40) REVERT: D 20 LYS cc_start: 0.9091 (mttm) cc_final: 0.8817 (mttm) REVERT: D 22 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7849 (mt-10) REVERT: D 58 GLU cc_start: 0.8682 (pm20) cc_final: 0.8319 (pm20) outliers start: 19 outliers final: 14 residues processed: 148 average time/residue: 0.2256 time to fit residues: 46.6650 Evaluate side-chains 148 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 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 = 0.3574 r_free = 0.3574 target = 0.109207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.070132 restraints weight = 16573.770| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.69 r_work: 0.2744 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9399 Z= 0.137 Angle : 0.551 7.976 12724 Z= 0.284 Chirality : 0.041 0.205 1481 Planarity : 0.003 0.045 1586 Dihedral : 3.930 17.106 1278 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.70 % Allowed : 15.20 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.57 (0.25), residues: 1163 helix: 2.16 (0.25), residues: 432 sheet: -0.69 (0.32), residues: 268 loop : -0.62 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 339 HIS 0.002 0.001 HIS B 188 PHE 0.020 0.001 PHE A 58 TYR 0.013 0.001 TYR C 59 ARG 0.005 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 469) hydrogen bonds : angle 4.18346 ( 1338) SS BOND : bond 0.00172 ( 1) SS BOND : angle 0.11265 ( 2) covalent geometry : bond 0.00313 ( 9398) covalent geometry : angle 0.55119 (12722) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLN cc_start: 0.8167 (mt0) cc_final: 0.7823 (mt0) REVERT: A 180 MET cc_start: 0.8147 (mtm) cc_final: 0.7088 (ppp) REVERT: A 182 TRP cc_start: 0.7235 (t-100) cc_final: 0.6994 (t60) REVERT: A 277 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7510 (mm) REVERT: C 9 GLN cc_start: 0.8282 (pp30) cc_final: 0.8077 (pp30) REVERT: C 37 ILE cc_start: 0.9447 (mt) cc_final: 0.9093 (tt) REVERT: C 130 GLU cc_start: 0.9196 (mp0) cc_final: 0.8964 (mp0) REVERT: C 217 MET cc_start: 0.9040 (ptp) cc_final: 0.8699 (ppp) REVERT: D 13 ARG cc_start: 0.8577 (ttp-110) cc_final: 0.8316 (ttm110) REVERT: D 18 GLN cc_start: 0.8773 (tp40) cc_final: 0.8346 (tp40) REVERT: D 20 LYS cc_start: 0.9084 (mttm) cc_final: 0.8808 (mttm) REVERT: D 22 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7796 (mt-10) REVERT: D 58 GLU cc_start: 0.8674 (pm20) cc_final: 0.8302 (pm20) outliers start: 17 outliers final: 15 residues processed: 143 average time/residue: 0.2166 time to fit residues: 42.9020 Evaluate side-chains 143 residues out of total 1022 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 0.0980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 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 = 0.3583 r_free = 0.3583 target = 0.109636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.070898 restraints weight = 16368.700| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 2.65 r_work: 0.2773 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9399 Z= 0.124 Angle : 0.556 16.692 12724 Z= 0.283 Chirality : 0.041 0.294 1481 Planarity : 0.003 0.045 1586 Dihedral : 3.901 16.960 1278 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.80 % Allowed : 15.10 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: 0.60 (0.25), residues: 1163 helix: 2.21 (0.25), residues: 433 sheet: -0.69 (0.32), residues: 263 loop : -0.63 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 339 HIS 0.002 0.000 HIS B 188 PHE 0.019 0.001 PHE A 58 TYR 0.010 0.001 TYR E 178 ARG 0.006 0.000 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.03359 ( 469) hydrogen bonds : angle 4.13915 ( 1338) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.10256 ( 2) covalent geometry : bond 0.00279 ( 9398) covalent geometry : angle 0.55612 (12722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5963.90 seconds wall clock time: 103 minutes 48.04 seconds (6228.04 seconds total)