Starting phenix.real_space_refine on Wed Feb 12 00:47:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d61_46585/02_2025/9d61_46585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d61_46585/02_2025/9d61_46585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d61_46585/02_2025/9d61_46585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d61_46585/02_2025/9d61_46585.map" model { file = "/net/cci-nas-00/data/ceres_data/9d61_46585/02_2025/9d61_46585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d61_46585/02_2025/9d61_46585.cif" } resolution = 3.58 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= 0.008 sd= 0.047 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 52 5.16 5 C 4399 2.51 5 N 1156 2.21 5 O 1288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6895 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2145 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 9, 'TRANS': 276} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 102 Chain: "C" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2569 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "D" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 395 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1752 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'JDC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.75, per 1000 atoms: 0.69 Number of scatterers: 6895 At special positions: 0 Unit cell: (93.168, 93.168, 120.342, 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 52 16.00 O 1288 8.00 N 1156 7.00 C 4399 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " 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: 1.73 Conformation dependent library (CDL) restraints added in 1.0 seconds 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1714 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 10 sheets defined 46.5% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 57 through 87 removed outlier: 4.082A pdb=" N ILE A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE A 62 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 110 removed outlier: 3.607A pdb=" N ILE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 126 through 161 removed outlier: 4.250A pdb=" N LEU A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ILE A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASP A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 3.715A pdb=" N LEU A 167 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 196 removed outlier: 3.769A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 236 Processing helix chain 'A' and resid 236 through 256 removed outlier: 3.952A pdb=" N SER A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 300 removed outlier: 3.644A pdb=" N CYS A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.615A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 333 removed outlier: 4.431A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Proline residue: A 327 - end of helix Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'C' and resid 3 through 25 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.599A pdb=" N ALA D 33 " --> pdb=" O LYS D 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 28 Processing helix chain 'B' and resid 28 through 33 removed outlier: 4.153A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 50 removed outlier: 3.632A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 50' Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.530A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 256 through 260 removed outlier: 4.079A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 removed outlier: 3.787A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 280 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 330 through 351 removed outlier: 3.902A pdb=" N PHE B 334 " --> pdb=" O LYS B 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 201 removed outlier: 3.679A pdb=" N GLY A 198 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS A 200 " --> pdb=" O GLU A 209 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU A 209 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.503A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.793A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 102 through 105 removed outlier: 3.665A pdb=" N ALA C 104 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR C 124 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 160 removed outlier: 3.779A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 191 through 192 removed outlier: 6.707A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.773A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 278 removed outlier: 4.395A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.080A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 185 through 189 removed outlier: 3.550A pdb=" N THR B 187 " --> pdb=" O MET B 198 " (cutoff:3.500A) 350 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.96 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: 2202 1.34 - 1.46: 1422 1.46 - 1.58: 3326 1.58 - 1.70: 0 1.70 - 1.82: 73 Bond restraints: 7023 Sorted by residual: bond pdb=" C THR A 288 " pdb=" N PRO A 289 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.19e-02 7.06e+03 2.76e+00 bond pdb=" C ILE A 58 " pdb=" N PRO A 59 " ideal model delta sigma weight residual 1.335 1.347 -0.012 9.40e-03 1.13e+04 1.72e+00 bond pdb=" CG1 ILE A 292 " pdb=" CD1 ILE A 292 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.49e+00 bond pdb=" CA GLU B 43 " pdb=" CB GLU B 43 " ideal model delta sigma weight residual 1.530 1.549 -0.019 1.69e-02 3.50e+03 1.27e+00 bond pdb=" N LYS B 270 " pdb=" CA LYS B 270 " ideal model delta sigma weight residual 1.460 1.474 -0.014 1.42e-02 4.96e+03 1.02e+00 ... (remaining 7018 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 9224 1.69 - 3.38: 264 3.38 - 5.08: 34 5.08 - 6.77: 14 6.77 - 8.46: 10 Bond angle restraints: 9546 Sorted by residual: angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.20 108.70 4.50 9.60e-01 1.09e+00 2.20e+01 angle pdb=" N ARG C 68 " pdb=" CA ARG C 68 " pdb=" CB ARG C 68 " ideal model delta sigma weight residual 114.17 109.41 4.76 1.14e+00 7.69e-01 1.74e+01 angle pdb=" C GLY B 42 " pdb=" N GLU B 43 " pdb=" CA GLU B 43 " ideal model delta sigma weight residual 121.54 128.04 -6.50 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C ASN B 269 " pdb=" N LYS B 270 " pdb=" CA LYS B 270 " ideal model delta sigma weight residual 122.82 127.57 -4.75 1.42e+00 4.96e-01 1.12e+01 angle pdb=" CA GLU B 43 " pdb=" CB GLU B 43 " pdb=" CG GLU B 43 " ideal model delta sigma weight residual 114.10 120.28 -6.18 2.00e+00 2.50e-01 9.54e+00 ... (remaining 9541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 3944 21.52 - 43.04: 238 43.04 - 64.55: 15 64.55 - 86.07: 3 86.07 - 107.59: 1 Dihedral angle restraints: 4201 sinusoidal: 1563 harmonic: 2638 Sorted by residual: dihedral pdb=" CA ILE D 28 " pdb=" C ILE D 28 " pdb=" N LYS D 29 " pdb=" CA LYS D 29 " ideal model delta harmonic sigma weight residual -180.00 -159.16 -20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" C3B JDC A 401 " pdb=" C2A JDC A 401 " pdb=" C3A JDC A 401 " pdb=" N2A JDC A 401 " ideal model delta sinusoidal sigma weight residual 57.91 -49.68 107.59 1 3.00e+01 1.11e-03 1.39e+01 ... (remaining 4198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 791 0.046 - 0.092: 268 0.092 - 0.139: 70 0.139 - 0.185: 5 0.185 - 0.231: 3 Chirality restraints: 1137 Sorted by residual: chirality pdb=" CB ILE C 157 " pdb=" CA ILE C 157 " pdb=" CG1 ILE C 157 " pdb=" CG2 ILE C 157 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CG LEU B 348 " pdb=" CB LEU B 348 " pdb=" CD1 LEU B 348 " pdb=" CD2 LEU B 348 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CG LEU A 309 " pdb=" CB LEU A 309 " pdb=" CD1 LEU A 309 " pdb=" CD2 LEU A 309 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 1134 not shown) Planarity restraints: 1199 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 141 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.86e+00 pdb=" CG ASN A 141 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 141 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 141 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 68 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.67e+00 pdb=" C ARG C 68 " 0.037 2.00e-02 2.50e+03 pdb=" O ARG C 68 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU C 69 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 124 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 125 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " -0.025 5.00e-02 4.00e+02 ... (remaining 1196 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1490 2.78 - 3.31: 6517 3.31 - 3.84: 11800 3.84 - 4.37: 13248 4.37 - 4.90: 23144 Nonbonded interactions: 56199 Sorted by model distance: nonbonded pdb=" O ASP A 105 " pdb=" OG1 THR A 109 " model vdw 2.249 3.040 nonbonded pdb=" O VAL A 284 " pdb=" OG1 THR A 288 " model vdw 2.258 3.040 nonbonded pdb=" O ALA A 317 " pdb=" OG1 THR A 321 " model vdw 2.288 3.040 nonbonded pdb=" OH TYR B 230 " pdb=" OG SER B 281 " model vdw 2.307 3.040 nonbonded pdb=" OG1 THR C 184 " pdb=" OD2 ASP C 205 " model vdw 2.324 3.040 ... (remaining 56194 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 group one per residue 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.530 Find NCS groups from input model: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 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 : 0.004 0.048 7023 Z= 0.240 Angle : 0.744 8.461 9546 Z= 0.402 Chirality : 0.048 0.231 1137 Planarity : 0.005 0.045 1199 Dihedral : 12.935 107.591 2484 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.57 (0.27), residues: 893 helix: -0.25 (0.25), residues: 372 sheet: -0.90 (0.43), residues: 157 loop : -1.87 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 339 HIS 0.004 0.001 HIS A 291 PHE 0.022 0.002 PHE C 278 TYR 0.018 0.002 TYR A 140 ARG 0.005 0.000 ARG D 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 TRP cc_start: 0.5448 (p-90) cc_final: 0.4780 (p-90) REVERT: C 17 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8537 (tm-30) REVERT: C 19 ARG cc_start: 0.8898 (mtm180) cc_final: 0.8553 (ptp-110) REVERT: C 57 LYS cc_start: 0.6640 (ttmt) cc_final: 0.5980 (ttmm) REVERT: C 246 ASP cc_start: 0.7556 (t0) cc_final: 0.7319 (t0) REVERT: C 255 LEU cc_start: 0.7040 (mm) cc_final: 0.6525 (tp) REVERT: B 17 LYS cc_start: 0.8543 (mtmt) cc_final: 0.7935 (mmmt) REVERT: B 33 GLU cc_start: 0.6486 (tp30) cc_final: 0.6254 (tp30) REVERT: B 243 MET cc_start: 0.7699 (tpp) cc_final: 0.6974 (tpt) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2528 time to fit residues: 67.1392 Evaluate side-chains 138 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN C 156 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 244 HIS B 333 GLN B 346 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.154456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.137296 restraints weight = 15073.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.138199 restraints weight = 11238.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.140338 restraints weight = 8734.460| |-----------------------------------------------------------------------------| r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7023 Z= 0.227 Angle : 0.651 10.715 9546 Z= 0.337 Chirality : 0.042 0.178 1137 Planarity : 0.004 0.044 1199 Dihedral : 6.054 107.919 1002 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.31 % Allowed : 11.85 % Favored : 84.85 % 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: 893 helix: 0.76 (0.27), residues: 368 sheet: -0.90 (0.42), residues: 159 loop : -1.83 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 339 HIS 0.006 0.001 HIS B 244 PHE 0.018 0.002 PHE C 241 TYR 0.014 0.002 TYR B 290 ARG 0.006 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 TYR cc_start: 0.7063 (m-80) cc_final: 0.6852 (m-10) REVERT: C 6 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7635 (tp-100) REVERT: C 214 ARG cc_start: 0.5116 (mmp-170) cc_final: 0.4808 (mmp-170) REVERT: C 255 LEU cc_start: 0.6823 (mm) cc_final: 0.6519 (tp) REVERT: D 21 MET cc_start: 0.7087 (tmm) cc_final: 0.6844 (tmm) REVERT: B 10 LYS cc_start: 0.7547 (mmpt) cc_final: 0.7290 (mmtt) REVERT: B 22 ASN cc_start: 0.8102 (p0) cc_final: 0.7675 (t0) REVERT: B 197 LYS cc_start: 0.7058 (mtmt) cc_final: 0.6724 (mtmt) REVERT: B 225 VAL cc_start: 0.5827 (p) cc_final: 0.5120 (p) REVERT: B 247 MET cc_start: 0.6778 (mtt) cc_final: 0.6484 (ptp) REVERT: B 318 GLU cc_start: 0.4163 (tp30) cc_final: 0.3762 (tp30) outliers start: 24 outliers final: 13 residues processed: 170 average time/residue: 0.2248 time to fit residues: 49.1061 Evaluate side-chains 147 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 350 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 7 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 0.0670 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN C 156 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN B 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.139325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.119140 restraints weight = 15086.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.121931 restraints weight = 9679.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.122946 restraints weight = 7185.027| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7023 Z= 0.322 Angle : 0.697 8.151 9546 Z= 0.366 Chirality : 0.045 0.162 1137 Planarity : 0.004 0.045 1199 Dihedral : 6.354 108.769 1002 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.99 % Allowed : 16.25 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.28), residues: 893 helix: 0.66 (0.27), residues: 373 sheet: -1.07 (0.41), residues: 154 loop : -1.86 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 339 HIS 0.010 0.002 HIS C 266 PHE 0.025 0.002 PHE C 241 TYR 0.037 0.002 TYR A 66 ARG 0.007 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 149 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.6320 (t0) cc_final: 0.5939 (t0) REVERT: A 138 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.6909 (t0) REVERT: A 139 TYR cc_start: 0.7170 (m-80) cc_final: 0.6771 (m-10) REVERT: A 312 TYR cc_start: 0.6810 (t80) cc_final: 0.6521 (t80) REVERT: C 214 ARG cc_start: 0.5339 (mmp-170) cc_final: 0.5088 (mmp-170) REVERT: C 255 LEU cc_start: 0.7149 (mm) cc_final: 0.6881 (tp) REVERT: D 17 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8118 (mm-30) REVERT: D 32 LYS cc_start: 0.8480 (tmtt) cc_final: 0.8093 (tmmt) REVERT: B 22 ASN cc_start: 0.8382 (p0) cc_final: 0.8134 (t0) REVERT: B 197 LYS cc_start: 0.7661 (mtmt) cc_final: 0.7257 (mmtt) REVERT: B 276 GLU cc_start: 0.7224 (pm20) cc_final: 0.6859 (pm20) outliers start: 29 outliers final: 19 residues processed: 164 average time/residue: 0.2267 time to fit residues: 47.3223 Evaluate side-chains 150 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 350 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 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 = 0.4437 r_free = 0.4437 target = 0.140450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.120377 restraints weight = 15144.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.121300 restraints weight = 10270.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.123349 restraints weight = 8488.006| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7023 Z= 0.249 Angle : 0.657 10.936 9546 Z= 0.338 Chirality : 0.042 0.175 1137 Planarity : 0.004 0.045 1199 Dihedral : 6.223 109.476 1002 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.27 % Allowed : 19.83 % Favored : 75.90 % 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: -0.80 (0.28), residues: 893 helix: 0.93 (0.28), residues: 379 sheet: -1.06 (0.42), residues: 154 loop : -1.89 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.004 0.001 HIS B 322 PHE 0.017 0.002 PHE C 241 TYR 0.014 0.002 TYR A 119 ARG 0.007 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ASP cc_start: 0.6329 (t0) cc_final: 0.6073 (t0) REVERT: C 114 CYS cc_start: 0.5897 (t) cc_final: 0.5401 (t) REVERT: C 255 LEU cc_start: 0.7198 (mm) cc_final: 0.6903 (tp) REVERT: D 17 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8162 (mm-30) REVERT: B 22 ASN cc_start: 0.8464 (p0) cc_final: 0.8236 (t0) REVERT: B 277 LYS cc_start: 0.7298 (mptp) cc_final: 0.6949 (ptpt) outliers start: 31 outliers final: 23 residues processed: 157 average time/residue: 0.2287 time to fit residues: 45.8143 Evaluate side-chains 152 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain D residue 29 LYS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 350 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN C 13 GLN C 156 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 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 = 0.4430 r_free = 0.4430 target = 0.139923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.120196 restraints weight = 14907.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.122751 restraints weight = 9860.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.123663 restraints weight = 7931.474| |-----------------------------------------------------------------------------| r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7023 Z= 0.237 Angle : 0.648 8.564 9546 Z= 0.337 Chirality : 0.042 0.166 1137 Planarity : 0.004 0.046 1199 Dihedral : 6.102 107.864 1002 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.27 % Allowed : 21.90 % Favored : 73.83 % 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: -0.67 (0.29), residues: 893 helix: 1.08 (0.28), residues: 373 sheet: -1.11 (0.43), residues: 150 loop : -1.75 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 211 HIS 0.004 0.001 HIS B 322 PHE 0.017 0.002 PHE C 241 TYR 0.012 0.001 TYR A 66 ARG 0.009 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6720 (mt) REVERT: A 105 ASP cc_start: 0.6567 (t0) cc_final: 0.6342 (t0) REVERT: A 335 GLU cc_start: 0.7023 (pt0) cc_final: 0.6770 (pp20) REVERT: C 114 CYS cc_start: 0.5687 (t) cc_final: 0.5356 (t) REVERT: C 233 CYS cc_start: 0.5721 (p) cc_final: 0.5515 (p) REVERT: C 255 LEU cc_start: 0.7227 (mm) cc_final: 0.6946 (tp) REVERT: D 15 LEU cc_start: 0.8724 (pp) cc_final: 0.8430 (pp) REVERT: D 17 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8201 (mm-30) REVERT: D 32 LYS cc_start: 0.8745 (ptpt) cc_final: 0.8469 (tmtt) REVERT: B 22 ASN cc_start: 0.8358 (p0) cc_final: 0.8149 (p0) REVERT: B 36 LEU cc_start: 0.8432 (mt) cc_final: 0.8067 (mt) REVERT: B 192 LYS cc_start: 0.7382 (mttm) cc_final: 0.7154 (mttm) outliers start: 31 outliers final: 23 residues processed: 163 average time/residue: 0.2297 time to fit residues: 47.7357 Evaluate side-chains 148 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 350 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 45 optimal weight: 0.0770 chunk 14 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 40 optimal weight: 0.0370 chunk 67 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN C 6 GLN C 13 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.141442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.121549 restraints weight = 14817.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.124022 restraints weight = 9599.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.124819 restraints weight = 7843.340| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7023 Z= 0.197 Angle : 0.631 9.113 9546 Z= 0.327 Chirality : 0.041 0.148 1137 Planarity : 0.004 0.044 1199 Dihedral : 6.012 106.041 1002 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.58 % Allowed : 23.28 % Favored : 73.14 % 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: -0.51 (0.29), residues: 893 helix: 1.29 (0.28), residues: 368 sheet: -1.08 (0.42), residues: 164 loop : -1.70 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.002 0.001 HIS B 188 PHE 0.028 0.001 PHE A 293 TYR 0.020 0.001 TYR A 246 ARG 0.008 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6634 (mt) REVERT: A 105 ASP cc_start: 0.6415 (t0) cc_final: 0.6211 (t0) REVERT: A 235 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.6395 (m-10) REVERT: C 114 CYS cc_start: 0.5617 (t) cc_final: 0.5276 (t) REVERT: C 233 CYS cc_start: 0.5705 (p) cc_final: 0.5488 (p) REVERT: C 255 LEU cc_start: 0.7164 (mm) cc_final: 0.6903 (tp) REVERT: D 15 LEU cc_start: 0.8661 (pp) cc_final: 0.8370 (pp) REVERT: D 17 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8203 (mm-30) REVERT: B 36 LEU cc_start: 0.8371 (mt) cc_final: 0.8104 (mt) REVERT: B 247 MET cc_start: 0.6935 (mtt) cc_final: 0.6556 (ptp) REVERT: B 277 LYS cc_start: 0.7250 (ptmm) cc_final: 0.6775 (ptpp) outliers start: 26 outliers final: 18 residues processed: 157 average time/residue: 0.2123 time to fit residues: 43.1419 Evaluate side-chains 150 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain C residue 6 GLN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 350 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 268 ASN C 156 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.138823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.119286 restraints weight = 14822.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.121034 restraints weight = 9727.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.121965 restraints weight = 7713.257| |-----------------------------------------------------------------------------| r_work (final): 0.4180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7023 Z= 0.259 Angle : 0.683 9.994 9546 Z= 0.353 Chirality : 0.042 0.143 1137 Planarity : 0.004 0.042 1199 Dihedral : 6.020 105.968 1002 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 4.13 % Allowed : 24.38 % Favored : 71.49 % 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: -0.59 (0.29), residues: 893 helix: 1.14 (0.28), residues: 367 sheet: -1.20 (0.41), residues: 166 loop : -1.58 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.003 0.001 HIS C 54 PHE 0.029 0.002 PHE A 293 TYR 0.019 0.002 TYR A 246 ARG 0.004 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6702 (mt) REVERT: A 235 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.6349 (m-10) REVERT: A 252 ARG cc_start: 0.7240 (tpt90) cc_final: 0.7030 (tpt90) REVERT: A 287 TRP cc_start: 0.7435 (t-100) cc_final: 0.7190 (t-100) REVERT: A 292 ILE cc_start: 0.5377 (OUTLIER) cc_final: 0.5017 (mp) REVERT: C 233 CYS cc_start: 0.5704 (p) cc_final: 0.5495 (p) REVERT: C 255 LEU cc_start: 0.7258 (mm) cc_final: 0.6976 (tp) REVERT: D 15 LEU cc_start: 0.8669 (pp) cc_final: 0.8391 (pp) REVERT: D 17 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8212 (mm-30) REVERT: B 36 LEU cc_start: 0.8388 (mt) cc_final: 0.8037 (mt) outliers start: 30 outliers final: 18 residues processed: 158 average time/residue: 0.2149 time to fit residues: 43.8154 Evaluate side-chains 148 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 350 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 268 ASN C 13 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** B 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.140942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.121318 restraints weight = 15077.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.123293 restraints weight = 10139.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.123588 restraints weight = 9575.757| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7023 Z= 0.215 Angle : 0.669 10.209 9546 Z= 0.345 Chirality : 0.042 0.146 1137 Planarity : 0.004 0.078 1199 Dihedral : 6.051 105.440 1002 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.44 % Allowed : 26.45 % Favored : 70.11 % 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: -0.52 (0.29), residues: 893 helix: 1.30 (0.28), residues: 360 sheet: -1.07 (0.42), residues: 160 loop : -1.67 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 99 HIS 0.002 0.001 HIS D 44 PHE 0.021 0.001 PHE A 293 TYR 0.017 0.002 TYR A 246 ARG 0.004 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6724 (mt) REVERT: A 235 PHE cc_start: 0.6644 (OUTLIER) cc_final: 0.6278 (m-10) REVERT: A 252 ARG cc_start: 0.7148 (tpt90) cc_final: 0.6862 (tpt170) REVERT: A 287 TRP cc_start: 0.7417 (t-100) cc_final: 0.7154 (t-100) REVERT: A 326 ASN cc_start: 0.7878 (t0) cc_final: 0.7634 (t0) REVERT: A 329 LEU cc_start: 0.7901 (tp) cc_final: 0.7558 (tt) REVERT: C 57 LYS cc_start: 0.6075 (ttpp) cc_final: 0.5725 (ttpp) REVERT: C 247 ASP cc_start: 0.7473 (t0) cc_final: 0.7168 (t0) REVERT: C 255 LEU cc_start: 0.7233 (mm) cc_final: 0.6981 (tp) REVERT: C 270 ILE cc_start: 0.8353 (mm) cc_final: 0.8117 (tp) REVERT: D 17 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8217 (mm-30) REVERT: B 36 LEU cc_start: 0.8285 (mt) cc_final: 0.7958 (mt) REVERT: B 247 MET cc_start: 0.6836 (mtt) cc_final: 0.6374 (ptp) REVERT: B 277 LYS cc_start: 0.7164 (ptmm) cc_final: 0.6906 (mptt) outliers start: 25 outliers final: 19 residues processed: 156 average time/residue: 0.2177 time to fit residues: 43.8389 Evaluate side-chains 150 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain B residue 17 LYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 350 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 0.0670 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.0870 chunk 78 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 268 ASN C 156 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.150823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.133096 restraints weight = 15315.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.133926 restraints weight = 11889.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.135361 restraints weight = 10279.115| |-----------------------------------------------------------------------------| r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7023 Z= 0.228 Angle : 0.712 10.092 9546 Z= 0.365 Chirality : 0.042 0.153 1137 Planarity : 0.004 0.074 1199 Dihedral : 6.140 105.272 1002 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 3.17 % Allowed : 26.86 % Favored : 69.97 % 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: -0.53 (0.29), residues: 893 helix: 1.24 (0.28), residues: 360 sheet: -1.06 (0.42), residues: 160 loop : -1.62 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 82 HIS 0.003 0.001 HIS C 54 PHE 0.015 0.001 PHE A 293 TYR 0.016 0.001 TYR A 246 ARG 0.003 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6701 (mt) REVERT: A 138 ASP cc_start: 0.7647 (OUTLIER) cc_final: 0.6937 (t0) REVERT: A 139 TYR cc_start: 0.6344 (m-10) cc_final: 0.6009 (m-10) REVERT: A 235 PHE cc_start: 0.6474 (OUTLIER) cc_final: 0.6176 (m-10) REVERT: A 326 ASN cc_start: 0.7926 (t0) cc_final: 0.7679 (t0) REVERT: A 329 LEU cc_start: 0.7990 (tp) cc_final: 0.7674 (tt) REVERT: C 57 LYS cc_start: 0.5828 (ttpp) cc_final: 0.5622 (ttpp) REVERT: C 247 ASP cc_start: 0.7300 (t0) cc_final: 0.7025 (t0) REVERT: C 255 LEU cc_start: 0.6990 (mm) cc_final: 0.6642 (pp) REVERT: D 17 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8161 (mm-30) REVERT: B 36 LEU cc_start: 0.8185 (mt) cc_final: 0.7879 (mt) outliers start: 23 outliers final: 18 residues processed: 152 average time/residue: 0.2100 time to fit residues: 41.4477 Evaluate side-chains 152 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 68 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 0.0370 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 0.1980 chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 268 ASN C 13 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.153707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.136682 restraints weight = 15274.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.138901 restraints weight = 11208.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.140670 restraints weight = 7921.219| |-----------------------------------------------------------------------------| r_work (final): 0.4465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7023 Z= 0.212 Angle : 0.733 11.422 9546 Z= 0.372 Chirality : 0.043 0.258 1137 Planarity : 0.004 0.046 1199 Dihedral : 6.035 104.067 1002 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.62 % Allowed : 27.13 % Favored : 70.25 % 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: -0.52 (0.29), residues: 893 helix: 1.17 (0.28), residues: 366 sheet: -1.06 (0.42), residues: 161 loop : -1.57 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 82 HIS 0.002 0.001 HIS C 142 PHE 0.012 0.001 PHE C 199 TYR 0.015 0.001 TYR A 66 ARG 0.005 0.000 ARG A 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6669 (mt) REVERT: A 206 ASP cc_start: 0.6566 (m-30) cc_final: 0.6331 (m-30) REVERT: A 235 PHE cc_start: 0.6413 (OUTLIER) cc_final: 0.6105 (m-10) REVERT: A 326 ASN cc_start: 0.7916 (t0) cc_final: 0.7692 (t0) REVERT: A 329 LEU cc_start: 0.8039 (tp) cc_final: 0.7734 (tt) REVERT: A 338 LYS cc_start: 0.5823 (pttt) cc_final: 0.5561 (tppt) REVERT: C 57 LYS cc_start: 0.5714 (ttpp) cc_final: 0.5502 (ttpp) REVERT: C 247 ASP cc_start: 0.7277 (t0) cc_final: 0.6996 (t0) REVERT: C 255 LEU cc_start: 0.6997 (mm) cc_final: 0.6638 (pp) REVERT: D 17 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8101 (mm-30) REVERT: B 22 ASN cc_start: 0.7784 (p0) cc_final: 0.7475 (t0) REVERT: B 36 LEU cc_start: 0.8018 (mt) cc_final: 0.7698 (mt) REVERT: B 247 MET cc_start: 0.6506 (mtt) cc_final: 0.6232 (ptp) outliers start: 19 outliers final: 16 residues processed: 150 average time/residue: 0.2090 time to fit residues: 40.5135 Evaluate side-chains 147 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 229 CYS Chi-restraints excluded: chain A residue 235 PHE Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 183 HIS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 350 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 23 optimal weight: 0.6980 chunk 51 optimal weight: 0.0030 chunk 65 optimal weight: 0.0030 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 46 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 ASN A 268 ASN C 156 GLN ** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.154629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.136970 restraints weight = 15123.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.138558 restraints weight = 10650.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.140554 restraints weight = 9170.115| |-----------------------------------------------------------------------------| r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7023 Z= 0.214 Angle : 0.737 13.317 9546 Z= 0.374 Chirality : 0.042 0.161 1137 Planarity : 0.003 0.041 1199 Dihedral : 5.944 102.792 1002 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.75 % Allowed : 27.41 % Favored : 69.83 % 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: -0.54 (0.29), residues: 893 helix: 1.25 (0.28), residues: 360 sheet: -1.12 (0.42), residues: 156 loop : -1.60 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 82 HIS 0.002 0.001 HIS C 142 PHE 0.011 0.001 PHE C 199 TYR 0.022 0.001 TYR A 66 ARG 0.005 0.000 ARG A 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2361.80 seconds wall clock time: 43 minutes 9.35 seconds (2589.35 seconds total)