Starting phenix.real_space_refine on Thu Feb 13 17:25:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vuh_32128/02_2025/7vuh_32128.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vuh_32128/02_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_32128/02_2025/7vuh_32128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vuh_32128/02_2025/7vuh_32128.map" model { file = "/net/cci-nas-00/data/ceres_data/7vuh_32128/02_2025/7vuh_32128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vuh_32128/02_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-5592/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: 4.90, per 1000 atoms: 0.59 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: 2.02 Conformation dependent library (CDL) restraints added in 891.3 milliseconds 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: 0.88 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: 2.34 Time building geometry restraints manager: 2.22 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: 0.940 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: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 20.770 Find NCS groups from input model: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.260 ------------------------------------------------------------------------------- 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 : 0.860 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: 0.2485 time to fit residues: 68.0641 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 : 0.952 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145556 restraints weight = 11530.950| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.90 r_work: 0.3662 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 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 : 0.893 Fit side-chains REVERT: A 49 ASP cc_start: 0.7360 (t0) cc_final: 0.6972 (t0) REVERT: A 221 MET cc_start: 0.8320 (ttp) cc_final: 0.8090 (ttp) REVERT: A 229 ASP cc_start: 0.7475 (p0) cc_final: 0.7174 (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: 0.7248 (p0) REVERT: A 330 PHE cc_start: 0.7623 (t80) cc_final: 0.7415 (t80) REVERT: A 360 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7559 (mm-30) REVERT: A 363 ARG cc_start: 0.7998 (tpp-160) cc_final: 0.7760 (tpp-160) REVERT: A 377 ASN cc_start: 0.7997 (m110) cc_final: 0.7567 (m-40) REVERT: B 43 ILE cc_start: 0.8446 (tp) cc_final: 0.8225 (pt) REVERT: B 277 SER cc_start: 0.8148 (p) cc_final: 0.7912 (p) REVERT: B 301 LYS cc_start: 0.7580 (mttm) cc_final: 0.7314 (mttm) REVERT: G 58 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7796 (mm-30) REVERT: R 247 MET cc_start: 0.5276 (ttm) cc_final: 0.3942 (mtt) REVERT: R 266 MET cc_start: 0.5808 (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: 0.7159 (mmp) outliers start: 7 outliers final: 6 residues processed: 212 average time/residue: 0.2472 time to fit residues: 68.4291 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 : 0.811 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 5.9990 chunk 81 optimal weight: 0.1980 chunk 5 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 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: 0.4360 ------------------------------------------------------------------------------- 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 = 0.3963 r_free = 0.3963 target = 0.160447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144623 restraints weight = 11813.640| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.89 r_work: 0.3654 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1425 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= 0.201 Angle : 0.550 5.912 11502 Z= 0.293 Chirality : 0.042 0.149 1299 Planarity : 0.005 0.062 1459 Dihedral : 5.328 53.395 1155 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.77 % Allowed : 13.86 % Favored : 84.37 % 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: -1.47 (0.26), residues: 1030 helix: 0.53 (0.29), residues: 378 sheet: -2.07 (0.32), residues: 193 loop : -1.72 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS R 113 PHE 0.014 0.001 PHE R 282 TYR 0.019 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: 16 poor density : 201 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7529 (p0) cc_final: 0.7220 (p0) REVERT: A 301 TYR cc_start: 0.6739 (m-80) cc_final: 0.6533 (t80) REVERT: A 313 ASP cc_start: 0.7514 (p0) cc_final: 0.7230 (p0) REVERT: A 330 PHE cc_start: 0.7613 (t80) cc_final: 0.7378 (t80) REVERT: A 360 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7479 (mm-30) REVERT: A 363 ARG cc_start: 0.7986 (tpp-160) cc_final: 0.7742 (tpp-160) REVERT: A 377 ASN cc_start: 0.7981 (m110) cc_final: 0.7492 (m-40) REVERT: B 234 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: B 318 LEU cc_start: 0.8157 (tp) cc_final: 0.7951 (tp) REVERT: G 58 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7794 (mm-30) REVERT: R 295 MET cc_start: 0.7489 (mmp) cc_final: 0.7244 (mmp) outliers start: 16 outliers final: 10 residues processed: 208 average time/residue: 0.2594 time to fit residues: 69.8381 Evaluate side-chains 201 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3933 r_free = 0.3933 target = 0.158153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.142401 restraints weight = 11761.452| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.87 r_work: 0.3633 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8482 Z= 0.301 Angle : 0.604 7.900 11502 Z= 0.319 Chirality : 0.044 0.163 1299 Planarity : 0.005 0.064 1459 Dihedral : 5.523 50.100 1155 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.77 % Allowed : 15.08 % Favored : 82.15 % 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: -1.46 (0.26), residues: 1030 helix: 0.53 (0.28), residues: 386 sheet: -1.93 (0.32), residues: 195 loop : -1.80 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.005 0.001 HIS R 180 PHE 0.017 0.002 PHE R 282 TYR 0.022 0.002 TYR R 253 ARG 0.007 0.001 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 224 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 199 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7517 (p0) cc_final: 0.7265 (p0) REVERT: A 301 TYR cc_start: 0.7056 (OUTLIER) cc_final: 0.6853 (t80) REVERT: A 313 ASP cc_start: 0.7541 (p0) cc_final: 0.7263 (p0) REVERT: A 330 PHE cc_start: 0.7642 (t80) cc_final: 0.7435 (t80) REVERT: A 360 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7540 (mm-30) REVERT: A 363 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7652 (tpp-160) REVERT: A 368 ASP cc_start: 0.7385 (m-30) cc_final: 0.6996 (t0) REVERT: B 55 LEU cc_start: 0.7779 (mt) cc_final: 0.7472 (mp) REVERT: B 84 SER cc_start: 0.7837 (OUTLIER) cc_final: 0.7526 (p) REVERT: G 58 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7738 (mm-30) REVERT: N 109 ASP cc_start: 0.7796 (p0) cc_final: 0.7589 (p0) REVERT: R 161 ILE cc_start: 0.7897 (mm) cc_final: 0.7646 (mt) REVERT: R 295 MET cc_start: 0.7536 (mmp) cc_final: 0.7307 (mmp) outliers start: 25 outliers final: 13 residues processed: 215 average time/residue: 0.2436 time to fit residues: 68.3770 Evaluate side-chains 209 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 301 TYR 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 155 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 200 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 9 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.159700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.142888 restraints weight = 11668.805| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.01 r_work: 0.3630 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8482 Z= 0.225 Angle : 0.577 6.724 11502 Z= 0.303 Chirality : 0.043 0.151 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.605 59.437 1155 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.22 % Allowed : 16.41 % Favored : 80.38 % 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: -1.32 (0.26), residues: 1030 helix: 0.65 (0.29), residues: 379 sheet: -1.75 (0.33), residues: 196 loop : -1.77 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.017 0.001 PHE R 282 TYR 0.020 0.001 TYR N 80 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 230 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7833 (t) cc_final: 0.7558 (p) REVERT: A 42 ARG cc_start: 0.8057 (mtm-85) cc_final: 0.7819 (mtm-85) REVERT: A 229 ASP cc_start: 0.7562 (p0) cc_final: 0.7286 (p0) REVERT: A 301 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.6655 (t80) REVERT: A 313 ASP cc_start: 0.7623 (p0) cc_final: 0.7309 (p0) REVERT: A 330 PHE cc_start: 0.7628 (t80) cc_final: 0.7426 (t80) REVERT: A 363 ARG cc_start: 0.7970 (tpp-160) cc_final: 0.7649 (tpp-160) REVERT: A 368 ASP cc_start: 0.7479 (m-30) cc_final: 0.7152 (t0) REVERT: B 55 LEU cc_start: 0.7784 (mt) cc_final: 0.7477 (mp) REVERT: B 84 SER cc_start: 0.7786 (OUTLIER) cc_final: 0.7459 (p) REVERT: B 212 ASP cc_start: 0.7346 (m-30) cc_final: 0.6824 (m-30) REVERT: B 219 ARG cc_start: 0.7824 (mmt-90) cc_final: 0.7457 (mmt-90) REVERT: B 292 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7140 (m-80) REVERT: G 58 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7726 (mm-30) REVERT: N 109 ASP cc_start: 0.7826 (p0) cc_final: 0.7563 (p0) REVERT: R 161 ILE cc_start: 0.7886 (mm) cc_final: 0.7631 (mt) REVERT: R 295 MET cc_start: 0.7438 (mmp) cc_final: 0.7195 (mmp) outliers start: 29 outliers final: 16 residues processed: 217 average time/residue: 0.2425 time to fit residues: 68.9006 Evaluate side-chains 217 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 301 TYR 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 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 74 ILE 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: 0.9980 chunk 96 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.157818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.141090 restraints weight = 11759.117| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.03 r_work: 0.3606 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8482 Z= 0.242 Angle : 0.583 6.577 11502 Z= 0.306 Chirality : 0.043 0.160 1299 Planarity : 0.005 0.067 1459 Dihedral : 5.487 54.484 1155 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.10 % Allowed : 17.18 % Favored : 79.71 % 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: -1.25 (0.26), residues: 1030 helix: 0.65 (0.28), residues: 386 sheet: -1.64 (0.34), residues: 196 loop : -1.73 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.019 0.001 PHE R 282 TYR 0.022 0.001 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 228 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 0.841 Fit side-chains REVERT: A 36 VAL cc_start: 0.7801 (t) cc_final: 0.7543 (p) REVERT: A 42 ARG cc_start: 0.8054 (mtm-85) cc_final: 0.7815 (mtm-85) REVERT: A 229 ASP cc_start: 0.7544 (p0) cc_final: 0.7292 (p0) REVERT: A 301 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.6749 (t80) REVERT: A 313 ASP cc_start: 0.7630 (p0) cc_final: 0.7311 (p0) REVERT: A 363 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7601 (tpp-160) REVERT: A 368 ASP cc_start: 0.7467 (m-30) cc_final: 0.7094 (t0) REVERT: B 55 LEU cc_start: 0.7791 (mt) cc_final: 0.7479 (mp) REVERT: B 84 SER cc_start: 0.7836 (OUTLIER) cc_final: 0.7448 (p) REVERT: B 219 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.7444 (mmt-90) REVERT: B 292 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7141 (m-80) REVERT: G 58 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7737 (mm-30) REVERT: N 109 ASP cc_start: 0.7871 (p0) cc_final: 0.7520 (p0) REVERT: R 161 ILE cc_start: 0.7877 (mm) cc_final: 0.7632 (mt) REVERT: R 295 MET cc_start: 0.7421 (mmp) cc_final: 0.7198 (mmp) outliers start: 28 outliers final: 18 residues processed: 215 average time/residue: 0.2413 time to fit residues: 68.0454 Evaluate side-chains 220 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 301 TYR 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 89 LYS 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 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: 0.9980 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3942 r_free = 0.3942 target = 0.158715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142294 restraints weight = 11665.192| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.94 r_work: 0.3630 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8482 Z= 0.263 Angle : 0.591 6.853 11502 Z= 0.312 Chirality : 0.044 0.160 1299 Planarity : 0.005 0.067 1459 Dihedral : 5.442 49.692 1155 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.44 % Allowed : 16.96 % 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: -1.22 (0.26), residues: 1030 helix: 0.63 (0.28), residues: 386 sheet: -1.61 (0.34), residues: 196 loop : -1.69 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.021 0.002 PHE R 282 TYR 0.022 0.002 TYR N 80 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 237 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 206 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7798 (t) cc_final: 0.7546 (p) REVERT: A 42 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7816 (mtm-85) REVERT: A 229 ASP cc_start: 0.7545 (p0) cc_final: 0.7325 (p0) REVERT: A 313 ASP cc_start: 0.7604 (p0) cc_final: 0.7269 (p0) REVERT: A 363 ARG cc_start: 0.7958 (tpp-160) cc_final: 0.7626 (tpp-160) REVERT: B 55 LEU cc_start: 0.7788 (mt) cc_final: 0.7381 (mp) REVERT: B 76 ASP cc_start: 0.7277 (t0) cc_final: 0.7008 (t0) REVERT: B 84 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7457 (p) REVERT: B 292 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: N 109 ASP cc_start: 0.7921 (p0) cc_final: 0.7701 (p0) REVERT: R 161 ILE cc_start: 0.7873 (mm) cc_final: 0.7620 (mt) REVERT: R 247 MET cc_start: 0.5422 (ttm) cc_final: 0.4872 (ttt) REVERT: R 252 LEU cc_start: 0.7731 (tp) cc_final: 0.7521 (tt) REVERT: R 266 MET cc_start: 0.5620 (ptp) cc_final: 0.5412 (ppp) REVERT: R 273 LEU cc_start: 0.7593 (mt) cc_final: 0.7317 (mt) REVERT: R 295 MET cc_start: 0.7414 (mmp) cc_final: 0.7190 (mmp) outliers start: 31 outliers final: 21 residues processed: 225 average time/residue: 0.2470 time to fit residues: 72.5914 Evaluate side-chains 227 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 229 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 74 ILE 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 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: 1.9990 chunk 96 optimal weight: 0.0770 chunk 44 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 73 optimal weight: 0.0170 chunk 8 optimal weight: 0.9980 chunk 88 optimal weight: 0.0570 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 overall best weight: 0.2694 ------------------------------------------------------------------------------- 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** R 281 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.159623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.142889 restraints weight = 11955.583| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.05 r_work: 0.3640 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.2216 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= 0.164 Angle : 0.551 6.270 11502 Z= 0.288 Chirality : 0.042 0.148 1299 Planarity : 0.004 0.066 1459 Dihedral : 5.163 44.201 1155 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.88 % Allowed : 17.96 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.26), residues: 1030 helix: 0.72 (0.28), residues: 381 sheet: -1.37 (0.35), residues: 194 loop : -1.60 (0.28), residues: 455 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 0.017 0.001 PHE A 330 TYR 0.020 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 226 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7778 (t) cc_final: 0.7554 (p) REVERT: A 42 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7791 (mtm-85) REVERT: A 229 ASP cc_start: 0.7527 (p0) cc_final: 0.7242 (p0) REVERT: A 313 ASP cc_start: 0.7624 (p0) cc_final: 0.7334 (p0) REVERT: A 360 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7470 (mm-30) REVERT: A 363 ARG cc_start: 0.7962 (tpp-160) cc_final: 0.7676 (tpp-160) REVERT: A 368 ASP cc_start: 0.7420 (m-30) cc_final: 0.7074 (t0) REVERT: B 55 LEU cc_start: 0.7714 (mt) cc_final: 0.7357 (mp) REVERT: B 76 ASP cc_start: 0.7221 (t0) cc_final: 0.6888 (t0) REVERT: B 212 ASP cc_start: 0.7228 (m-30) cc_final: 0.6947 (m-30) REVERT: B 292 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7137 (m-80) REVERT: N 109 ASP cc_start: 0.7845 (p0) cc_final: 0.7600 (p0) REVERT: R 48 VAL cc_start: 0.6953 (t) cc_final: 0.6734 (p) REVERT: R 161 ILE cc_start: 0.7825 (mm) cc_final: 0.7584 (mt) REVERT: R 252 LEU cc_start: 0.7510 (tp) cc_final: 0.7302 (tt) REVERT: R 295 MET cc_start: 0.7385 (mmp) cc_final: 0.7141 (mmp) outliers start: 26 outliers final: 17 residues processed: 216 average time/residue: 0.2523 time to fit residues: 70.9148 Evaluate side-chains 212 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 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 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 234 PHE 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 74 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 5 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 81 optimal weight: 0.6980 chunk 82 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 230 ASN ** B 340 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 = 0.3948 r_free = 0.3948 target = 0.159076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142877 restraints weight = 11855.532| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.94 r_work: 0.3650 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3505 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8482 Z= 0.234 Angle : 0.589 7.013 11502 Z= 0.308 Chirality : 0.043 0.153 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.281 43.283 1155 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 3.10 % Allowed : 18.29 % 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: -1.09 (0.26), residues: 1030 helix: 0.64 (0.28), residues: 387 sheet: -1.34 (0.35), residues: 194 loop : -1.61 (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 0.040 0.002 PHE A 330 TYR 0.023 0.001 TYR N 80 ARG 0.008 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 230 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 36 VAL cc_start: 0.7777 (t) cc_final: 0.7549 (p) REVERT: A 229 ASP cc_start: 0.7559 (p0) cc_final: 0.7279 (p0) REVERT: A 313 ASP cc_start: 0.7592 (p0) cc_final: 0.7271 (p0) REVERT: A 360 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7425 (mm-30) REVERT: A 363 ARG cc_start: 0.7967 (tpp-160) cc_final: 0.7624 (tpp-160) REVERT: A 368 ASP cc_start: 0.7349 (m-30) cc_final: 0.7016 (t0) REVERT: B 212 ASP cc_start: 0.7255 (m-30) cc_final: 0.6833 (m-30) REVERT: B 292 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: N 109 ASP cc_start: 0.7913 (p0) cc_final: 0.7651 (p0) REVERT: R 161 ILE cc_start: 0.7831 (mm) cc_final: 0.7596 (mt) REVERT: R 295 MET cc_start: 0.7376 (mmp) cc_final: 0.7156 (mmp) outliers start: 28 outliers final: 20 residues processed: 219 average time/residue: 0.2401 time to fit residues: 68.5209 Evaluate side-chains 222 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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 327 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 74 ILE 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 266 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** 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 = 0.3947 r_free = 0.3947 target = 0.159136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.142828 restraints weight = 11800.556| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.95 r_work: 0.3629 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2319 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= 0.254 Angle : 0.616 8.837 11502 Z= 0.321 Chirality : 0.044 0.154 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.475 49.278 1155 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.55 % Allowed : 19.29 % Favored : 78.16 % 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: 0.60 (0.28), residues: 387 sheet: -1.39 (0.34), residues: 196 loop : -1.64 (0.28), residues: 447 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 0.038 0.002 PHE A 330 TYR 0.023 0.001 TYR N 80 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 225 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.861 Fit side-chains REVERT: A 36 VAL cc_start: 0.7763 (t) cc_final: 0.7520 (p) REVERT: A 229 ASP cc_start: 0.7603 (p0) cc_final: 0.7342 (p0) REVERT: A 313 ASP cc_start: 0.7616 (p0) cc_final: 0.7291 (p0) REVERT: A 363 ARG cc_start: 0.7969 (tpp-160) cc_final: 0.7621 (tpp-160) REVERT: A 368 ASP cc_start: 0.7407 (m-30) cc_final: 0.7052 (t0) REVERT: B 212 ASP cc_start: 0.7244 (m-30) cc_final: 0.6782 (m-30) REVERT: B 292 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: N 109 ASP cc_start: 0.7923 (p0) cc_final: 0.7666 (p0) REVERT: R 161 ILE cc_start: 0.7828 (mm) cc_final: 0.7575 (mt) REVERT: R 273 LEU cc_start: 0.7588 (mt) cc_final: 0.7310 (mt) REVERT: R 295 MET cc_start: 0.7417 (mmp) cc_final: 0.7128 (mmp) outliers start: 23 outliers final: 21 residues processed: 219 average time/residue: 0.2390 time to fit residues: 68.4788 Evaluate side-chains 223 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 239 ASN 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 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 327 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain R residue 74 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 0.0470 chunk 6 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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 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 = 0.3957 r_free = 0.3957 target = 0.159893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.143351 restraints weight = 11896.178| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.04 r_work: 0.3645 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2353 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= 0.208 Angle : 0.587 6.897 11502 Z= 0.309 Chirality : 0.043 0.153 1299 Planarity : 0.005 0.066 1459 Dihedral : 5.454 50.756 1155 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.66 % Allowed : 19.29 % 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: -1.11 (0.26), residues: 1030 helix: 0.58 (0.28), residues: 387 sheet: -1.35 (0.35), residues: 196 loop : -1.59 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS R 113 PHE 0.021 0.002 PHE R 282 TYR 0.021 0.001 TYR N 80 ARG 0.009 0.001 ARG A 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4597.54 seconds wall clock time: 82 minutes 8.34 seconds (4928.34 seconds total)