Starting phenix.real_space_refine on Thu Mar 13 20:24:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vuh_32128/03_2025/7vuh_32128.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuh_32128/03_2025/7vuh_32128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vuh_32128/03_2025/7vuh_32128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuh_32128/03_2025/7vuh_32128.map" model { file = "/net/cci-nas-00/data/ceres_data/7vuh_32128/03_2025/7vuh_32128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuh_32128/03_2025/7vuh_32128.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1050 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians S 50 5.16 5 Cl 1 4.86 5 C 5292 2.51 5 N 1436 2.21 5 O 1523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8302 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1970 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2313 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'7ZQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.32, per 1000 atoms: 0.64 Number of scatterers: 8302 At special positions: 0 Unit cell: (76.96, 99.84, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 50 16.00 O 1523 8.00 N 1436 7.00 C 5292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 2.27 Conformation dependent library (CDL) restraints added in 1.0 seconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 39.0% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 3.734A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.530A pdb=" N LEU A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.675A pdb=" N ALA A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 292 removed outlier: 3.730A pdb=" N LEU A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 321 through 340 removed outlier: 3.649A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 381 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.540A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 74 through 77 removed outlier: 3.623A pdb=" N ASN N 77 " --> pdb=" O ASN N 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 74 through 77' Processing helix chain 'R' and resid 24 through 54 Proline residue: R 29 - end of helix Proline residue: R 42 - end of helix removed outlier: 3.843A pdb=" N GLN R 53 " --> pdb=" O ILE R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 59 removed outlier: 3.614A pdb=" N ARG R 58 " --> pdb=" O VAL R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 83 removed outlier: 4.149A pdb=" N ASN R 64 " --> pdb=" O LYS R 60 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 91 Processing helix chain 'R' and resid 101 through 132 removed outlier: 3.594A pdb=" N LEU R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) Proline residue: R 121 - end of helix Processing helix chain 'R' and resid 143 through 160 removed outlier: 3.645A pdb=" N VAL R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR R 153 " --> pdb=" O ILE R 149 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE R 154 " --> pdb=" O VAL R 150 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR R 155 " --> pdb=" O SER R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 192 removed outlier: 3.715A pdb=" N HIS R 181 " --> pdb=" O THR R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 212 removed outlier: 4.003A pdb=" N LEU R 202 " --> pdb=" O ILE R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 254 removed outlier: 4.214A pdb=" N THR R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE R 237 " --> pdb=" O ILE R 233 " (cutoff:3.500A) Proline residue: R 243 - end of helix removed outlier: 3.955A pdb=" N LEU R 252 " --> pdb=" O ILE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 261 removed outlier: 3.592A pdb=" N TRP R 261 " --> pdb=" O GLN R 258 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 258 through 261' Processing helix chain 'R' and resid 262 through 284 removed outlier: 4.148A pdb=" N MET R 266 " --> pdb=" O LEU R 262 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR R 278 " --> pdb=" O ALA R 274 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA R 279 " --> pdb=" O LEU R 275 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N PHE R 282 " --> pdb=" O THR R 278 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 300 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.617A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.719A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.547A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.853A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.461A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.505A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 191 removed outlier: 3.554A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.533A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.360A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.570A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 59 through 60 removed outlier: 6.502A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1059 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: 2.28 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1334 1.31 - 1.44: 2377 1.44 - 1.56: 4700 1.56 - 1.69: 0 1.69 - 1.82: 71 Bond restraints: 8482 Sorted by residual: bond pdb=" C9 7ZQ R 401 " pdb=" N2 7ZQ R 401 " ideal model delta sigma weight residual 1.341 1.447 -0.106 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C7 7ZQ R 401 " pdb=" N1 7ZQ R 401 " ideal model delta sigma weight residual 1.344 1.448 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" C3 7ZQ R 401 " pdb="CL1 7ZQ R 401 " ideal model delta sigma weight residual 1.732 1.784 -0.052 2.00e-02 2.50e+03 6.72e+00 bond pdb=" C7 7ZQ R 401 " pdb=" O1 7ZQ R 401 " ideal model delta sigma weight residual 1.222 1.182 0.040 2.00e-02 2.50e+03 3.95e+00 bond pdb=" C9 7ZQ R 401 " pdb=" O2 7ZQ R 401 " ideal model delta sigma weight residual 1.219 1.180 0.039 2.00e-02 2.50e+03 3.77e+00 ... (remaining 8477 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 11129 1.56 - 3.12: 307 3.12 - 4.68: 43 4.68 - 6.24: 16 6.24 - 7.80: 7 Bond angle restraints: 11502 Sorted by residual: angle pdb=" N ILE R 118 " pdb=" CA ILE R 118 " pdb=" C ILE R 118 " ideal model delta sigma weight residual 111.81 107.53 4.28 8.60e-01 1.35e+00 2.47e+01 angle pdb=" C SER R 160 " pdb=" N ILE R 161 " pdb=" CA ILE R 161 " ideal model delta sigma weight residual 120.24 122.90 -2.66 6.30e-01 2.52e+00 1.79e+01 angle pdb=" C VAL R 191 " pdb=" N TYR R 192 " pdb=" CA TYR R 192 " ideal model delta sigma weight residual 122.17 116.39 5.78 1.54e+00 4.22e-01 1.41e+01 angle pdb=" C PHE R 27 " pdb=" N VAL R 28 " pdb=" CA VAL R 28 " ideal model delta sigma weight residual 120.24 122.30 -2.06 6.30e-01 2.52e+00 1.07e+01 angle pdb=" N GLY B 116 " pdb=" CA GLY B 116 " pdb=" C GLY B 116 " ideal model delta sigma weight residual 111.56 114.56 -3.00 1.01e+00 9.80e-01 8.84e+00 ... (remaining 11497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4568 17.34 - 34.69: 384 34.69 - 52.03: 74 52.03 - 69.38: 8 69.38 - 86.72: 12 Dihedral angle restraints: 5046 sinusoidal: 1999 harmonic: 3047 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -29.67 -56.33 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CA ASN R 168 " pdb=" C ASN R 168 " pdb=" N ILE R 169 " pdb=" CA ILE R 169 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TRP R 117 " pdb=" C TRP R 117 " pdb=" N ILE R 118 " pdb=" CA ILE R 118 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 798 0.033 - 0.065: 327 0.065 - 0.098: 115 0.098 - 0.130: 53 0.130 - 0.163: 6 Chirality restraints: 1299 Sorted by residual: chirality pdb=" CA LYS A 283 " pdb=" N LYS A 283 " pdb=" C LYS A 283 " pdb=" CB LYS A 283 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CB ILE R 104 " pdb=" CA ILE R 104 " pdb=" CG1 ILE R 104 " pdb=" CG2 ILE R 104 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CG LEU A 46 " pdb=" CB LEU A 46 " pdb=" CD1 LEU A 46 " pdb=" CD2 LEU A 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 1296 not shown) Planarity restraints: 1459 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE R 82 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.33e+00 pdb=" C PHE R 82 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE R 82 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL R 83 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 141 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO R 142 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO R 142 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 142 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 87 " -0.010 2.00e-02 2.50e+03 2.00e-02 4.00e+00 pdb=" C LEU R 87 " 0.035 2.00e-02 2.50e+03 pdb=" O LEU R 87 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU R 88 " -0.012 2.00e-02 2.50e+03 ... (remaining 1456 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 149 2.66 - 3.22: 8177 3.22 - 3.78: 13172 3.78 - 4.34: 18332 4.34 - 4.90: 29767 Nonbonded interactions: 69597 Sorted by model distance: nonbonded pdb=" OH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 2.099 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.131 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.137 3.040 nonbonded pdb=" OD1 ASP A 249 " pdb=" NZ LYS A 283 " model vdw 2.163 3.120 nonbonded pdb=" OD2 ASP B 27 " pdb=" OG SER G 31 " model vdw 2.197 3.040 ... (remaining 69592 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 22.630 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 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 0.106 8482 Z= 0.261 Angle : 0.656 7.796 11502 Z= 0.364 Chirality : 0.044 0.163 1299 Planarity : 0.004 0.051 1459 Dihedral : 13.682 86.724 3070 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -1.87 (0.26), residues: 1030 helix: 0.32 (0.28), residues: 380 sheet: -2.64 (0.33), residues: 182 loop : -1.94 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.020 0.002 PHE R 79 TYR 0.015 0.001 TYR R 253 ARG 0.010 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.6520 (t0) cc_final: 0.6168 (t0) REVERT: A 248 VAL cc_start: 0.8214 (p) cc_final: 0.7980 (m) REVERT: A 313 ASP cc_start: 0.7203 (p0) cc_final: 0.6800 (p0) REVERT: A 368 ASP cc_start: 0.6576 (m-30) cc_final: 0.6062 (m-30) REVERT: A 377 ASN cc_start: 0.7683 (m110) cc_final: 0.7413 (m-40) REVERT: B 277 SER cc_start: 0.7897 (p) cc_final: 0.7622 (p) REVERT: G 58 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7160 (mm-30) REVERT: R 141 TYR cc_start: 0.7993 (p90) cc_final: 0.7622 (p90) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.2480 time to fit residues: 68.1767 Evaluate side-chains 201 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN R 181 HIS ** R 277 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 = 0.3970 r_free = 0.3970 target = 0.161081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145541 restraints weight = 11530.949| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.90 r_work: 0.3661 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8482 Z= 0.224 Angle : 0.599 8.609 11502 Z= 0.316 Chirality : 0.044 0.163 1299 Planarity : 0.005 0.055 1459 Dihedral : 5.512 52.993 1155 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.78 % Allowed : 10.20 % Favored : 89.02 % 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: -1.64 (0.26), residues: 1030 helix: 0.35 (0.28), residues: 388 sheet: -2.39 (0.32), residues: 184 loop : -1.73 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 234 HIS 0.008 0.001 HIS R 113 PHE 0.019 0.002 PHE R 282 TYR 0.018 0.002 TYR R 253 ARG 0.004 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 0.839 Fit side-chains REVERT: A 49 ASP cc_start: 0.7363 (t0) cc_final: 0.6974 (t0) REVERT: A 221 MET cc_start: 0.8321 (ttp) cc_final: 0.8090 (ttp) REVERT: A 229 ASP cc_start: 0.7479 (p0) cc_final: 0.7177 (p0) REVERT: A 301 TYR cc_start: 0.6797 (m-80) cc_final: 0.6566 (t80) REVERT: A 313 ASP cc_start: 0.7513 (p0) cc_final: 0.7249 (p0) REVERT: A 330 PHE cc_start: 0.7623 (t80) cc_final: 0.7416 (t80) REVERT: A 363 ARG cc_start: 0.7997 (tpp-160) cc_final: 0.7759 (tpp-160) REVERT: A 377 ASN cc_start: 0.7996 (m110) cc_final: 0.7566 (m-40) REVERT: B 43 ILE cc_start: 0.8446 (tp) cc_final: 0.8225 (pt) REVERT: B 277 SER cc_start: 0.8149 (p) cc_final: 0.7912 (p) REVERT: B 301 LYS cc_start: 0.7580 (mttm) cc_final: 0.7315 (mttm) REVERT: G 58 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7794 (mm-30) REVERT: R 247 MET cc_start: 0.5274 (ttm) cc_final: 0.3938 (mtt) REVERT: R 266 MET cc_start: 0.5809 (ptp) cc_final: 0.5089 (ppp) REVERT: R 277 ASN cc_start: 0.7702 (t0) cc_final: 0.7492 (t0) REVERT: R 295 MET cc_start: 0.7431 (mmp) cc_final: 0.7158 (mmp) outliers start: 7 outliers final: 6 residues processed: 212 average time/residue: 0.2371 time to fit residues: 65.7648 Evaluate side-chains 204 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 198 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 5 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 84 optimal weight: 0.1980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 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 = 0.3943 r_free = 0.3943 target = 0.158987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.142795 restraints weight = 11841.446| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.97 r_work: 0.3641 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8482 Z= 0.222 Angle : 0.561 6.018 11502 Z= 0.298 Chirality : 0.043 0.151 1299 Planarity : 0.005 0.062 1459 Dihedral : 5.372 52.482 1155 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.88 % Allowed : 13.53 % Favored : 84.59 % 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: -1.49 (0.26), residues: 1030 helix: 0.52 (0.29), residues: 378 sheet: -2.07 (0.32), residues: 193 loop : -1.74 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.004 0.001 HIS R 113 PHE 0.015 0.001 PHE R 282 TYR 0.020 0.001 TYR N 80 ARG 0.007 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7531 (p0) cc_final: 0.7239 (p0) REVERT: A 313 ASP cc_start: 0.7528 (p0) cc_final: 0.7240 (p0) REVERT: A 330 PHE cc_start: 0.7639 (t80) cc_final: 0.7390 (t80) REVERT: A 363 ARG cc_start: 0.7989 (tpp-160) cc_final: 0.7729 (tpp-160) REVERT: A 377 ASN cc_start: 0.8026 (m110) cc_final: 0.7542 (m-40) REVERT: B 212 ASP cc_start: 0.7303 (m-30) cc_final: 0.6795 (m-30) REVERT: B 234 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: B 277 SER cc_start: 0.8162 (p) cc_final: 0.7920 (p) REVERT: G 58 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7815 (mm-30) REVERT: R 295 MET cc_start: 0.7524 (mmp) cc_final: 0.7292 (mmp) outliers start: 17 outliers final: 10 residues processed: 208 average time/residue: 0.2503 time to fit residues: 67.6804 Evaluate side-chains 202 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 25 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 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 = 0.3943 r_free = 0.3943 target = 0.159030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142619 restraints weight = 11698.721| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.94 r_work: 0.3630 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8482 Z= 0.279 Angle : 0.589 6.878 11502 Z= 0.312 Chirality : 0.044 0.161 1299 Planarity : 0.005 0.064 1459 Dihedral : 5.475 50.253 1155 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.66 % Allowed : 14.97 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.45 (0.26), residues: 1030 helix: 0.52 (0.28), residues: 386 sheet: -1.93 (0.32), residues: 196 loop : -1.77 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.004 0.001 HIS R 180 PHE 0.017 0.002 PHE R 282 TYR 0.022 0.002 TYR R 253 ARG 0.007 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7532 (p0) cc_final: 0.7260 (p0) REVERT: A 313 ASP cc_start: 0.7573 (p0) cc_final: 0.7298 (p0) REVERT: A 330 PHE cc_start: 0.7630 (t80) cc_final: 0.7422 (t80) REVERT: A 363 ARG cc_start: 0.7954 (tpp-160) cc_final: 0.7627 (tpp-160) REVERT: A 368 ASP cc_start: 0.7452 (m-30) cc_final: 0.7064 (t0) REVERT: B 55 LEU cc_start: 0.7782 (mt) cc_final: 0.7489 (mp) REVERT: B 84 SER cc_start: 0.7809 (OUTLIER) cc_final: 0.7477 (p) REVERT: B 212 ASP cc_start: 0.7294 (m-30) cc_final: 0.6864 (m-30) REVERT: B 219 ARG cc_start: 0.7748 (mmt-90) cc_final: 0.7452 (mmt-90) REVERT: B 234 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7424 (m-80) REVERT: B 318 LEU cc_start: 0.8175 (tp) cc_final: 0.7974 (tp) REVERT: G 58 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7722 (mm-30) REVERT: N 109 ASP cc_start: 0.7807 (p0) cc_final: 0.7559 (p0) REVERT: R 161 ILE cc_start: 0.7900 (mm) cc_final: 0.7644 (mt) REVERT: R 295 MET cc_start: 0.7438 (mmp) cc_final: 0.7210 (mmp) outliers start: 24 outliers final: 14 residues processed: 220 average time/residue: 0.2367 time to fit residues: 68.3598 Evaluate side-chains 212 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 9 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 34 optimal weight: 0.1980 chunk 90 optimal weight: 0.0980 chunk 83 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 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 = 0.3939 r_free = 0.3939 target = 0.158587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141950 restraints weight = 11768.527| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.04 r_work: 0.3626 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8482 Z= 0.195 Angle : 0.563 6.715 11502 Z= 0.296 Chirality : 0.043 0.149 1299 Planarity : 0.005 0.065 1459 Dihedral : 5.471 58.443 1155 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.44 % Allowed : 16.96 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 1030 helix: 0.66 (0.29), residues: 379 sheet: -1.68 (0.33), residues: 196 loop : -1.70 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 113 PHE 0.017 0.001 PHE R 282 TYR 0.020 0.001 TYR N 80 ARG 0.008 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7806 (mtm-85) REVERT: A 229 ASP cc_start: 0.7571 (p0) cc_final: 0.7270 (p0) REVERT: A 313 ASP cc_start: 0.7605 (p0) cc_final: 0.7336 (p0) REVERT: A 363 ARG cc_start: 0.7951 (tpp-160) cc_final: 0.7653 (tpp-160) REVERT: A 368 ASP cc_start: 0.7453 (m-30) cc_final: 0.7126 (t0) REVERT: B 55 LEU cc_start: 0.7763 (mt) cc_final: 0.7444 (mp) REVERT: B 84 SER cc_start: 0.7769 (OUTLIER) cc_final: 0.7401 (p) REVERT: B 234 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: N 109 ASP cc_start: 0.7787 (p0) cc_final: 0.7540 (p0) REVERT: R 161 ILE cc_start: 0.7874 (mm) cc_final: 0.7620 (mt) REVERT: R 295 MET cc_start: 0.7426 (mmp) cc_final: 0.7187 (mmp) outliers start: 22 outliers final: 15 residues processed: 213 average time/residue: 0.2788 time to fit residues: 78.2425 Evaluate side-chains 211 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 281 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 27 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 21 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 12 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.159084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.142693 restraints weight = 11701.040| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.93 r_work: 0.3640 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8482 Z= 0.249 Angle : 0.582 6.763 11502 Z= 0.306 Chirality : 0.043 0.150 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.399 51.325 1155 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.22 % Allowed : 16.52 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.26), residues: 1030 helix: 0.66 (0.28), residues: 386 sheet: -1.58 (0.34), residues: 195 loop : -1.68 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.029 0.002 PHE A 330 TYR 0.020 0.001 TYR R 253 ARG 0.008 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.954 Fit side-chains REVERT: A 36 VAL cc_start: 0.7839 (t) cc_final: 0.7580 (p) REVERT: A 42 ARG cc_start: 0.8053 (mtm-85) cc_final: 0.7819 (mtm-85) REVERT: A 229 ASP cc_start: 0.7527 (p0) cc_final: 0.7284 (p0) REVERT: A 313 ASP cc_start: 0.7577 (p0) cc_final: 0.7293 (p0) REVERT: A 363 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.7630 (tpp-160) REVERT: A 368 ASP cc_start: 0.7405 (m-30) cc_final: 0.7034 (t0) REVERT: B 55 LEU cc_start: 0.7810 (mt) cc_final: 0.7495 (mp) REVERT: B 84 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7443 (p) REVERT: B 234 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: B 292 PHE cc_start: 0.7601 (OUTLIER) cc_final: 0.7170 (m-80) REVERT: N 109 ASP cc_start: 0.7852 (p0) cc_final: 0.7504 (p0) REVERT: R 161 ILE cc_start: 0.7887 (mm) cc_final: 0.7643 (mt) REVERT: R 295 MET cc_start: 0.7441 (mmp) cc_final: 0.7223 (mmp) outliers start: 29 outliers final: 19 residues processed: 219 average time/residue: 0.2692 time to fit residues: 78.0429 Evaluate side-chains 221 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 281 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** R 277 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 = 0.3934 r_free = 0.3934 target = 0.158080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141382 restraints weight = 11757.443| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.03 r_work: 0.3624 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8482 Z= 0.219 Angle : 0.568 6.717 11502 Z= 0.299 Chirality : 0.043 0.163 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.224 44.287 1155 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.55 % Allowed : 17.07 % Favored : 79.38 % 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: -1.11 (0.26), residues: 1030 helix: 0.69 (0.28), residues: 387 sheet: -1.49 (0.34), residues: 193 loop : -1.63 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.021 0.002 PHE A 330 TYR 0.023 0.001 TYR N 80 ARG 0.009 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.923 Fit side-chains REVERT: A 36 VAL cc_start: 0.7804 (t) cc_final: 0.7558 (p) REVERT: A 42 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7805 (mtm-85) REVERT: A 49 ASP cc_start: 0.7269 (t0) cc_final: 0.6898 (t0) REVERT: A 229 ASP cc_start: 0.7582 (p0) cc_final: 0.7307 (p0) REVERT: A 313 ASP cc_start: 0.7582 (p0) cc_final: 0.7275 (p0) REVERT: A 363 ARG cc_start: 0.7952 (tpp-160) cc_final: 0.7622 (tpp-160) REVERT: B 55 LEU cc_start: 0.7791 (mt) cc_final: 0.7384 (mp) REVERT: B 76 ASP cc_start: 0.7269 (t0) cc_final: 0.6979 (t0) REVERT: B 84 SER cc_start: 0.7824 (OUTLIER) cc_final: 0.7448 (p) REVERT: B 234 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: B 292 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7139 (m-80) REVERT: N 109 ASP cc_start: 0.7843 (p0) cc_final: 0.7624 (p0) REVERT: R 117 TRP cc_start: 0.8078 (m100) cc_final: 0.7870 (m100) REVERT: R 161 ILE cc_start: 0.7887 (mm) cc_final: 0.7637 (mt) REVERT: R 247 MET cc_start: 0.5281 (ttm) cc_final: 0.4669 (ttt) REVERT: R 252 LEU cc_start: 0.7696 (tp) cc_final: 0.7484 (tt) REVERT: R 266 MET cc_start: 0.5657 (ptp) cc_final: 0.5402 (ppp) REVERT: R 295 MET cc_start: 0.7465 (mmp) cc_final: 0.7219 (mmp) outliers start: 32 outliers final: 21 residues processed: 229 average time/residue: 0.2735 time to fit residues: 82.1328 Evaluate side-chains 233 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 281 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 96 optimal weight: 0.0060 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 0.4980 chunk 73 optimal weight: 0.0050 chunk 8 optimal weight: 1.9990 chunk 88 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 overall best weight: 0.2408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 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 = 0.3974 r_free = 0.3974 target = 0.161315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.144913 restraints weight = 11885.541| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.96 r_work: 0.3669 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8482 Z= 0.163 Angle : 0.551 6.609 11502 Z= 0.288 Chirality : 0.042 0.133 1299 Planarity : 0.005 0.066 1459 Dihedral : 4.905 44.312 1155 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.77 % Allowed : 18.40 % Favored : 78.82 % 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: -0.98 (0.26), residues: 1030 helix: 0.75 (0.28), residues: 381 sheet: -1.27 (0.36), residues: 193 loop : -1.56 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.030 0.001 PHE A 330 TYR 0.019 0.001 TYR N 80 ARG 0.008 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 1.541 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7801 (t) cc_final: 0.7571 (p) REVERT: A 42 ARG cc_start: 0.8000 (mtm-85) cc_final: 0.7775 (mtm-85) REVERT: A 49 ASP cc_start: 0.7214 (t0) cc_final: 0.6845 (t0) REVERT: A 229 ASP cc_start: 0.7527 (p0) cc_final: 0.7202 (p0) REVERT: A 313 ASP cc_start: 0.7561 (p0) cc_final: 0.7269 (p0) REVERT: A 363 ARG cc_start: 0.7968 (tpp-160) cc_final: 0.7725 (tpp-160) REVERT: A 368 ASP cc_start: 0.7358 (m-30) cc_final: 0.7027 (t0) REVERT: B 55 LEU cc_start: 0.7805 (mt) cc_final: 0.7437 (mp) REVERT: B 76 ASP cc_start: 0.7184 (t0) cc_final: 0.6863 (t0) REVERT: B 292 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: N 109 ASP cc_start: 0.7816 (p0) cc_final: 0.7534 (p0) REVERT: R 148 VAL cc_start: 0.7207 (m) cc_final: 0.6914 (p) REVERT: R 252 LEU cc_start: 0.7483 (tp) cc_final: 0.7258 (tt) REVERT: R 295 MET cc_start: 0.7437 (mmp) cc_final: 0.7193 (mmp) outliers start: 25 outliers final: 17 residues processed: 212 average time/residue: 0.3555 time to fit residues: 101.7285 Evaluate side-chains 210 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 251 HIS Chi-restraints excluded: chain R residue 281 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 81 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 40 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.0870 chunk 97 optimal weight: 0.6980 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 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 = 0.3970 r_free = 0.3970 target = 0.160884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144445 restraints weight = 11867.220| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.95 r_work: 0.3673 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8482 Z= 0.194 Angle : 0.578 11.977 11502 Z= 0.300 Chirality : 0.042 0.145 1299 Planarity : 0.005 0.078 1459 Dihedral : 4.974 44.836 1155 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.22 % Allowed : 18.85 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.98 (0.26), residues: 1030 helix: 0.70 (0.28), residues: 387 sheet: -1.24 (0.36), residues: 193 loop : -1.53 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 220 PHE 0.027 0.001 PHE A 330 TYR 0.020 0.001 TYR N 80 ARG 0.009 0.000 ARG A 332 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.023 Fit side-chains REVERT: A 36 VAL cc_start: 0.7755 (t) cc_final: 0.7532 (p) REVERT: A 49 ASP cc_start: 0.7290 (t0) cc_final: 0.6912 (t0) REVERT: A 229 ASP cc_start: 0.7574 (p0) cc_final: 0.7288 (p0) REVERT: A 313 ASP cc_start: 0.7545 (p0) cc_final: 0.7241 (p0) REVERT: A 363 ARG cc_start: 0.7957 (tpp-160) cc_final: 0.7666 (tpp-160) REVERT: A 368 ASP cc_start: 0.7378 (m-30) cc_final: 0.7059 (t0) REVERT: B 55 LEU cc_start: 0.7713 (mt) cc_final: 0.7345 (mp) REVERT: B 76 ASP cc_start: 0.7176 (t0) cc_final: 0.6827 (t0) REVERT: B 292 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: N 109 ASP cc_start: 0.7887 (p0) cc_final: 0.7608 (p0) REVERT: R 161 ILE cc_start: 0.7808 (mm) cc_final: 0.7585 (mt) REVERT: R 235 SER cc_start: 0.7409 (t) cc_final: 0.6764 (p) REVERT: R 252 LEU cc_start: 0.7462 (tp) cc_final: 0.7233 (tt) REVERT: R 266 MET cc_start: 0.5568 (ptp) cc_final: 0.5355 (ppp) REVERT: R 295 MET cc_start: 0.7435 (mmp) cc_final: 0.7118 (mmp) outliers start: 20 outliers final: 15 residues processed: 211 average time/residue: 0.2581 time to fit residues: 71.1669 Evaluate side-chains 210 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 196 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 10 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 44 optimal weight: 0.0060 chunk 8 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 92 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 81 optimal weight: 0.2980 chunk 50 optimal weight: 0.2980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 281 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.162033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.145571 restraints weight = 11818.776| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.96 r_work: 0.3683 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8482 Z= 0.185 Angle : 0.569 7.253 11502 Z= 0.298 Chirality : 0.042 0.183 1299 Planarity : 0.005 0.075 1459 Dihedral : 4.958 45.946 1155 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.44 % Allowed : 18.96 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.26), residues: 1030 helix: 0.64 (0.28), residues: 388 sheet: -1.15 (0.36), residues: 193 loop : -1.45 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.043 0.002 PHE A 305 TYR 0.020 0.001 TYR N 80 ARG 0.010 0.000 ARG A 332 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.922 Fit side-chains REVERT: A 49 ASP cc_start: 0.7281 (t0) cc_final: 0.6902 (t0) REVERT: A 229 ASP cc_start: 0.7546 (p0) cc_final: 0.7277 (p0) REVERT: A 313 ASP cc_start: 0.7555 (p0) cc_final: 0.7253 (p0) REVERT: A 363 ARG cc_start: 0.7967 (tpp-160) cc_final: 0.7694 (tpp-160) REVERT: A 368 ASP cc_start: 0.7391 (m-30) cc_final: 0.7072 (t0) REVERT: B 55 LEU cc_start: 0.7796 (mt) cc_final: 0.7442 (mp) REVERT: B 76 ASP cc_start: 0.7100 (t0) cc_final: 0.6724 (t0) REVERT: B 188 MET cc_start: 0.7129 (mtp) cc_final: 0.6912 (mmm) REVERT: B 198 LEU cc_start: 0.7769 (mp) cc_final: 0.7545 (mm) REVERT: B 292 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7177 (m-80) REVERT: N 109 ASP cc_start: 0.7875 (p0) cc_final: 0.7582 (p0) REVERT: R 148 VAL cc_start: 0.7260 (m) cc_final: 0.6949 (p) REVERT: R 161 ILE cc_start: 0.7807 (mm) cc_final: 0.7577 (mt) REVERT: R 266 MET cc_start: 0.5694 (ptp) cc_final: 0.5337 (ppp) REVERT: R 295 MET cc_start: 0.7431 (mmp) cc_final: 0.7118 (mmp) outliers start: 22 outliers final: 19 residues processed: 208 average time/residue: 0.2861 time to fit residues: 78.8418 Evaluate side-chains 211 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 115 SER Chi-restraints excluded: chain R residue 119 THR Chi-restraints excluded: chain R residue 120 VAL Chi-restraints excluded: chain R residue 123 THR Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 251 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 68 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 0.0170 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 32 optimal weight: 0.3980 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 44 ASN R 251 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.162619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.146521 restraints weight = 11926.217| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.95 r_work: 0.3694 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8482 Z= 0.175 Angle : 0.580 6.606 11502 Z= 0.302 Chirality : 0.042 0.167 1299 Planarity : 0.005 0.065 1459 Dihedral : 5.315 42.260 1155 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.33 % Allowed : 19.40 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.27), residues: 1030 helix: 0.72 (0.28), residues: 389 sheet: -1.13 (0.36), residues: 195 loop : -1.38 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 271 HIS 0.003 0.001 HIS A 347 PHE 0.023 0.001 PHE R 282 TYR 0.021 0.001 TYR N 80 ARG 0.013 0.000 ARG A 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5048.44 seconds wall clock time: 89 minutes 50.19 seconds (5390.19 seconds total)