Starting phenix.real_space_refine on Tue Mar 3 21:15:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jvq_22510/03_2026/7jvq_22510.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jvq_22510/03_2026/7jvq_22510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jvq_22510/03_2026/7jvq_22510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jvq_22510/03_2026/7jvq_22510.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jvq_22510/03_2026/7jvq_22510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jvq_22510/03_2026/7jvq_22510.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5439 2.51 5 N 1449 2.21 5 O 1541 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8485 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2273 Classifications: {'peptide': 286} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1989 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} 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: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 214 Unusual residues: {'CLR': 5, 'OR9': 1, 'PLM': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Time building chain proxies: 1.80, per 1000 atoms: 0.21 Number of scatterers: 8485 At special positions: 0 Unit cell: (95.316, 98.358, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1541 8.00 N 1449 7.00 C 5439 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 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: 0.65 Conformation dependent library (CDL) restraints added in 302.9 milliseconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 43.6% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'R' and resid 21 through 51 removed outlier: 3.597A pdb=" N LEU R 25 " --> pdb=" O SER R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 57 removed outlier: 3.825A pdb=" N LYS R 57 " --> pdb=" O HIS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 removed outlier: 3.998A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 removed outlier: 3.752A pdb=" N LYS R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 127 removed outlier: 4.481A pdb=" N ILE R 98 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA R 101 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER R 110 " --> pdb=" O CYS R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 135 Processing helix chain 'R' and resid 136 through 162 removed outlier: 3.634A pdb=" N ALA R 140 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 191 through 203 Processing helix chain 'R' and resid 203 through 242 Processing helix chain 'R' and resid 265 through 298 Proline residue: R 287 - end of helix removed outlier: 4.092A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 309 through 331 removed outlier: 4.358A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU R 326 " --> pdb=" O ALA R 322 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 96 through 103 removed outlier: 3.661A pdb=" N CYS A 99 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.935A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 154 removed outlier: 4.100A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 164 removed outlier: 3.824A pdb=" N ASP A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 183 through 205 removed outlier: 4.241A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.571A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.579A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.947A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.580A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.770A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'N' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.351A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL A 86 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU A 45 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.599A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.596A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.144A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.896A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.634A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.758A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.731A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.473A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP N 50 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 430 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2456 1.34 - 1.46: 2093 1.46 - 1.59: 4046 1.59 - 1.71: 0 1.71 - 1.83: 76 Bond restraints: 8671 Sorted by residual: bond pdb=" C ILE R 205 " pdb=" N PRO R 206 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.52e+00 bond pdb=" C MET R 78 " pdb=" N PRO R 79 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.30e-02 5.92e+03 3.46e+00 bond pdb=" C ILE R 157 " pdb=" N PRO R 158 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.23e-02 6.61e+03 2.93e+00 bond pdb=" C THR R 136 " pdb=" N PRO R 137 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.87e+00 bond pdb=" C5 CLR R 502 " pdb=" C6 CLR R 502 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 8666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 11180 1.99 - 3.98: 516 3.98 - 5.97: 45 5.97 - 7.97: 15 7.97 - 9.96: 4 Bond angle restraints: 11760 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.99 -9.45 1.91e+00 2.74e-01 2.45e+01 angle pdb=" C ILE R 294 " pdb=" N LEU R 295 " pdb=" CA LEU R 295 " ideal model delta sigma weight residual 121.62 126.94 -5.32 1.57e+00 4.06e-01 1.15e+01 angle pdb=" N LEU R 286 " pdb=" CA LEU R 286 " pdb=" C LEU R 286 " ideal model delta sigma weight residual 109.81 116.93 -7.12 2.21e+00 2.05e-01 1.04e+01 angle pdb=" N LEU R 295 " pdb=" CA LEU R 295 " pdb=" C LEU R 295 " ideal model delta sigma weight residual 113.77 118.01 -4.24 1.32e+00 5.74e-01 1.03e+01 angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 123.93 128.85 -4.92 1.54e+00 4.22e-01 1.02e+01 ... (remaining 11755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.88: 5154 14.88 - 29.75: 223 29.75 - 44.63: 43 44.63 - 59.50: 2 59.50 - 74.38: 3 Dihedral angle restraints: 5425 sinusoidal: 2369 harmonic: 3056 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 163.67 -70.67 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CA MET R 135 " pdb=" C MET R 135 " pdb=" N THR R 136 " pdb=" CA THR R 136 " ideal model delta harmonic sigma weight residual 180.00 155.08 24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LEU B 198 " pdb=" C LEU B 198 " pdb=" N PHE B 199 " pdb=" CA PHE B 199 " ideal model delta harmonic sigma weight residual 180.00 156.51 23.49 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 5422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1149 0.084 - 0.168: 148 0.168 - 0.252: 20 0.252 - 0.336: 5 0.336 - 0.420: 6 Chirality restraints: 1328 Sorted by residual: chirality pdb=" C14 CLR R 506 " pdb=" C13 CLR R 506 " pdb=" C15 CLR R 506 " pdb=" C8 CLR R 506 " both_signs ideal model delta sigma weight residual False -2.32 -2.74 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 1325 not shown) Planarity restraints: 1462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 207 " 0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C VAL R 207 " -0.068 2.00e-02 2.50e+03 pdb=" O VAL R 207 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA R 208 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 218 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.27e+00 pdb=" C TYR R 218 " -0.053 2.00e-02 2.50e+03 pdb=" O TYR R 218 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG R 219 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 114 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.03e+00 pdb=" C LEU R 114 " 0.049 2.00e-02 2.50e+03 pdb=" O LEU R 114 " -0.018 2.00e-02 2.50e+03 pdb=" N CYS R 115 " -0.017 2.00e-02 2.50e+03 ... (remaining 1459 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1840 2.79 - 3.32: 7461 3.32 - 3.85: 13404 3.85 - 4.37: 15541 4.37 - 4.90: 27678 Nonbonded interactions: 65924 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.270 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.329 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.344 3.040 nonbonded pdb=" NE2 GLN B 75 " pdb=" O VAL B 100 " model vdw 2.358 3.120 ... (remaining 65919 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.820 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.820 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 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 0.057 8675 Z= 0.242 Angle : 0.924 9.957 11768 Z= 0.510 Chirality : 0.064 0.420 1328 Planarity : 0.007 0.060 1462 Dihedral : 8.730 74.381 3429 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.23), residues: 1031 helix: -1.60 (0.21), residues: 408 sheet: -0.36 (0.34), residues: 219 loop : -2.01 (0.26), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 237 TYR 0.018 0.002 TYR B 289 PHE 0.035 0.003 PHE R 141 TRP 0.031 0.003 TRP R 80 HIS 0.011 0.003 HIS R 53 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8671) covalent geometry : angle 0.92306 (11760) SS BOND : bond 0.00242 ( 4) SS BOND : angle 2.03592 ( 8) hydrogen bonds : bond 0.11045 ( 430) hydrogen bonds : angle 6.53123 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 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: 0 poor density : 216 time to evaluate : 0.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8101 (tp30) cc_final: 0.7818 (tm-30) REVERT: A 20 ARG cc_start: 0.7684 (tpt170) cc_final: 0.7189 (ttp-110) REVERT: A 35 GLN cc_start: 0.7724 (mt0) cc_final: 0.7425 (pt0) REVERT: A 145 LYS cc_start: 0.8362 (mttt) cc_final: 0.8147 (mttm) REVERT: A 202 THR cc_start: 0.7396 (m) cc_final: 0.6929 (p) REVERT: A 233 ASP cc_start: 0.8268 (m-30) cc_final: 0.7974 (m-30) REVERT: B 97 SER cc_start: 0.8212 (p) cc_final: 0.7884 (t) REVERT: B 118 ASP cc_start: 0.8247 (p0) cc_final: 0.8002 (p0) REVERT: B 137 ARG cc_start: 0.7430 (ttm-80) cc_final: 0.7078 (ttt180) REVERT: B 163 ASP cc_start: 0.7664 (p0) cc_final: 0.7377 (p0) REVERT: B 181 THR cc_start: 0.7655 (p) cc_final: 0.7234 (t) REVERT: B 239 ASN cc_start: 0.8232 (m-40) cc_final: 0.8031 (m-40) REVERT: B 246 ASP cc_start: 0.7711 (m-30) cc_final: 0.7404 (m-30) REVERT: N 105 ARG cc_start: 0.7686 (mtm180) cc_final: 0.7053 (pmt-80) outliers start: 0 outliers final: 3 residues processed: 216 average time/residue: 0.6481 time to fit residues: 147.3120 Evaluate side-chains 132 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 129 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain N residue 70 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN R 334 ASN A 64 HIS B 259 GLN B 295 ASN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.189396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.140456 restraints weight = 8516.053| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.29 r_work: 0.3419 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8675 Z= 0.276 Angle : 0.693 8.260 11768 Z= 0.372 Chirality : 0.047 0.176 1328 Planarity : 0.006 0.053 1462 Dihedral : 6.013 38.528 1528 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.22 % Allowed : 10.21 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.24), residues: 1031 helix: 0.88 (0.24), residues: 400 sheet: -0.24 (0.33), residues: 230 loop : -1.48 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 96 TYR 0.015 0.002 TYR N 94 PHE 0.021 0.003 PHE R 129 TRP 0.019 0.003 TRP B 339 HIS 0.010 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00647 ( 8671) covalent geometry : angle 0.69205 (11760) SS BOND : bond 0.00346 ( 4) SS BOND : angle 1.75519 ( 8) hydrogen bonds : bond 0.06579 ( 430) hydrogen bonds : angle 5.22650 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 78 MET cc_start: 0.7920 (mtt) cc_final: 0.7700 (mmt) REVERT: A 16 GLU cc_start: 0.7377 (tp30) cc_final: 0.7009 (tm-30) REVERT: A 20 ARG cc_start: 0.6953 (tpt170) cc_final: 0.6639 (ttp-110) REVERT: A 32 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7466 (ttpp) REVERT: A 42 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.6632 (mpp-170) REVERT: A 92 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7718 (mt-10) REVERT: A 102 ASP cc_start: 0.6000 (p0) cc_final: 0.5319 (p0) REVERT: A 167 PHE cc_start: 0.8293 (t80) cc_final: 0.8079 (t80) REVERT: A 169 ARG cc_start: 0.7500 (ttp-110) cc_final: 0.6646 (ttt180) REVERT: A 202 THR cc_start: 0.7271 (m) cc_final: 0.7034 (p) REVERT: A 217 CYS cc_start: 0.8294 (m) cc_final: 0.7897 (t) REVERT: A 226 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6374 (mtt90) REVERT: A 242 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7370 (tt0) REVERT: B 59 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7992 (t80) REVERT: B 97 SER cc_start: 0.7477 (p) cc_final: 0.7205 (t) REVERT: B 119 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8205 (p0) REVERT: B 134 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6409 (pmt170) REVERT: B 217 MET cc_start: 0.7843 (pmm) cc_final: 0.7596 (pmm) REVERT: B 303 ASP cc_start: 0.7264 (t0) cc_final: 0.6952 (m-30) REVERT: N 49 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.8080 (m) REVERT: N 105 ARG cc_start: 0.7454 (mtm180) cc_final: 0.6634 (pmt170) outliers start: 38 outliers final: 19 residues processed: 171 average time/residue: 0.5441 time to fit residues: 99.3433 Evaluate side-chains 140 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 39 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 91 optimal weight: 0.0020 chunk 69 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS B 176 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN B 295 ASN N 31 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.196468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.147865 restraints weight = 8295.855| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.31 r_work: 0.3499 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8675 Z= 0.117 Angle : 0.510 6.005 11768 Z= 0.273 Chirality : 0.041 0.148 1328 Planarity : 0.004 0.053 1462 Dihedral : 5.435 42.608 1528 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.33 % Allowed : 11.99 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.26), residues: 1031 helix: 2.15 (0.25), residues: 402 sheet: -0.08 (0.33), residues: 228 loop : -1.21 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 96 TYR 0.009 0.001 TYR B 85 PHE 0.011 0.001 PHE B 199 TRP 0.012 0.001 TRP A 133 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8671) covalent geometry : angle 0.50901 (11760) SS BOND : bond 0.00211 ( 4) SS BOND : angle 1.11543 ( 8) hydrogen bonds : bond 0.05110 ( 430) hydrogen bonds : angle 4.75617 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7577 (mm) REVERT: R 94 SER cc_start: 0.8622 (p) cc_final: 0.8380 (p) REVERT: A 21 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7043 (tm-30) REVERT: A 35 GLN cc_start: 0.7214 (mt0) cc_final: 0.6921 (pt0) REVERT: A 55 THR cc_start: 0.7646 (OUTLIER) cc_final: 0.7388 (p) REVERT: A 92 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7620 (mt-10) REVERT: A 169 ARG cc_start: 0.7121 (ttp-110) cc_final: 0.6273 (ttt180) REVERT: A 202 THR cc_start: 0.7223 (m) cc_final: 0.6876 (p) REVERT: A 217 CYS cc_start: 0.8301 (m) cc_final: 0.7911 (t) REVERT: A 242 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7372 (tt0) REVERT: B 13 GLN cc_start: 0.7040 (tp40) cc_final: 0.6426 (tp40) REVERT: B 97 SER cc_start: 0.7569 (p) cc_final: 0.7055 (m) REVERT: B 134 ARG cc_start: 0.7007 (pmt170) cc_final: 0.6090 (mmt-90) REVERT: B 186 ASP cc_start: 0.6473 (m-30) cc_final: 0.6236 (m-30) REVERT: B 217 MET cc_start: 0.7925 (pmm) cc_final: 0.7610 (pmm) REVERT: B 277 SER cc_start: 0.9035 (t) cc_final: 0.8776 (p) REVERT: B 303 ASP cc_start: 0.7256 (t0) cc_final: 0.6935 (m-30) REVERT: N 71 SER cc_start: 0.7735 (OUTLIER) cc_final: 0.7376 (p) REVERT: N 105 ARG cc_start: 0.7435 (mtm180) cc_final: 0.6687 (pmt-80) outliers start: 39 outliers final: 20 residues processed: 151 average time/residue: 0.5074 time to fit residues: 82.0509 Evaluate side-chains 135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.188649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.141235 restraints weight = 8508.986| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.41 r_work: 0.3353 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8675 Z= 0.208 Angle : 0.583 8.818 11768 Z= 0.312 Chirality : 0.044 0.166 1328 Planarity : 0.004 0.049 1462 Dihedral : 5.683 36.115 1524 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 5.55 % Allowed : 13.43 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.26), residues: 1031 helix: 2.14 (0.25), residues: 399 sheet: -0.33 (0.32), residues: 229 loop : -0.97 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 96 TYR 0.012 0.002 TYR A 191 PHE 0.019 0.002 PHE N 108 TRP 0.014 0.002 TRP R 123 HIS 0.007 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 8671) covalent geometry : angle 0.58017 (11760) SS BOND : bond 0.00283 ( 4) SS BOND : angle 2.22560 ( 8) hydrogen bonds : bond 0.05789 ( 430) hydrogen bonds : angle 4.78655 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 124 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7361 (mm) REVERT: R 94 SER cc_start: 0.8772 (p) cc_final: 0.8535 (p) REVERT: R 342 SER cc_start: 0.6932 (m) cc_final: 0.6725 (p) REVERT: A 20 ARG cc_start: 0.6865 (tpt170) cc_final: 0.6541 (ttp80) REVERT: A 42 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.6788 (mpp-170) REVERT: A 55 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7481 (p) REVERT: A 92 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7764 (mt-10) REVERT: A 169 ARG cc_start: 0.7044 (ttp-110) cc_final: 0.6201 (ttt180) REVERT: A 202 THR cc_start: 0.7318 (m) cc_final: 0.7025 (p) REVERT: A 217 CYS cc_start: 0.8277 (m) cc_final: 0.7860 (t) REVERT: A 242 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7384 (tt0) REVERT: A 244 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6773 (tp30) REVERT: B 13 GLN cc_start: 0.7059 (tp40) cc_final: 0.6570 (tp40) REVERT: B 59 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7765 (t80) REVERT: B 96 ARG cc_start: 0.7726 (mtp-110) cc_final: 0.7448 (ttm110) REVERT: B 134 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6636 (pmt170) REVERT: B 217 MET cc_start: 0.7886 (pmm) cc_final: 0.7507 (pmm) REVERT: B 277 SER cc_start: 0.9018 (t) cc_final: 0.8693 (p) REVERT: B 303 ASP cc_start: 0.7291 (t0) cc_final: 0.6920 (m-30) REVERT: N 49 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.8263 (m) REVERT: N 71 SER cc_start: 0.7646 (OUTLIER) cc_final: 0.7321 (p) REVERT: N 105 ARG cc_start: 0.7443 (mtm180) cc_final: 0.6520 (pmt-80) REVERT: N 110 VAL cc_start: 0.7864 (t) cc_final: 0.7658 (p) outliers start: 50 outliers final: 24 residues processed: 151 average time/residue: 0.5561 time to fit residues: 89.5098 Evaluate side-chains 147 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.193177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.145486 restraints weight = 8397.212| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.46 r_work: 0.3403 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8675 Z= 0.125 Angle : 0.533 10.081 11768 Z= 0.282 Chirality : 0.041 0.151 1328 Planarity : 0.003 0.050 1462 Dihedral : 5.603 51.394 1524 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.11 % Allowed : 15.32 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.26), residues: 1031 helix: 2.41 (0.25), residues: 399 sheet: -0.24 (0.32), residues: 228 loop : -0.90 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.008 0.001 TYR A 191 PHE 0.014 0.001 PHE R 51 TRP 0.012 0.001 TRP R 123 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8671) covalent geometry : angle 0.52198 (11760) SS BOND : bond 0.01066 ( 4) SS BOND : angle 4.17203 ( 8) hydrogen bonds : bond 0.05007 ( 430) hydrogen bonds : angle 4.56505 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7355 (mm) REVERT: R 94 SER cc_start: 0.8756 (p) cc_final: 0.8322 (t) REVERT: R 153 LEU cc_start: 0.7809 (mp) cc_final: 0.7570 (tt) REVERT: R 160 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.6475 (mp10) REVERT: A 21 GLU cc_start: 0.7396 (tm-30) cc_final: 0.7113 (tm-30) REVERT: A 42 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.6613 (mpp-170) REVERT: A 55 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7479 (p) REVERT: A 64 HIS cc_start: 0.6165 (OUTLIER) cc_final: 0.5527 (t-170) REVERT: A 92 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: A 169 ARG cc_start: 0.7009 (ttp-110) cc_final: 0.6170 (ttt180) REVERT: A 202 THR cc_start: 0.7257 (m) cc_final: 0.6928 (p) REVERT: A 217 CYS cc_start: 0.8281 (m) cc_final: 0.7856 (t) REVERT: A 238 MET cc_start: 0.7961 (ttp) cc_final: 0.7733 (ttp) REVERT: A 242 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7339 (tt0) REVERT: A 244 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: B 13 GLN cc_start: 0.7182 (tp40) cc_final: 0.6811 (tp40) REVERT: B 59 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7792 (t80) REVERT: B 96 ARG cc_start: 0.7701 (mtp-110) cc_final: 0.7443 (ttm110) REVERT: B 97 SER cc_start: 0.8065 (t) cc_final: 0.7753 (m) REVERT: B 134 ARG cc_start: 0.7115 (pmt170) cc_final: 0.6108 (mmt-90) REVERT: B 155 ASN cc_start: 0.6791 (t0) cc_final: 0.6530 (t0) REVERT: B 217 MET cc_start: 0.7984 (pmm) cc_final: 0.7600 (pmm) REVERT: B 277 SER cc_start: 0.8967 (t) cc_final: 0.8657 (p) REVERT: B 303 ASP cc_start: 0.7274 (t0) cc_final: 0.6871 (m-30) REVERT: N 71 SER cc_start: 0.7624 (OUTLIER) cc_final: 0.7419 (p) REVERT: N 105 ARG cc_start: 0.7328 (mtm180) cc_final: 0.6519 (pmt-80) outliers start: 37 outliers final: 18 residues processed: 144 average time/residue: 0.5812 time to fit residues: 89.1380 Evaluate side-chains 139 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 160 GLN Chi-restraints excluded: chain R residue 290 ILE Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN B 36 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 35 ASN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.190705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.144280 restraints weight = 8328.168| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.33 r_work: 0.3402 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8675 Z= 0.130 Angle : 0.514 8.607 11768 Z= 0.273 Chirality : 0.041 0.146 1328 Planarity : 0.003 0.050 1462 Dihedral : 5.393 43.772 1524 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.66 % Allowed : 14.98 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1031 helix: 2.50 (0.25), residues: 401 sheet: -0.24 (0.32), residues: 229 loop : -0.89 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.021 0.001 TYR N 60 PHE 0.011 0.001 PHE B 199 TRP 0.013 0.001 TRP R 123 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8671) covalent geometry : angle 0.50817 (11760) SS BOND : bond 0.00558 ( 4) SS BOND : angle 3.03891 ( 8) hydrogen bonds : bond 0.04914 ( 430) hydrogen bonds : angle 4.51141 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7421 (mm) REVERT: R 94 SER cc_start: 0.8740 (p) cc_final: 0.8342 (t) REVERT: R 160 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.6550 (mp10) REVERT: A 42 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.6663 (mpp-170) REVERT: A 55 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7521 (p) REVERT: A 64 HIS cc_start: 0.6200 (OUTLIER) cc_final: 0.5527 (t-170) REVERT: A 92 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7606 (mt-10) REVERT: A 169 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6216 (ttt180) REVERT: A 202 THR cc_start: 0.7237 (m) cc_final: 0.6941 (p) REVERT: A 217 CYS cc_start: 0.8300 (m) cc_final: 0.7863 (t) REVERT: A 242 GLN cc_start: 0.7784 (tm-30) cc_final: 0.7346 (tt0) REVERT: A 244 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6524 (mp0) REVERT: B 13 GLN cc_start: 0.7208 (tp40) cc_final: 0.6880 (tp40) REVERT: B 59 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7775 (t80) REVERT: B 76 ASP cc_start: 0.8656 (p0) cc_final: 0.8396 (p0) REVERT: B 96 ARG cc_start: 0.7715 (mtp-110) cc_final: 0.7421 (ttm110) REVERT: B 100 VAL cc_start: 0.8444 (t) cc_final: 0.8105 (p) REVERT: B 134 ARG cc_start: 0.6980 (pmt170) cc_final: 0.6009 (mmt-90) REVERT: B 155 ASN cc_start: 0.6850 (t0) cc_final: 0.6592 (t0) REVERT: B 196 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7633 (p) REVERT: B 217 MET cc_start: 0.7923 (pmm) cc_final: 0.7663 (pmm) REVERT: B 277 SER cc_start: 0.8987 (t) cc_final: 0.8653 (p) REVERT: B 303 ASP cc_start: 0.7256 (t0) cc_final: 0.6906 (m-30) REVERT: N 71 SER cc_start: 0.7690 (OUTLIER) cc_final: 0.7469 (p) REVERT: N 105 ARG cc_start: 0.7416 (mtm180) cc_final: 0.6625 (pmt-80) outliers start: 42 outliers final: 24 residues processed: 143 average time/residue: 0.5850 time to fit residues: 89.2167 Evaluate side-chains 143 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 160 GLN Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.192047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.145882 restraints weight = 8485.026| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.22 r_work: 0.3410 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8675 Z= 0.130 Angle : 0.514 7.648 11768 Z= 0.270 Chirality : 0.041 0.145 1328 Planarity : 0.003 0.048 1462 Dihedral : 5.321 40.470 1524 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.66 % Allowed : 15.09 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1031 helix: 2.57 (0.25), residues: 401 sheet: -0.29 (0.32), residues: 229 loop : -0.81 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.018 0.001 TYR N 60 PHE 0.011 0.001 PHE N 103 TRP 0.011 0.001 TRP R 123 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8671) covalent geometry : angle 0.50911 (11760) SS BOND : bond 0.00376 ( 4) SS BOND : angle 2.64986 ( 8) hydrogen bonds : bond 0.04864 ( 430) hydrogen bonds : angle 4.47023 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7427 (mm) REVERT: R 94 SER cc_start: 0.8765 (p) cc_final: 0.8369 (t) REVERT: A 21 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6955 (tm-30) REVERT: A 42 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.6676 (mpp-170) REVERT: A 55 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7531 (p) REVERT: A 64 HIS cc_start: 0.6207 (OUTLIER) cc_final: 0.5526 (t-170) REVERT: A 82 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7395 (t-170) REVERT: A 92 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: A 169 ARG cc_start: 0.6979 (ttp-110) cc_final: 0.6164 (ttt180) REVERT: A 202 THR cc_start: 0.7254 (m) cc_final: 0.6962 (p) REVERT: A 217 CYS cc_start: 0.8314 (m) cc_final: 0.7827 (t) REVERT: A 238 MET cc_start: 0.7961 (ttp) cc_final: 0.7727 (ttp) REVERT: A 242 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7318 (tt0) REVERT: A 244 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6586 (mp0) REVERT: B 59 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7887 (t80) REVERT: B 76 ASP cc_start: 0.8699 (p0) cc_final: 0.8432 (p0) REVERT: B 96 ARG cc_start: 0.7703 (mtp-110) cc_final: 0.7394 (ttm110) REVERT: B 100 VAL cc_start: 0.8413 (t) cc_final: 0.8089 (p) REVERT: B 134 ARG cc_start: 0.7020 (pmt170) cc_final: 0.6067 (mmt-90) REVERT: B 155 ASN cc_start: 0.6832 (t0) cc_final: 0.6563 (t0) REVERT: B 196 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7484 (p) REVERT: B 217 MET cc_start: 0.7929 (pmm) cc_final: 0.7668 (pmm) REVERT: B 277 SER cc_start: 0.8991 (t) cc_final: 0.8761 (m) REVERT: B 303 ASP cc_start: 0.7306 (t0) cc_final: 0.6975 (m-30) REVERT: N 105 ARG cc_start: 0.7520 (mtm180) cc_final: 0.6681 (pmt-80) outliers start: 42 outliers final: 27 residues processed: 138 average time/residue: 0.5655 time to fit residues: 83.2437 Evaluate side-chains 146 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 chunk 14 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.192922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146459 restraints weight = 8329.812| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.40 r_work: 0.3415 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8675 Z= 0.115 Angle : 0.487 6.919 11768 Z= 0.257 Chirality : 0.040 0.131 1328 Planarity : 0.003 0.047 1462 Dihedral : 5.086 37.942 1524 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 4.22 % Allowed : 15.87 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.26), residues: 1031 helix: 2.74 (0.25), residues: 402 sheet: -0.21 (0.32), residues: 230 loop : -0.74 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.009 0.001 TYR N 117 PHE 0.010 0.001 PHE N 108 TRP 0.012 0.001 TRP R 123 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 8671) covalent geometry : angle 0.48306 (11760) SS BOND : bond 0.00425 ( 4) SS BOND : angle 2.49689 ( 8) hydrogen bonds : bond 0.04636 ( 430) hydrogen bonds : angle 4.37273 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7412 (mm) REVERT: R 94 SER cc_start: 0.8754 (p) cc_final: 0.8372 (t) REVERT: A 42 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.6661 (mpp-170) REVERT: A 55 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7564 (p) REVERT: A 64 HIS cc_start: 0.6235 (OUTLIER) cc_final: 0.5504 (t-170) REVERT: A 82 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7321 (t-170) REVERT: A 92 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: A 169 ARG cc_start: 0.6875 (ttp-110) cc_final: 0.6099 (ttt180) REVERT: A 202 THR cc_start: 0.7210 (m) cc_final: 0.6913 (p) REVERT: A 217 CYS cc_start: 0.8292 (m) cc_final: 0.7817 (t) REVERT: A 242 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7320 (tt0) REVERT: A 244 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: B 59 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.7883 (t80) REVERT: B 76 ASP cc_start: 0.8692 (p0) cc_final: 0.8415 (p0) REVERT: B 96 ARG cc_start: 0.7716 (mtp-110) cc_final: 0.7406 (ttm110) REVERT: B 100 VAL cc_start: 0.8393 (t) cc_final: 0.8076 (p) REVERT: B 134 ARG cc_start: 0.7021 (pmt170) cc_final: 0.6015 (mmt-90) REVERT: B 155 ASN cc_start: 0.6847 (t0) cc_final: 0.6584 (t0) REVERT: B 196 THR cc_start: 0.7592 (OUTLIER) cc_final: 0.7333 (p) REVERT: B 217 MET cc_start: 0.7919 (pmm) cc_final: 0.7659 (pmm) REVERT: B 277 SER cc_start: 0.9025 (t) cc_final: 0.8790 (m) REVERT: B 303 ASP cc_start: 0.7375 (t0) cc_final: 0.6964 (m-30) REVERT: N 7 SER cc_start: 0.7196 (OUTLIER) cc_final: 0.6943 (p) REVERT: N 105 ARG cc_start: 0.7530 (mtm180) cc_final: 0.6686 (pmt-80) outliers start: 38 outliers final: 22 residues processed: 140 average time/residue: 0.5651 time to fit residues: 84.3279 Evaluate side-chains 140 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 61 optimal weight: 0.0060 chunk 20 optimal weight: 7.9990 chunk 75 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 49 optimal weight: 0.1980 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 119 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.193037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146697 restraints weight = 8389.091| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.43 r_work: 0.3477 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8675 Z= 0.107 Angle : 0.489 7.831 11768 Z= 0.256 Chirality : 0.040 0.136 1328 Planarity : 0.003 0.045 1462 Dihedral : 4.899 37.967 1524 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.88 % Allowed : 16.87 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.26), residues: 1031 helix: 2.78 (0.25), residues: 405 sheet: -0.14 (0.33), residues: 230 loop : -0.70 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.021 0.001 TYR N 60 PHE 0.009 0.001 PHE B 199 TRP 0.012 0.001 TRP R 123 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8671) covalent geometry : angle 0.48557 (11760) SS BOND : bond 0.00355 ( 4) SS BOND : angle 2.34431 ( 8) hydrogen bonds : bond 0.04477 ( 430) hydrogen bonds : angle 4.30643 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7512 (mm) REVERT: R 94 SER cc_start: 0.8734 (p) cc_final: 0.8345 (t) REVERT: A 21 GLU cc_start: 0.7342 (tm-30) cc_final: 0.6757 (tm-30) REVERT: A 42 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.6722 (mpp-170) REVERT: A 55 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7586 (p) REVERT: A 64 HIS cc_start: 0.6279 (OUTLIER) cc_final: 0.5568 (t-170) REVERT: A 82 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7673 (t-90) REVERT: A 169 ARG cc_start: 0.6795 (ttp-110) cc_final: 0.6034 (ttt180) REVERT: A 202 THR cc_start: 0.7270 (m) cc_final: 0.7047 (p) REVERT: A 217 CYS cc_start: 0.8336 (m) cc_final: 0.7885 (t) REVERT: A 242 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7373 (tt0) REVERT: A 244 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: B 59 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7974 (t80) REVERT: B 96 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7448 (ttm110) REVERT: B 100 VAL cc_start: 0.8433 (t) cc_final: 0.8135 (p) REVERT: B 134 ARG cc_start: 0.7033 (pmt170) cc_final: 0.5981 (mmt-90) REVERT: B 155 ASN cc_start: 0.6895 (t0) cc_final: 0.6634 (t0) REVERT: B 186 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6490 (m-30) REVERT: B 196 THR cc_start: 0.7600 (OUTLIER) cc_final: 0.7323 (p) REVERT: B 217 MET cc_start: 0.7980 (pmm) cc_final: 0.7670 (pmm) REVERT: B 303 ASP cc_start: 0.7404 (t0) cc_final: 0.7020 (m-30) REVERT: N 105 ARG cc_start: 0.7589 (mtm180) cc_final: 0.6760 (pmt-80) outliers start: 35 outliers final: 21 residues processed: 129 average time/residue: 0.5438 time to fit residues: 74.9829 Evaluate side-chains 135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.0570 chunk 62 optimal weight: 5.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.190256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.143204 restraints weight = 8433.754| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.43 r_work: 0.3488 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8675 Z= 0.138 Angle : 0.511 6.450 11768 Z= 0.269 Chirality : 0.041 0.177 1328 Planarity : 0.003 0.045 1462 Dihedral : 5.004 37.724 1524 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.33 % Allowed : 17.65 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.26), residues: 1031 helix: 2.56 (0.25), residues: 407 sheet: -0.17 (0.33), residues: 229 loop : -0.67 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 197 TYR 0.018 0.001 TYR N 60 PHE 0.010 0.001 PHE N 108 TRP 0.012 0.001 TRP R 123 HIS 0.004 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8671) covalent geometry : angle 0.50671 (11760) SS BOND : bond 0.00390 ( 4) SS BOND : angle 2.72586 ( 8) hydrogen bonds : bond 0.04842 ( 430) hydrogen bonds : angle 4.40536 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: R 35 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7560 (mm) REVERT: R 94 SER cc_start: 0.8747 (p) cc_final: 0.8368 (t) REVERT: A 42 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6885 (mpp-170) REVERT: A 55 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7561 (p) REVERT: A 64 HIS cc_start: 0.6323 (OUTLIER) cc_final: 0.5609 (t-170) REVERT: A 169 ARG cc_start: 0.6888 (ttp-110) cc_final: 0.6125 (ttt180) REVERT: A 202 THR cc_start: 0.7520 (m) cc_final: 0.7281 (p) REVERT: A 217 CYS cc_start: 0.8356 (m) cc_final: 0.7903 (t) REVERT: A 242 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7444 (tt0) REVERT: A 244 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.6803 (mp0) REVERT: B 13 GLN cc_start: 0.7341 (tp40) cc_final: 0.7112 (tp40) REVERT: B 59 TYR cc_start: 0.8749 (OUTLIER) cc_final: 0.8059 (t80) REVERT: B 96 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7505 (ttm110) REVERT: B 100 VAL cc_start: 0.8480 (t) cc_final: 0.8168 (p) REVERT: B 134 ARG cc_start: 0.7083 (pmt170) cc_final: 0.6150 (mmt-90) REVERT: B 155 ASN cc_start: 0.6969 (t0) cc_final: 0.6718 (t0) REVERT: B 196 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7341 (p) REVERT: B 217 MET cc_start: 0.8010 (pmm) cc_final: 0.7714 (pmm) REVERT: B 303 ASP cc_start: 0.7486 (t0) cc_final: 0.7135 (m-30) REVERT: N 105 ARG cc_start: 0.7641 (mtm180) cc_final: 0.6828 (pmt-80) outliers start: 30 outliers final: 22 residues processed: 133 average time/residue: 0.5498 time to fit residues: 78.2646 Evaluate side-chains 138 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 118 SER Chi-restraints excluded: chain R residue 155 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.186188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138389 restraints weight = 8500.781| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.49 r_work: 0.3320 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8675 Z= 0.234 Angle : 0.617 7.916 11768 Z= 0.325 Chirality : 0.045 0.230 1328 Planarity : 0.004 0.045 1462 Dihedral : 5.743 39.346 1524 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 3.55 % Allowed : 17.54 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1031 helix: 2.18 (0.24), residues: 407 sheet: -0.22 (0.33), residues: 225 loop : -0.74 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 314 TYR 0.021 0.002 TYR A 163 PHE 0.023 0.002 PHE N 108 TRP 0.015 0.002 TRP B 169 HIS 0.006 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00555 ( 8671) covalent geometry : angle 0.60984 (11760) SS BOND : bond 0.00487 ( 4) SS BOND : angle 3.61843 ( 8) hydrogen bonds : bond 0.05930 ( 430) hydrogen bonds : angle 4.73231 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3478.03 seconds wall clock time: 59 minutes 50.39 seconds (3590.39 seconds total)