Starting phenix.real_space_refine on Thu Mar 13 08:17:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jvq_22510/03_2025/7jvq_22510.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jvq_22510/03_2025/7jvq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jvq_22510/03_2025/7jvq_22510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jvq_22510/03_2025/7jvq_22510.map" model { file = "/net/cci-nas-00/data/ceres_data/7jvq_22510/03_2025/7jvq_22510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jvq_22510/03_2025/7jvq_22510.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.26, per 1000 atoms: 0.62 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: 2.29 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.84 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: 2.27 Time building geometry restraints manager: 2.64 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.950 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.340 ------------------------------------------------------------------------------- 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 8671 Z= 0.289 Angle : 0.923 9.957 11760 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 : 4.24 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.031 0.003 TRP R 80 HIS 0.011 0.003 HIS R 53 PHE 0.035 0.003 PHE R 141 TYR 0.018 0.002 TYR B 289 ARG 0.009 0.001 ARG A 237 *********************** 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 : 0.801 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: 1.3214 time to fit residues: 302.0685 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 : 0.974 ------------------------------------------------------------------------------- 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 85 optimal weight: 6.9990 chunk 76 optimal weight: 0.0470 chunk 42 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 41 ASN R 327 ASN R 334 ASN A 64 HIS B 259 GLN B 340 ASN N 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.205170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.158011 restraints weight = 8299.257| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.48 r_work: 0.3548 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8671 Z= 0.163 Angle : 0.537 9.000 11760 Z= 0.286 Chirality : 0.041 0.144 1328 Planarity : 0.005 0.049 1462 Dihedral : 5.328 33.863 1528 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.33 % Allowed : 11.21 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.25), residues: 1031 helix: 1.18 (0.25), residues: 411 sheet: 0.08 (0.34), residues: 230 loop : -1.49 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 133 HIS 0.005 0.001 HIS A 209 PHE 0.013 0.001 PHE R 141 TYR 0.014 0.001 TYR A 163 ARG 0.010 0.001 ARG B 96 *********************** 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 181 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 278 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5934 (ttm) REVERT: A 20 ARG cc_start: 0.6819 (tpt170) cc_final: 0.6505 (ttp-110) REVERT: A 35 GLN cc_start: 0.7134 (mt0) cc_final: 0.6865 (pt0) REVERT: A 92 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7366 (mt-10) REVERT: A 93 ARG cc_start: 0.7893 (ptp-170) cc_final: 0.7687 (ptp-170) REVERT: A 169 ARG cc_start: 0.7335 (ttp-110) cc_final: 0.6502 (ttt180) REVERT: A 202 THR cc_start: 0.6891 (m) cc_final: 0.6652 (p) REVERT: B 59 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.7864 (t80) REVERT: B 97 SER cc_start: 0.7758 (p) cc_final: 0.7504 (t) REVERT: B 134 ARG cc_start: 0.6711 (pmt170) cc_final: 0.5659 (mmt-90) REVERT: B 181 THR cc_start: 0.7332 (p) cc_final: 0.7101 (t) REVERT: B 217 MET cc_start: 0.7885 (pmm) cc_final: 0.7665 (pmm) REVERT: N 105 ARG cc_start: 0.7340 (mtm180) cc_final: 0.6555 (pmt-80) outliers start: 30 outliers final: 18 residues processed: 171 average time/residue: 1.0638 time to fit residues: 194.9110 Evaluate side-chains 138 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 278 MET 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 92 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL 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 51 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 75 optimal weight: 0.0060 chunk 77 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN B 340 ASN N 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.201098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.155146 restraints weight = 8456.338| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.19 r_work: 0.3691 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8671 Z= 0.191 Angle : 0.516 7.487 11760 Z= 0.278 Chirality : 0.041 0.143 1328 Planarity : 0.004 0.044 1462 Dihedral : 5.004 30.788 1528 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.44 % Allowed : 12.32 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.26), residues: 1031 helix: 2.02 (0.25), residues: 412 sheet: -0.00 (0.32), residues: 230 loop : -1.21 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 123 HIS 0.004 0.001 HIS A 209 PHE 0.012 0.001 PHE B 151 TYR 0.015 0.001 TYR N 60 ARG 0.004 0.000 ARG B 96 *********************** 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 162 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 122 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7516 (mm) REVERT: R 94 SER cc_start: 0.8344 (p) cc_final: 0.8073 (p) REVERT: R 275 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.8285 (m) REVERT: A 20 ARG cc_start: 0.7030 (tpt170) cc_final: 0.6770 (ttp-110) REVERT: A 21 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7051 (tm-30) REVERT: A 42 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.6704 (mpp-170) REVERT: A 55 THR cc_start: 0.7637 (OUTLIER) cc_final: 0.7418 (p) REVERT: A 92 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7668 (mt-10) REVERT: A 169 ARG cc_start: 0.7329 (ttp-110) cc_final: 0.6420 (ttt180) REVERT: A 202 THR cc_start: 0.7391 (m) cc_final: 0.7126 (p) REVERT: A 217 CYS cc_start: 0.8370 (m) cc_final: 0.8064 (t) REVERT: A 226 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.6964 (mtt90) REVERT: A 242 GLN cc_start: 0.7758 (tm-30) cc_final: 0.7430 (tm-30) REVERT: B 13 GLN cc_start: 0.7081 (tp40) cc_final: 0.6493 (tp40) REVERT: B 59 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.8012 (t80) REVERT: B 97 SER cc_start: 0.7674 (p) cc_final: 0.7132 (m) REVERT: B 134 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6142 (pmt170) REVERT: B 163 ASP cc_start: 0.7544 (p0) cc_final: 0.7305 (p0) REVERT: B 217 MET cc_start: 0.8017 (pmm) cc_final: 0.7755 (pmm) REVERT: N 105 ARG cc_start: 0.7541 (mtm180) cc_final: 0.6816 (pmt-80) outliers start: 40 outliers final: 21 residues processed: 147 average time/residue: 1.3555 time to fit residues: 214.3841 Evaluate side-chains 142 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 86 ILE Chi-restraints excluded: chain R residue 118 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 92 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 201 SER 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 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 245 SER 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 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 91 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.200739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.153477 restraints weight = 8383.681| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.43 r_work: 0.3496 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8671 Z= 0.160 Angle : 0.480 6.086 11760 Z= 0.257 Chirality : 0.040 0.136 1328 Planarity : 0.004 0.059 1462 Dihedral : 4.731 30.204 1526 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.66 % Allowed : 12.87 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1031 helix: 2.53 (0.25), residues: 402 sheet: -0.03 (0.33), residues: 230 loop : -0.97 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 123 HIS 0.004 0.001 HIS A 209 PHE 0.014 0.001 PHE R 51 TYR 0.020 0.001 TYR N 60 ARG 0.014 0.000 ARG B 96 *********************** 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 166 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7208 (mm) REVERT: R 94 SER cc_start: 0.8550 (p) cc_final: 0.8313 (p) REVERT: R 233 ARG cc_start: 0.6995 (ttm-80) cc_final: 0.6739 (ttp80) REVERT: R 278 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5991 (ttm) REVERT: A 20 ARG cc_start: 0.6795 (tpt170) cc_final: 0.6489 (ttp-110) REVERT: A 38 ARG cc_start: 0.7727 (mpt180) cc_final: 0.7464 (mmt-90) REVERT: A 42 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.6379 (mpp-170) REVERT: A 55 THR cc_start: 0.7456 (OUTLIER) cc_final: 0.7250 (p) REVERT: A 92 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7558 (mt-10) REVERT: A 169 ARG cc_start: 0.7054 (ttp-110) cc_final: 0.6208 (ttt180) REVERT: A 202 THR cc_start: 0.7046 (m) cc_final: 0.6801 (p) REVERT: A 217 CYS cc_start: 0.8254 (m) cc_final: 0.7883 (t) REVERT: A 233 ASP cc_start: 0.7732 (m-30) cc_final: 0.7519 (m-30) REVERT: A 242 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7230 (tt0) REVERT: B 13 GLN cc_start: 0.7155 (tp40) cc_final: 0.6490 (tp40) REVERT: B 97 SER cc_start: 0.7314 (p) cc_final: 0.6829 (m) REVERT: B 134 ARG cc_start: 0.6948 (pmt170) cc_final: 0.5939 (mmt-90) REVERT: B 217 MET cc_start: 0.7875 (pmm) cc_final: 0.7514 (pmm) REVERT: B 277 SER cc_start: 0.9062 (t) cc_final: 0.8782 (p) REVERT: N 105 ARG cc_start: 0.7441 (mtm180) cc_final: 0.6616 (pmt-80) outliers start: 42 outliers final: 18 residues processed: 147 average time/residue: 1.1410 time to fit residues: 179.6939 Evaluate side-chains 131 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 278 MET 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 75 GLN 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 B residue 114 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 245 SER 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 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL 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 25 optimal weight: 0.5980 chunk 81 optimal weight: 8.9990 chunk 86 optimal weight: 0.0470 chunk 32 optimal weight: 0.4980 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 0.0870 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.201158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.155816 restraints weight = 8216.992| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.16 r_work: 0.3675 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8671 Z= 0.130 Angle : 0.466 7.169 11760 Z= 0.248 Chirality : 0.039 0.135 1328 Planarity : 0.003 0.048 1462 Dihedral : 4.482 29.940 1524 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.22 % Allowed : 14.87 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1031 helix: 2.74 (0.25), residues: 402 sheet: 0.06 (0.33), residues: 230 loop : -0.95 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 123 HIS 0.003 0.001 HIS A 82 PHE 0.011 0.001 PHE B 199 TYR 0.019 0.001 TYR A 163 ARG 0.005 0.000 ARG B 96 *********************** 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 142 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7409 (mm) REVERT: A 21 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6998 (tm-30) REVERT: A 32 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7363 (ttpp) REVERT: A 55 THR cc_start: 0.7557 (OUTLIER) cc_final: 0.7353 (p) REVERT: A 60 MET cc_start: 0.5329 (OUTLIER) cc_final: 0.5092 (pmt) REVERT: A 92 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7649 (mt-10) REVERT: A 169 ARG cc_start: 0.7097 (ttp-110) cc_final: 0.6282 (ttt180) REVERT: A 202 THR cc_start: 0.7119 (m) cc_final: 0.6855 (p) REVERT: A 217 CYS cc_start: 0.8363 (m) cc_final: 0.8028 (t) REVERT: A 233 ASP cc_start: 0.7841 (m-30) cc_final: 0.7612 (m-30) REVERT: A 242 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7331 (tt0) REVERT: B 13 GLN cc_start: 0.7226 (tp40) cc_final: 0.6893 (tp40) REVERT: B 96 ARG cc_start: 0.7853 (mtp-110) cc_final: 0.7620 (ttm110) REVERT: B 97 SER cc_start: 0.7523 (p) cc_final: 0.7057 (m) REVERT: B 134 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.5921 (mmt-90) REVERT: B 217 MET cc_start: 0.7998 (pmm) cc_final: 0.7701 (pmm) REVERT: N 105 ARG cc_start: 0.7513 (mtm180) cc_final: 0.6810 (pmt-80) outliers start: 29 outliers final: 18 residues processed: 131 average time/residue: 1.2118 time to fit residues: 169.6458 Evaluate side-chains 121 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 32 LYS 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 171 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain G residue 27 ARG Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 33 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 42 optimal weight: 0.0000 chunk 85 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.192685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.145179 restraints weight = 8334.779| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.47 r_work: 0.3403 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8671 Z= 0.255 Angle : 0.529 7.056 11760 Z= 0.285 Chirality : 0.042 0.141 1328 Planarity : 0.004 0.048 1462 Dihedral : 4.805 29.510 1524 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.44 % Allowed : 14.87 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1031 helix: 2.56 (0.25), residues: 403 sheet: -0.10 (0.33), residues: 229 loop : -0.90 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 123 HIS 0.006 0.002 HIS B 54 PHE 0.015 0.002 PHE N 108 TYR 0.011 0.002 TYR A 191 ARG 0.007 0.001 ARG R 233 *********************** 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 161 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7239 (mm) REVERT: R 94 SER cc_start: 0.8692 (p) cc_final: 0.8240 (t) REVERT: A 32 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7250 (ttpp) REVERT: A 42 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.6644 (mpp-170) REVERT: A 55 THR cc_start: 0.7544 (OUTLIER) cc_final: 0.7331 (p) REVERT: A 60 MET cc_start: 0.5127 (OUTLIER) cc_final: 0.4366 (ptp) REVERT: A 64 HIS cc_start: 0.6204 (OUTLIER) cc_final: 0.5546 (t-170) REVERT: A 92 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7679 (mt-10) REVERT: A 169 ARG cc_start: 0.7139 (ttp-110) cc_final: 0.6290 (ttt180) REVERT: A 202 THR cc_start: 0.7110 (m) cc_final: 0.6882 (p) REVERT: A 217 CYS cc_start: 0.8247 (m) cc_final: 0.7827 (t) REVERT: A 242 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7353 (tt0) REVERT: B 96 ARG cc_start: 0.7684 (mtp-110) cc_final: 0.7414 (ttm110) REVERT: B 97 SER cc_start: 0.7271 (p) cc_final: 0.6855 (m) REVERT: B 134 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6597 (pmt170) REVERT: B 186 ASP cc_start: 0.7030 (m-30) cc_final: 0.6824 (m-30) REVERT: B 217 MET cc_start: 0.7971 (pmm) cc_final: 0.7644 (pmm) REVERT: B 303 ASP cc_start: 0.7167 (t0) cc_final: 0.6796 (m-30) REVERT: N 7 SER cc_start: 0.7268 (OUTLIER) cc_final: 0.7040 (p) REVERT: N 105 ARG cc_start: 0.7480 (mtm180) cc_final: 0.6677 (pmt-80) outliers start: 40 outliers final: 21 residues processed: 147 average time/residue: 1.0231 time to fit residues: 162.2753 Evaluate side-chains 145 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 275 SER Chi-restraints excluded: chain R residue 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 60 MET 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 B residue 67 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 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 59 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 1 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 66 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 28 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.193559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146342 restraints weight = 8358.325| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.49 r_work: 0.3413 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8671 Z= 0.202 Angle : 0.511 8.678 11760 Z= 0.271 Chirality : 0.041 0.139 1328 Planarity : 0.003 0.049 1462 Dihedral : 4.807 29.178 1524 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.88 % Allowed : 15.54 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.26), residues: 1031 helix: 2.60 (0.25), residues: 404 sheet: -0.17 (0.32), residues: 229 loop : -0.71 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 123 HIS 0.004 0.001 HIS A 209 PHE 0.015 0.001 PHE R 51 TYR 0.020 0.001 TYR N 60 ARG 0.004 0.000 ARG R 227 *********************** 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 144 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7271 (mm) REVERT: R 94 SER cc_start: 0.8669 (p) cc_final: 0.8174 (t) REVERT: A 21 GLU cc_start: 0.7452 (tm-30) cc_final: 0.7068 (tm-30) REVERT: A 32 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7215 (ttpp) REVERT: A 42 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.6633 (mpp-170) REVERT: A 55 THR cc_start: 0.7671 (OUTLIER) cc_final: 0.7450 (p) REVERT: A 60 MET cc_start: 0.5084 (OUTLIER) cc_final: 0.4232 (ptp) REVERT: A 64 HIS cc_start: 0.6275 (OUTLIER) cc_final: 0.5548 (t-170) REVERT: A 92 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7694 (mt-10) REVERT: A 169 ARG cc_start: 0.6927 (ttp-110) cc_final: 0.6106 (ttt180) REVERT: A 202 THR cc_start: 0.7083 (m) cc_final: 0.6830 (p) REVERT: A 217 CYS cc_start: 0.8237 (m) cc_final: 0.7950 (m) REVERT: A 242 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7268 (tt0) REVERT: A 244 GLU cc_start: 0.6925 (tp30) cc_final: 0.6393 (mp0) REVERT: B 96 ARG cc_start: 0.7752 (mtp-110) cc_final: 0.7463 (ttm110) REVERT: B 134 ARG cc_start: 0.6934 (OUTLIER) cc_final: 0.5934 (mmt-90) REVERT: B 217 MET cc_start: 0.7957 (pmm) cc_final: 0.7627 (pmm) REVERT: B 303 ASP cc_start: 0.7184 (t0) cc_final: 0.6823 (m-30) REVERT: B 325 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7322 (mmm) REVERT: N 7 SER cc_start: 0.7259 (OUTLIER) cc_final: 0.7029 (p) REVERT: N 105 ARG cc_start: 0.7441 (mtm180) cc_final: 0.6548 (pmt-80) outliers start: 35 outliers final: 23 residues processed: 132 average time/residue: 1.1957 time to fit residues: 168.9722 Evaluate side-chains 135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 32 LYS Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 60 MET 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 B residue 67 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 MET 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 59 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 Chi-restraints excluded: chain N residue 120 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 49 optimal weight: 0.1980 chunk 58 optimal weight: 0.8980 chunk 5 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.195128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.147854 restraints weight = 8453.686| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.53 r_work: 0.3429 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8671 Z= 0.156 Angle : 0.485 8.126 11760 Z= 0.259 Chirality : 0.040 0.136 1328 Planarity : 0.003 0.049 1462 Dihedral : 4.681 29.156 1524 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.77 % Allowed : 15.76 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1031 helix: 2.70 (0.25), residues: 404 sheet: -0.20 (0.32), residues: 231 loop : -0.62 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 123 HIS 0.004 0.001 HIS A 82 PHE 0.011 0.001 PHE B 199 TYR 0.018 0.001 TYR N 60 ARG 0.004 0.000 ARG R 227 *********************** 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 150 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 116 time to evaluate : 1.540 Fit side-chains revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7281 (mm) REVERT: R 94 SER cc_start: 0.8655 (p) cc_final: 0.8178 (t) REVERT: R 233 ARG cc_start: 0.6893 (ttm-80) cc_final: 0.6622 (ttp80) REVERT: A 20 ARG cc_start: 0.6692 (tpt170) cc_final: 0.6367 (ttp80) REVERT: A 32 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7193 (ttpp) REVERT: A 42 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.6605 (mpp-170) REVERT: A 55 THR cc_start: 0.7674 (OUTLIER) cc_final: 0.7456 (p) REVERT: A 60 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.4236 (ptp) REVERT: A 64 HIS cc_start: 0.6297 (OUTLIER) cc_final: 0.5558 (t-170) REVERT: A 92 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7621 (mt-10) REVERT: A 169 ARG cc_start: 0.6913 (ttp-110) cc_final: 0.6123 (ttt180) REVERT: A 217 CYS cc_start: 0.8277 (m) cc_final: 0.7996 (m) REVERT: A 242 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7255 (tt0) REVERT: A 244 GLU cc_start: 0.6992 (tp30) cc_final: 0.6465 (mp0) REVERT: B 76 ASP cc_start: 0.8641 (p0) cc_final: 0.8401 (p0) REVERT: B 96 ARG cc_start: 0.7759 (mtp-110) cc_final: 0.7483 (ttm110) REVERT: B 100 VAL cc_start: 0.8575 (t) cc_final: 0.8298 (p) REVERT: B 134 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.5867 (mmt-90) REVERT: B 176 GLN cc_start: 0.8186 (mt0) cc_final: 0.7764 (mt0) REVERT: B 217 MET cc_start: 0.7957 (pmm) cc_final: 0.7625 (pmm) REVERT: B 303 ASP cc_start: 0.7218 (t0) cc_final: 0.6831 (m-30) REVERT: B 314 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.8037 (ptt180) REVERT: N 7 SER cc_start: 0.7258 (OUTLIER) cc_final: 0.7029 (p) REVERT: N 105 ARG cc_start: 0.7386 (mtm180) cc_final: 0.6543 (pmt-80) REVERT: N 109 ASP cc_start: 0.7336 (p0) cc_final: 0.6881 (p0) outliers start: 34 outliers final: 21 residues processed: 139 average time/residue: 1.1801 time to fit residues: 176.2945 Evaluate side-chains 140 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 294 ILE Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 60 MET 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 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 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 27 ARG 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 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 84 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 327 ASN B 36 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.195665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.146837 restraints weight = 8459.199| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.45 r_work: 0.3491 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8671 Z= 0.189 Angle : 0.529 9.423 11760 Z= 0.278 Chirality : 0.041 0.136 1328 Planarity : 0.003 0.049 1462 Dihedral : 4.761 41.232 1524 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.88 % Allowed : 16.76 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.26), residues: 1031 helix: 2.72 (0.25), residues: 399 sheet: -0.32 (0.32), residues: 232 loop : -0.64 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 123 HIS 0.004 0.001 HIS A 82 PHE 0.015 0.001 PHE N 108 TYR 0.019 0.001 TYR A 163 ARG 0.004 0.000 ARG R 227 *********************** 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 : 0.970 Fit side-chains revert: symmetry clash REVERT: R 35 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7368 (mm) REVERT: R 94 SER cc_start: 0.8665 (p) cc_final: 0.8180 (t) REVERT: R 233 ARG cc_start: 0.7041 (ttm-80) cc_final: 0.6765 (ttp80) REVERT: A 21 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6661 (tm-30) REVERT: A 32 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.7287 (ttpp) REVERT: A 42 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.6772 (mpp-170) REVERT: A 55 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7614 (p) REVERT: A 64 HIS cc_start: 0.6387 (OUTLIER) cc_final: 0.5654 (t-170) REVERT: A 92 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7699 (mt-10) REVERT: A 169 ARG cc_start: 0.6895 (ttp-110) cc_final: 0.6119 (ttt180) REVERT: A 217 CYS cc_start: 0.8480 (m) cc_final: 0.8161 (m) REVERT: A 233 ASP cc_start: 0.7920 (m-30) cc_final: 0.7662 (t0) REVERT: A 242 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7334 (tt0) REVERT: A 244 GLU cc_start: 0.7205 (tp30) cc_final: 0.6669 (mp0) REVERT: B 96 ARG cc_start: 0.7854 (mtp-110) cc_final: 0.7587 (ttm110) REVERT: B 100 VAL cc_start: 0.8640 (t) cc_final: 0.8373 (p) REVERT: B 134 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.5959 (mmt-90) REVERT: B 176 GLN cc_start: 0.8267 (mt0) cc_final: 0.7892 (mt0) REVERT: B 217 MET cc_start: 0.7985 (pmm) cc_final: 0.7680 (pmm) REVERT: B 303 ASP cc_start: 0.7317 (t0) cc_final: 0.6977 (m-30) REVERT: N 7 SER cc_start: 0.7338 (OUTLIER) cc_final: 0.7104 (p) REVERT: N 105 ARG cc_start: 0.7407 (mtm180) cc_final: 0.6652 (pmt-80) outliers start: 35 outliers final: 22 residues processed: 129 average time/residue: 1.1441 time to fit residues: 157.7881 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 : 0.910 ------------------------------------------------------------------------------- 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 32 LYS 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 B residue 67 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 325 MET 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 59 SER Chi-restraints excluded: chain N residue 83 MET 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 55 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 26 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 220 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.195666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.149354 restraints weight = 8349.429| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.31 r_work: 0.3624 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8671 Z= 0.149 Angle : 0.488 7.188 11760 Z= 0.259 Chirality : 0.040 0.135 1328 Planarity : 0.003 0.049 1462 Dihedral : 4.529 40.467 1524 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.22 % Allowed : 17.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.26), residues: 1031 helix: 2.81 (0.25), residues: 404 sheet: -0.27 (0.32), residues: 232 loop : -0.65 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 123 HIS 0.004 0.001 HIS A 82 PHE 0.009 0.001 PHE N 27 TYR 0.007 0.001 TYR N 117 ARG 0.003 0.000 ARG B 256 ********************** 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 144 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 35 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7648 (mm) REVERT: R 94 SER cc_start: 0.8523 (p) cc_final: 0.8017 (t) REVERT: R 233 ARG cc_start: 0.7182 (ttm-80) cc_final: 0.6936 (ttp80) REVERT: A 42 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.6892 (mpp-170) REVERT: A 55 THR cc_start: 0.7921 (OUTLIER) cc_final: 0.7692 (p) REVERT: A 169 ARG cc_start: 0.6838 (ttp-110) cc_final: 0.6113 (ttt180) REVERT: A 217 CYS cc_start: 0.8548 (m) cc_final: 0.8266 (m) REVERT: A 242 GLN cc_start: 0.7856 (tm-30) cc_final: 0.7406 (tt0) REVERT: A 244 GLU cc_start: 0.7259 (tp30) cc_final: 0.6776 (mp0) REVERT: B 96 ARG cc_start: 0.7952 (mtp-110) cc_final: 0.7685 (ttm110) REVERT: B 100 VAL cc_start: 0.8665 (t) cc_final: 0.8446 (p) REVERT: B 134 ARG cc_start: 0.6960 (pmt170) cc_final: 0.6013 (mmt-90) REVERT: B 176 GLN cc_start: 0.8320 (mt0) cc_final: 0.7993 (mt0) REVERT: B 194 PRO cc_start: 0.8076 (Cg_exo) cc_final: 0.7859 (Cg_endo) REVERT: B 217 MET cc_start: 0.8017 (pmm) cc_final: 0.7724 (pmm) REVERT: B 303 ASP cc_start: 0.7352 (t0) cc_final: 0.7141 (m-30) REVERT: N 7 SER cc_start: 0.7513 (OUTLIER) cc_final: 0.7308 (p) REVERT: N 105 ARG cc_start: 0.7424 (mtm180) cc_final: 0.6599 (pmt-80) outliers start: 29 outliers final: 19 residues processed: 135 average time/residue: 1.1007 time to fit residues: 159.0669 Evaluate side-chains 135 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 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 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 171 THR 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 184 THR Chi-restraints excluded: chain B residue 258 ASP 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 57 SER Chi-restraints excluded: chain N residue 59 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 83 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.190715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.144374 restraints weight = 8546.364| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.33 r_work: 0.3562 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8671 Z= 0.275 Angle : 0.569 7.378 11760 Z= 0.300 Chirality : 0.043 0.218 1328 Planarity : 0.004 0.050 1462 Dihedral : 4.958 39.299 1524 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.33 % Allowed : 17.98 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1031 helix: 2.59 (0.25), residues: 401 sheet: -0.43 (0.32), residues: 233 loop : -0.66 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 123 HIS 0.006 0.002 HIS B 54 PHE 0.025 0.002 PHE N 108 TYR 0.021 0.002 TYR A 163 ARG 0.006 0.000 ARG B 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7109.71 seconds wall clock time: 125 minutes 6.73 seconds (7506.73 seconds total)