Starting phenix.real_space_refine on Sat Dec 28 22:00:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vuh_32128/12_2024/7vuh_32128.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuh_32128/12_2024/7vuh_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_32128/12_2024/7vuh_32128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuh_32128/12_2024/7vuh_32128.map" model { file = "/net/cci-nas-00/data/ceres_data/7vuh_32128/12_2024/7vuh_32128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuh_32128/12_2024/7vuh_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.33, 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: 2.55 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: 0.91 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: 2.68 Time building geometry restraints manager: 2.73 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: 0.010 Normalize map: mean=0, sd=1: 1.090 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: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.110 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.870 ------------------------------------------------------------------------------- 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 : 0.958 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: 0.2428 time to fit residues: 66.7302 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 : 0.927 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 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 : 0.840 Fit side-chains REVERT: A 49 ASP cc_start: 0.6468 (t0) cc_final: 0.6107 (t0) REVERT: A 221 MET cc_start: 0.7784 (ttp) cc_final: 0.7553 (ttp) REVERT: A 229 ASP cc_start: 0.7076 (p0) cc_final: 0.6847 (p0) REVERT: A 313 ASP cc_start: 0.7198 (p0) cc_final: 0.6909 (p0) REVERT: A 360 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6567 (mm-30) REVERT: A 377 ASN cc_start: 0.7803 (m110) cc_final: 0.7441 (m-40) REVERT: B 277 SER cc_start: 0.7805 (p) cc_final: 0.7601 (p) REVERT: B 301 LYS cc_start: 0.7270 (mttm) cc_final: 0.6994 (mttm) REVERT: G 58 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7146 (mm-30) REVERT: R 247 MET cc_start: 0.4348 (ttm) cc_final: 0.2931 (mtt) outliers start: 7 outliers final: 6 residues processed: 212 average time/residue: 0.2483 time to fit residues: 68.5408 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 : 0.851 ------------------------------------------------------------------------------- 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 50 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 0.1980 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.1414 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= 0.208 Angle : 0.566 6.118 11502 Z= 0.301 Chirality : 0.043 0.149 1299 Planarity : 0.005 0.062 1459 Dihedral : 5.383 52.965 1155 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.77 % Allowed : 13.75 % Favored : 84.48 % 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: 0.56 (0.29), residues: 375 sheet: -2.08 (0.32), residues: 193 loop : -1.78 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.005 0.001 HIS R 113 PHE 0.020 0.002 PHE A 330 TYR 0.019 0.001 TYR N 80 ARG 0.006 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 216 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.951 Fit side-chains REVERT: A 229 ASP cc_start: 0.7111 (p0) cc_final: 0.6883 (p0) REVERT: A 313 ASP cc_start: 0.7204 (p0) cc_final: 0.6902 (p0) REVERT: A 360 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6506 (mm-30) REVERT: A 368 ASP cc_start: 0.6808 (m-30) cc_final: 0.6594 (m-30) REVERT: A 377 ASN cc_start: 0.7792 (m110) cc_final: 0.7414 (m-40) REVERT: B 34 THR cc_start: 0.6128 (p) cc_final: 0.5763 (p) REVERT: G 58 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7139 (mm-30) outliers start: 16 outliers final: 9 residues processed: 208 average time/residue: 0.2662 time to fit residues: 71.6204 Evaluate side-chains 203 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 200 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8482 Z= 0.263 Angle : 0.588 7.932 11502 Z= 0.309 Chirality : 0.044 0.154 1299 Planarity : 0.005 0.065 1459 Dihedral : 5.570 51.829 1155 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 2.22 % Allowed : 15.85 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.26), residues: 1030 helix: 0.57 (0.28), residues: 382 sheet: -1.89 (0.33), residues: 195 loop : -1.84 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.003 0.001 HIS R 180 PHE 0.017 0.002 PHE R 282 TYR 0.020 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 215 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 313 ASP cc_start: 0.7214 (p0) cc_final: 0.6905 (p0) REVERT: B 84 SER cc_start: 0.7303 (OUTLIER) cc_final: 0.7044 (p) REVERT: G 58 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7094 (mm-30) REVERT: R 161 ILE cc_start: 0.7748 (mm) cc_final: 0.7490 (mt) outliers start: 20 outliers final: 11 residues processed: 208 average time/residue: 0.2561 time to fit residues: 69.3327 Evaluate side-chains 202 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 187 VAL 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 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.4980 chunk 72 optimal weight: 0.0870 chunk 40 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.1839 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= 0.216 Angle : 0.570 7.890 11502 Z= 0.299 Chirality : 0.043 0.148 1299 Planarity : 0.005 0.065 1459 Dihedral : 5.615 58.190 1155 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.22 % Allowed : 16.85 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 1030 helix: 0.67 (0.28), residues: 382 sheet: -1.69 (0.34), residues: 196 loop : -1.76 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.024 0.002 PHE A 330 TYR 0.020 0.001 TYR R 253 ARG 0.007 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 223 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7920 (mtm-85) cc_final: 0.7649 (mtm-85) REVERT: A 313 ASP cc_start: 0.7223 (p0) cc_final: 0.6916 (p0) REVERT: A 360 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6501 (mm-30) REVERT: A 368 ASP cc_start: 0.6765 (m-30) cc_final: 0.6447 (t0) REVERT: B 55 LEU cc_start: 0.7466 (mt) cc_final: 0.7208 (mp) REVERT: B 84 SER cc_start: 0.7225 (OUTLIER) cc_final: 0.6935 (p) REVERT: G 58 GLU cc_start: 0.7365 (mm-30) cc_final: 0.7065 (mm-30) REVERT: R 161 ILE cc_start: 0.7741 (mm) cc_final: 0.7488 (mt) REVERT: R 266 MET cc_start: 0.4822 (ppp) cc_final: 0.4391 (ppp) outliers start: 20 outliers final: 16 residues processed: 213 average time/residue: 0.2510 time to fit residues: 69.4853 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 : 0.912 ------------------------------------------------------------------------------- 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 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 247 MET 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 87 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 8482 Z= 0.328 Angle : 0.627 8.164 11502 Z= 0.330 Chirality : 0.045 0.164 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.780 53.979 1155 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.77 % Allowed : 16.63 % Favored : 79.60 % 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: -1.37 (0.26), residues: 1030 helix: 0.68 (0.28), residues: 380 sheet: -1.76 (0.33), residues: 200 loop : -1.87 (0.27), residues: 450 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 0.031 0.002 PHE A 330 TYR 0.023 0.002 TYR N 80 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 238 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7573 (t) cc_final: 0.7319 (p) REVERT: A 313 ASP cc_start: 0.7224 (p0) cc_final: 0.6913 (p0) REVERT: A 368 ASP cc_start: 0.6772 (m-30) cc_final: 0.6480 (t0) REVERT: B 55 LEU cc_start: 0.7538 (mt) cc_final: 0.7256 (mp) REVERT: B 212 ASP cc_start: 0.6382 (m-30) cc_final: 0.5850 (m-30) REVERT: B 292 PHE cc_start: 0.7036 (OUTLIER) cc_final: 0.6714 (m-80) REVERT: N 109 ASP cc_start: 0.7683 (p0) cc_final: 0.7393 (p0) REVERT: R 161 ILE cc_start: 0.7753 (mm) cc_final: 0.7511 (mt) REVERT: R 266 MET cc_start: 0.4930 (ppp) cc_final: 0.4594 (ppp) outliers start: 34 outliers final: 19 residues processed: 222 average time/residue: 0.2438 time to fit residues: 70.7269 Evaluate side-chains 221 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE 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 247 MET 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 11 optimal weight: 0.0470 chunk 55 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 0.0000 chunk 59 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 overall best weight: 0.4882 ------------------------------------------------------------------------------- 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 251 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.2102 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= 0.216 Angle : 0.587 7.904 11502 Z= 0.308 Chirality : 0.043 0.163 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.651 52.253 1155 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.44 % Allowed : 17.29 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.26), residues: 1030 helix: 0.68 (0.28), residues: 385 sheet: -1.57 (0.34), residues: 196 loop : -1.74 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.031 0.002 PHE A 330 TYR 0.022 0.001 TYR R 253 ARG 0.008 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 238 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7563 (t) cc_final: 0.7340 (p) REVERT: A 42 ARG cc_start: 0.7898 (mtm-85) cc_final: 0.7669 (mtm-85) REVERT: A 313 ASP cc_start: 0.7220 (p0) cc_final: 0.6878 (p0) REVERT: A 368 ASP cc_start: 0.6767 (m-30) cc_final: 0.6467 (t0) REVERT: B 55 LEU cc_start: 0.7475 (mt) cc_final: 0.7085 (mp) REVERT: B 76 ASP cc_start: 0.6758 (t0) cc_final: 0.6466 (t0) REVERT: B 84 SER cc_start: 0.7300 (OUTLIER) cc_final: 0.7020 (p) REVERT: B 150 ARG cc_start: 0.8115 (mmt-90) cc_final: 0.7860 (mmt-90) REVERT: B 292 PHE cc_start: 0.6979 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: B 314 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7940 (ttp-170) REVERT: G 58 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7006 (mm-30) REVERT: N 109 ASP cc_start: 0.7662 (p0) cc_final: 0.7401 (p0) REVERT: R 161 ILE cc_start: 0.7718 (mm) cc_final: 0.7461 (mt) REVERT: R 266 MET cc_start: 0.4963 (ppp) cc_final: 0.4639 (ppp) outliers start: 31 outliers final: 23 residues processed: 224 average time/residue: 0.2753 time to fit residues: 81.8472 Evaluate side-chains 228 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET 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 331 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 376 MET 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 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 35 ASN 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 196 CYS Chi-restraints excluded: chain R residue 247 MET Chi-restraints excluded: chain R residue 251 HIS 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 29 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 251 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8482 Z= 0.263 Angle : 0.615 8.715 11502 Z= 0.321 Chirality : 0.044 0.156 1299 Planarity : 0.005 0.067 1459 Dihedral : 5.741 53.226 1155 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.44 % Allowed : 17.96 % 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: -1.24 (0.26), residues: 1030 helix: 0.68 (0.28), residues: 383 sheet: -1.52 (0.34), residues: 194 loop : -1.80 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.007 0.001 HIS R 251 PHE 0.040 0.002 PHE A 330 TYR 0.024 0.002 TYR R 253 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 233 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 202 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7529 (t) cc_final: 0.7311 (p) REVERT: A 313 ASP cc_start: 0.7226 (p0) cc_final: 0.6886 (p0) REVERT: A 368 ASP cc_start: 0.6786 (m-30) cc_final: 0.6488 (t0) REVERT: B 55 LEU cc_start: 0.7497 (mt) cc_final: 0.7088 (mp) REVERT: B 76 ASP cc_start: 0.6763 (t0) cc_final: 0.6440 (t0) REVERT: B 84 SER cc_start: 0.7318 (OUTLIER) cc_final: 0.7032 (p) REVERT: B 212 ASP cc_start: 0.6611 (m-30) cc_final: 0.6374 (m-30) REVERT: B 219 ARG cc_start: 0.7117 (mmt-90) cc_final: 0.6807 (mmt-90) REVERT: B 292 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: G 58 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6981 (mm-30) REVERT: N 31 ASN cc_start: 0.6389 (m-40) cc_final: 0.6094 (m-40) REVERT: N 109 ASP cc_start: 0.7783 (p0) cc_final: 0.7525 (p0) REVERT: R 161 ILE cc_start: 0.7724 (mm) cc_final: 0.7481 (mt) REVERT: R 266 MET cc_start: 0.4867 (ppp) cc_final: 0.4586 (ppp) outliers start: 31 outliers final: 24 residues processed: 220 average time/residue: 0.2582 time to fit residues: 74.3774 Evaluate side-chains 225 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 218 ASN 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 146 LEU 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 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 247 MET 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 90 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 251 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8482 Z= 0.257 Angle : 0.615 8.836 11502 Z= 0.321 Chirality : 0.044 0.155 1299 Planarity : 0.005 0.067 1459 Dihedral : 5.800 57.539 1155 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.44 % Allowed : 18.51 % Favored : 78.05 % 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: -1.20 (0.26), residues: 1030 helix: 0.72 (0.28), residues: 383 sheet: -1.45 (0.35), residues: 193 loop : -1.81 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.005 0.001 HIS R 251 PHE 0.039 0.002 PHE A 330 TYR 0.024 0.002 TYR R 253 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 231 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7515 (t) cc_final: 0.7294 (p) REVERT: A 313 ASP cc_start: 0.7224 (p0) cc_final: 0.6883 (p0) REVERT: A 368 ASP cc_start: 0.6731 (m-30) cc_final: 0.6443 (t0) REVERT: B 55 LEU cc_start: 0.7489 (mt) cc_final: 0.7091 (mp) REVERT: B 76 ASP cc_start: 0.6742 (t0) cc_final: 0.6436 (t0) REVERT: B 84 SER cc_start: 0.7320 (OUTLIER) cc_final: 0.7004 (p) REVERT: B 198 LEU cc_start: 0.7530 (mm) cc_final: 0.7301 (mp) REVERT: B 219 ARG cc_start: 0.7053 (mmt-90) cc_final: 0.6776 (mmt-90) REVERT: B 292 PHE cc_start: 0.7026 (OUTLIER) cc_final: 0.6699 (m-80) REVERT: B 314 ARG cc_start: 0.8231 (ttt180) cc_final: 0.7971 (ttp-170) REVERT: G 58 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6967 (mm-30) REVERT: N 109 ASP cc_start: 0.7792 (p0) cc_final: 0.7538 (p0) REVERT: R 161 ILE cc_start: 0.7727 (mm) cc_final: 0.7470 (mt) REVERT: R 266 MET cc_start: 0.4891 (ppp) cc_final: 0.4663 (ppp) outliers start: 31 outliers final: 24 residues processed: 220 average time/residue: 0.2492 time to fit residues: 71.3449 Evaluate side-chains 225 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET 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 260 LEU 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 146 LEU Chi-restraints excluded: chain B residue 218 CYS 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 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 247 MET Chi-restraints excluded: chain R residue 251 HIS Chi-restraints excluded: chain R residue 281 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 80 optimal weight: 0.0030 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 0.0970 chunk 85 optimal weight: 0.2980 chunk 24 optimal weight: 2.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 251 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8482 Z= 0.203 Angle : 0.607 8.603 11502 Z= 0.316 Chirality : 0.043 0.156 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.730 58.663 1155 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.10 % Allowed : 18.96 % Favored : 77.94 % 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: -1.16 (0.26), residues: 1030 helix: 0.65 (0.28), residues: 387 sheet: -1.40 (0.35), residues: 196 loop : -1.73 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.008 0.001 HIS R 251 PHE 0.032 0.002 PHE A 330 TYR 0.023 0.001 TYR R 253 ARG 0.009 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 226 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 198 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7511 (t) cc_final: 0.7309 (p) REVERT: A 42 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7675 (mtm-85) REVERT: A 313 ASP cc_start: 0.7223 (p0) cc_final: 0.6890 (p0) REVERT: A 368 ASP cc_start: 0.6773 (m-30) cc_final: 0.6466 (t0) REVERT: B 55 LEU cc_start: 0.7449 (mt) cc_final: 0.7055 (mp) REVERT: B 76 ASP cc_start: 0.6746 (t0) cc_final: 0.6399 (t0) REVERT: B 212 ASP cc_start: 0.6407 (m-30) cc_final: 0.6049 (m-30) REVERT: B 292 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6653 (m-80) REVERT: G 58 GLU cc_start: 0.7264 (mm-30) cc_final: 0.7040 (mm-30) REVERT: N 109 ASP cc_start: 0.7687 (p0) cc_final: 0.7425 (p0) REVERT: R 161 ILE cc_start: 0.7702 (mm) cc_final: 0.7450 (mt) REVERT: R 266 MET cc_start: 0.4874 (ppp) cc_final: 0.4666 (ppp) outliers start: 28 outliers final: 23 residues processed: 215 average time/residue: 0.2517 time to fit residues: 70.5634 Evaluate side-chains 219 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 260 LEU 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 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE 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 247 MET Chi-restraints excluded: chain R residue 281 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 0.0470 chunk 57 optimal weight: 5.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 230 ASN ** B 340 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 = 0.3937 r_free = 0.3937 target = 0.158349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141874 restraints weight = 11632.251| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.02 r_work: 0.3618 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2312 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= 0.226 Angle : 0.610 8.572 11502 Z= 0.317 Chirality : 0.044 0.154 1299 Planarity : 0.005 0.067 1459 Dihedral : 5.750 59.436 1155 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.99 % Allowed : 19.18 % Favored : 77.83 % 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: -1.15 (0.26), residues: 1030 helix: 0.68 (0.28), residues: 386 sheet: -1.37 (0.35), residues: 196 loop : -1.74 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS R 113 PHE 0.026 0.002 PHE A 330 TYR 0.022 0.001 TYR N 80 ARG 0.009 0.000 ARG A 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2329.10 seconds wall clock time: 43 minutes 12.36 seconds (2592.36 seconds total)